William Degrado, PhD

De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties.

Journal of the American Chemical Society

Mann SI, Lin Z, Tan SK, Zhu J, Widel ZXW, Bakanas I, Mansergh JP, Liu R, Kelly MJS, Wu Y, Wells JA, Therien MJ, DeGrado WF

Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes.

Science advances

Grau B, Kormos R, Bañó-Polo M, Chen K, García-Murria MJ, Hajredini F, Sánchez Del Pino MM, Jo H, Martínez-Gil L, von Heijne G, DeGrado WF, Mingarro I

Emergence of binding and catalysis from a designed generalist binding protein.

bioRxiv : the preprint server for biology

Chen Y, Bhattacharya S, Bergmann L, Correy GJ, Tan S, Hou K, Biel J, Lu L, Bakanas I, Polizzi NF, Fraser JS, DeGrado WF

A Cooperative Model for Symmetric Ligand Binding to Protein Fibrils.

bioRxiv : the preprint server for biology

Smith MS, DeGrado WF, Grabe M, Shoichet BK

Design of a light and Ca2+ switchable organic-peptide hybrid.

Proceedings of the National Academy of Sciences of the United States of America

Khaleel ZH, No YH, Kim NH, Bae DH, Wu Y, Kim S, Choi H, Lee DE, Jeong SY, Ko YJ, Kim SG, Suh M, Kim JC, DeGrado WF, Kim KH, Kim YH

A designed Zn 2+ sensor domain transmits binding information to transmembrane histidine kinases.

bioRxiv : the preprint server for biology

Hatstat AK, Kormos R, Xu V, DeGrado WF

Methods for high throughput discovery of fluoroprobes that recognize tau fibril polymorphs.

bioRxiv : the preprint server for biology

Carroll EC, Yang H, Jones JG, Oehler A, Charvat AF, Montgomery KM, Yung A, Millbern Z, Vinueza NR, DeGrado WF, Mordes DA, Condello C, Gestwicki JE

SuFEx Chemistry Enables Covalent Assembly of a 280-kDa 18-Subunit Pore-Forming Complex.

Journal of the American Chemical Society

Schnaider L, Tan S, Singh PR, Capuano F, Scott AJ, Hambley R, Lu L, Yang H, Wallace EJ, Jo H, DeGrado WF

IL-13 and IL-17A activate ß1 integrin through an NF-kB/Rho kinase/PIP5K1? pathway to enhance force transmission in airway smooth muscle.

Proceedings of the National Academy of Sciences of the United States of America

Ngo U, Shi Y, Woodruff P, Shokat K, DeGrado W, Jo H, Sheppard D, Sundaram AB

Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats.

Proceedings of the National Academy of Sciences of the United States of America

Celona B, Salomonsson SE, Wu H, Dang B, Kratochvil HT, Clelland CD, DeGrado WF, Black BL

ProBASS - a language model with sequence and structural features for predicting the effect of mutations on binding affinity.

bioRxiv : the preprint server for biology

Gurusinghe SNS, Wu Y, DeGrado W, Shifman JM

Patterning and folding of intestinal villi by active mesenchymal dewetting.

Cell

Huycke TR, Häkkinen TJ, Miyazaki H, Srivastava V, Barruet E, McGinnis CS, Kalantari A, Cornwall-Scoones J, Vaka D, Zhu Q, Jo H, Oria R, Weaver VM, DeGrado WF, Thomson M, Garikipati K, Boffelli D, Klein OD, Gartner ZJ

IL-13 and IL-17A Activate β1 Integrin through an NF-kB/Rho kinase/PIP5K1γ pathway to Enhance Force Transmission in Airway Smooth Muscle.

bioRxiv : the preprint server for biology

Ngo U, Shi Y, Woodruff P, Shokat K, DeGrado W, Jo H, Sheppard D, Sundaram AB

De novo design of drug-binding proteins with predictable binding energy and specificity.

Science (New York, N.Y.)

Lu L, Gou X, Tan SK, Mann SI, Yang H, Zhong X, Gazgalis D, Valdiviezo J, Jo H, Wu Y, Diolaiti ME, Ashworth A, Polizzi NF, DeGrado WF

De novo design of peptides that bind specific conformers of α-synuclein.

Chemical science

Wallace HM, Yang H, Tan S, Pan HS, Yang R, Xu J, Jo H, Condello C, Polizzi NF, DeGrado WF

De novo-designed transmembrane proteins bind and regulate a cytokine receptor.

Nature chemical biology

Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF

An enhanced broad-spectrum peptide inhibits Omicron variants in vivo.

Cell reports. Medicine

Bi W, Tang K, Chen G, Xie Y, Polizzi NF, DeGrado WF, Yuan S, Dang B

Docking for Molecules That Bind in a Symmetric Stack with SymDOCK.

Journal of chemical information and modeling

Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK

De novo design of drug-binding proteins with predictable binding energy and specificity.

bioRxiv : the preprint server for biology

Lu L, Gou X, Tan SK, Mann SI, Yang H, Zhong X, Gazgalis D, Valdiviezo J, Jo H, Wu Y, Diolaiti ME, Ashworth A, Polizzi NF, DeGrado WF

De novo Design of Peptides that Bind Specific Conformers of α-Synuclein.

bioRxiv : the preprint server for biology

Wallace HM, Yang H, Tan S, Pan HS, Yang R, Xu J, Jo H, Condello C, Polizzi NF, DeGrado WF

Docking for molecules that bind in a symmetric stack with SymDOCK.

bioRxiv : the preprint server for biology

Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK

Hexamethylene amiloride binds the SARS-CoV-2 envelope protein at the protein-lipid interface.

Protein science : a publication of the Protein Society

Somberg NH, Medeiros-Silva J, Jo H, Wang J, DeGrado WF, Hong M

Patterning and folding of intestinal villi by active mesenchymal dewetting.

bioRxiv : the preprint server for biology

Huycke TR, Miyazaki H, Häkkinen TJ, Srivastava V, Barruet E, McGinnis CS, Kalantari A, Cornwall-Scoones J, Vaka D, Zhu Q, Jo H, DeGrado WF, Thomson M, Garikipati K, Boffelli D, Klein OD, Gartner ZJ

Transient water wires mediate selective proton transport in designed channel proteins.

Nature chemistry

Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF

Stacked binding of a PET ligand to Alzheimer's tau paired helical filaments.

Nature communications

Merz GE, Chalkley MJ, Tan SK, Tse E, Lee J, Prusiner SB, Paras NA, DeGrado WF, Southworth DR

A host defense peptide mimetic, brilacidin, potentiates caspofungin antifungal activity against human pathogenic fungi.

Nature communications

Dos Reis TF, de Castro PA, Bastos RW, Pinzan CF, Souza PFN, Ackloo S, Hossain MA, Drewry DH, Alkhazraji S, Ibrahim AS, Jo H, Lightfoot JD, Adams EM, Fuller KK, deGrado WF, Goldman GH

EMBER multidimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains.

Proceedings of the National Academy of Sciences of the United States of America

Yang H, Yuan P, Wu Y, Shi M, Caro CD, Tengeiji A, Yamanoi S, Inoue M, DeGrado WF, Condello C

Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology.

bioRxiv : the preprint server for biology

Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF

EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains.

bioRxiv : the preprint server for biology

Yang H, Yuan P, Wu Y, Shi M, Caro CD, Tengeiji A, Yamanoi S, Inoue M, DeGrado WF, Condello C

Aβ and Tau Prions Causing Alzheimer's Disease.

Methods in molecular biology (Clifton, N.J.)

Condello C, Merz GE, Aoyagi A, DeGrado WF, Prusiner SB

Solution of the protein structure prediction problem at last: crucial innovations and next frontiers.

Faculty reviews

Agard DA, Bowman GR, DeGrado W, Dokholyan NV, Zhou HX

SARS-CoV-2 Envelope Protein Forms Clustered Pentamers in Lipid Bilayers.

Biochemistry

Somberg NH, Wu WW, Medeiros-Silva J, Dregni AJ, Jo H, DeGrado WF, Hong M

Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.

Nature structural & molecular biology

Arrigoni C, Lolicato M, Shaya D, Rohaim A, Findeisen F, Fong LK, Colleran CM, Dominik P, Kim SS, Schuermann JP, DeGrado WF, Grabe M, Kossiakoff AA, Minor DL

Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides.

Chemical science

Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado WF, Fujimori DG

The CD3ζ adaptor structure determines functional differences between human and mouse CD16 Fc receptor signaling.

The Journal of experimental medicine

Aguilar OA, Fong LK, Ishiyama K, DeGrado WF, Lanier LL

Brilacidin, a COVID-19 drug candidate, demonstrates broad-spectrum antiviral activity against human coronaviruses OC43, 229E, and NL63 through targeting both the virus and the host cell.

Journal of medical virology

Hu Y, Jo H, DeGrado WF, Wang J

Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ.

Proceedings of the National Academy of Sciences of the United States of America

Belsare KD, Wu H, Mondal D, Bond A, Castillo E, Jin J, Jo H, Roush AE, Pilla KB, Sali A, Condello C, DeGrado WF

Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.

Journal of the American Chemical Society

Watkins LC, DeGrado WF, Voth GA

Emergence of distinct and heterogeneous strains of amyloid beta with advanced Alzheimer's disease pathology in Down syndrome.

Acta neuropathologica communications

Maxwell AM, Yuan P, Rivera BM, Schaaf W, Mladinov M, Prasher VP, Robinson AC, DeGrado WF, Condello C

Behaviour and interactions of proteins and peptides with and within membranes; from simple models to cellular membranes: general discussion.

Faraday discussions

Aguilar M, Al Nahas K, Barrera F, Bassereau P, Bastos M, Beales P, Bechinger B, Bonev B, Brand I, Chattopadhyay A, DeGrado W, Fuchs P, Garcia Saez AJ, Hoogenboom B, Kapoor S, Milán Rodríguez P, Molloy J, O'Shea P, Pabst G, Pal S, Rice A, Roux A, Sanderson J, Seddon J, Tamm LK, Vijayakumar A

Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides.

Faraday discussions

Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF

Theoretical and experimental comparisons of simple peptide-membrane systems; towards defining the reaction space: general discussion.

Faraday discussions

Aguilar MI, Al Nahas K, Barrera FN, Bassereau P, Bechinger B, Brand I, Chattopadhyay A, Clarke RJ, DeGrado WF, Deplazes E, Fletcher M, Fraternali F, Fuchs P, Garcia-Saez AJ, Gilbert R, Hoogenboom BW, Jarin Z, O'Shea P, Pabst G, Pal S, Sanderson JM, Seddon JM, Sengupta D, Siegel DP, Srivastava A, Tieleman DP, Tripathy M, Utterström J, Vácha R, Vanni S, Voth GA

Theoretical and experimental studies of complex peptide-membrane systems: general discussion.

Faraday discussions

Aguilar M, Al Nahas K, Barrera F, Bassereau P, Bastos M, Beales P, Bechinger B, Bonev B, Brand I, Chattopadhyay A, Clarke RJ, DeGrado W, Deplazes E, Garcia Saez AJ, Hoogenboom B, Lund R, Milán Rodríguez P, O'Shea P, Pabst G, Pal S, Roux A, Sanderson J, Semeraro EF, Sengupta D, Siegel DP, van 't Hag L, Vijayakumar A, Zoranic L

Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ.

eLife

Mensa B, Polizzi NF, Molnar KS, Natale AM, Lemmin T, DeGrado WF

Cleavage of talin by calpain promotes platelet-mediated fibrin clot contraction.

Blood advances

Fong KP, Molnar KS, Agard N, Litvinov RI, Kim OV, Wells JA, Weisel JW, DeGrado WF, Bennett JS

De novo metalloprotein design.

Nature reviews. Chemistry

Chalkley MJ, Mann SI, DeGrado WF

Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity.

Biochemistry

Thomaston JL, Samways ML, Konstantinidi A, Ma C, Hu Y, Bruce Macdonald HE, Wang J, Essex JW, DeGrado WF, Kolocouris A

Elucidation of the molecular interactions that enable stable assembly and structural diversity in multicomponent immune receptors.

Proceedings of the National Academy of Sciences of the United States of America

Fong LK, Chalkley MJ, Tan SK, Grabe M, DeGrado WF

Integrin α2β1 regulates collagen I tethering to modulate hyperresponsiveness in reactive airway disease models.

The Journal of clinical investigation

Liu S, Ngo U, Tang XZ, Ren X, Qiu W, Huang X, DeGrado W, Allen CD, Jo H, Sheppard D, Sundaram AB

Visualization of Platelet Integrins via Two-Photon Microscopy Using Anti-transmembrane Domain Peptides Containing a Blue Fluorescent Amino Acid.

Biochemistry

Fong KP, Ahmed IA, Mravic M, Jo H, Kim OV, Litvinov RI, Weisel JW, DeGrado WF, Gai F, Bennett JS

Inclusion of the C-Terminal Domain in the β-Sheet Core of Heparin-Fibrillized Three-Repeat Tau Protein Revealed by Solid-State Nuclear Magnetic Resonance Spectroscopy.

Journal of the American Chemical Society

Dregni AJ, Wang HK, Wu H, Duan P, Jin J, DeGrado WF, Hong M

Constructing ion channels from water-soluble α-helical barrels.

Nature chemistry

Scott AJ, Niitsu A, Kratochvil HT, Lang EJM, Sengel JT, Dawson WM, Mahendran KR, Mravic M, Thomson AR, Brady RL, Liu L, Mulholland AJ, Bayley H, DeGrado WF, Wallace MI, Woolfson DN

Protein design-scapes generated by microfluidic DNA assembly elucidate domain coupling in the bacterial histidine kinase CpxA.

Proceedings of the National Academy of Sciences of the United States of America

Clark IC, Mensa B, Ochs CJ, Schmidt NW, Mravic M, Quintana FJ, DeGrado WF, Abate AR

Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site.

Journal of the American Chemical Society

Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V

De Novo Design, Solution Characterization, and Crystallographic Structure of an Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing a Mn(V) Species.

Journal of the American Chemical Society

Mann SI, Nayak A, Gassner GT, Therien MJ, DeGrado WF

Allosteric cooperation in a de novo-designed two-domain protein.

Proceedings of the National Academy of Sciences of the United States of America

Pirro F, Schmidt N, Lincoff J, Widel ZX, Polizzi NF, Liu L, Therien MJ, Grabe M, Chino M, Lombardi A, DeGrado WF

Platform to Discover Protease-Activated Antibiotics and Application to Siderophore-Antibiotic Conjugates.

Journal of the American Chemical Society

Boyce JH, Dang B, Ary B, Edmondson Q, Craik CS, DeGrado WF, Seiple IB

Dual antagonists of α5β1/αvβ1 integrin for airway hyperresponsiveness.

Bioorganic & medicinal chemistry letters

Sundaram A, Chen C, Isik Reed N, Liu S, Ki Yeon S, McIntosh J, Tang YZ, Yang H, Adler M, Beresis R, Seiple IB, Sheppard D, DeGrado WF, Jo H

Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics.

Journal of the American Chemical Society

Watkins LC, DeGrado WF, Voth GA

Prion biology: implications for Alzheimer's disease therapeutics.

The Lancet. Neurology

Condello C, DeGrado WF, Prusiner SB

A defined structural unit enables de novo design of small-molecule-binding proteins.

Science (New York, N.Y.)

Polizzi NF, DeGrado WF

Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding.

ACS chemical biology

Newberry RW, Arhar T, Costello J, Hartoularos GC, Maxwell AM, Naing ZZC, Pittman M, Reddy NR, Schwarz DMC, Wassarman DR, Wu TS, Barrero D, Caggiano C, Catching A, Cavazos TB, Estes LS, Faust B, Fink EA, Goldman MA, Gomez YK, Gordon MG, Gunsalus LM, Hoppe N, Jaime-Garza M, Johnson MC, Jones MG, Kung AF, Lopez KE, Lumpe J, Martyn C, McCarthy EE, Miller-Vedam LE, Navarro EJ, Palar A, Pellegrino J, Saylor W, Stephens CA, Strickland J, Torosyan H, Wankowicz SA, Wong DR, Wong G, Redding S, Chow ED, DeGrado WF, Kampmann M

Deep mutational scanning reveals the structural basis for α-synuclein activity.

Nature chemical biology

Newberry RW, Leong JT, Chow ED, Kampmann M, DeGrado WF

De novo protein design, a retrospective.

Quarterly reviews of biophysics

Korendovych IV, DeGrado WF

X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance.

Biochemistry

Thomaston JL, Konstantinidi A, Liu L, Lambrinidis G, Tan J, Caffrey M, Wang J, Degrado WF, Kolocouris A

De novo design of a homo-trimeric amantadine-binding protein.

eLife

Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D

A disease-associated mutation in fibrillin-1 differentially regulates integrin-mediated cell adhesion.

The Journal of biological chemistry

Del Cid JS, Reed NI, Molnar K, Liu S, Dang B, Jensen SA, DeGrado W, Handford PA, Sheppard D, Sundaram AB

In vitro 0N4R tau fibrils contain a monomorphic β-sheet core enclosed by dynamically heterogeneous fuzzy coat segments.

Proceedings of the National Academy of Sciences of the United States of America

Dregni AJ, Mandala VS, Wu H, Elkins MR, Wang HK, Hung I, DeGrado WF, Hong M

Modulating Integrin αIIbβ3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts.

Biochemistry

Tan SK, Fong KP, Polizzi NF, Sternisha A, Slusky JSG, Yoon K, DeGrado WF, Bennett JS

Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel.

Journal of the American Chemical Society

Watkins LC, Liang R, Swanson JMJ, DeGrado WF, Voth GA

X-ray Crystal Structure of the Influenza A M2 Proton Channel S31N Mutant in Two Conformational States: An Open and Shut Case.

Journal of the American Chemical Society

Thomaston JL, Wu Y, Polizzi N, Liu L, Wang J, DeGrado WF

Unique transmembrane domain interactions differentially modulate integrin αvβ3 and αIIbβ3 function.

Proceedings of the National Academy of Sciences of the United States of America

Litvinov RI, Mravic M, Zhu H, Weisel JW, DeGrado WF, Bennett JS

Genetically Introducing Biochemically Reactive Amino Acids Dehydroalanine and Dehydrobutyrine in Proteins.

Journal of the American Chemical Society

Yang B, Wang N, Schnier PD, Zheng F, Zhu H, Polizzi NF, Ittuveetil A, Saikam V, DeGrado WF, Wang Q, Wang PG, Wang L

Aβ and tau prion-like activities decline with longevity in the Alzheimer's disease human brain.

Science translational medicine

Aoyagi A, Condello C, Stöhr J, Yue W, Rivera BM, Lee JC, Woerman AL, Halliday G, van Duinen S, Ingelsson M, Lannfelt L, Graff C, Bird TD, Keene CD, Seeley WW, DeGrado WF, Prusiner SB

Synthesis and application of the blue fluorescent amino acid l-4-cyanotryptophan to assess peptide-membrane interactions.

Chemical communications (Cambridge, England)

Zhang K, Ahmed IA, Kratochvil HT, DeGrado WF, Gai F, Jo H

Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly.

Journal of the American Chemical Society

Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF

De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities.

Accounts of chemical research

Lombardi A, Pirro F, Maglio O, Chino M, DeGrado WF

Packing of apolar side chains enables accurate design of highly stable membrane proteins.

Science (New York, N.Y.)

Mravic M, Thomaston JL, Tucker M, Solomon PE, Liu L, DeGrado WF

SNAC-tag for sequence-specific chemical protein cleavage.

Nature methods

Dang B, Mravic M, Hu H, Schmidt N, Mensa B, DeGrado WF

Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study.

The journal of physical chemistry. B

Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F

4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics.

Molecules (Basel, Switzerland)

Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F

Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations.

Cancer cell

Pahuja KB, Nguyen TT, Jaiswal BS, Prabhash K, Thaker TM, Senger K, Chaudhuri S, Kljavin NM, Antony A, Phalke S, Kumar P, Mravic M, Stawiski EW, Vargas D, Durinck S, Gupta R, Khanna-Gupta A, Trabucco SE, Sokol ES, Hartmaier RJ, Singh A, Chougule A, Trivedi V, Dutt A, Patil V, Joshi A, Noronha V, Ziai J, Banavali SD, Ramprasad V, DeGrado WF, Bueno R, Jura N, Seshagiri S

Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry.

Proceedings of the National Academy of Sciences of the United States of America

Yang B, Wu H, Schnier PD, Liu Y, Liu J, Wang N, DeGrado WF, Wang L

Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters.

Journal of the American Chemical Society

Thomaston JL, Polizzi NF, Konstantinidi A, Wang J, Kolocouris A, DeGrado WF

Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster.

Biopolymers

Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF

Building and Breaking Bonds via a Compact S-Propargyl-Cysteine to Chemically Control Enzymes and Modify Proteins.

Angewandte Chemie (International ed. in English)

Liu J, Cheng R, Wu H, Li S, Wang PG, DeGrado WF, Rozovsky S, Wang L

Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule.

Biochemistry

Bokoch MP, Jo H, Valcourt JR, Srinivasan Y, Pan AC, Capponi S, Grabe M, Dror RO, Shaw DE, DeGrado WF, Coughlin SR

Designed peptides that assemble into cross-α amyloid-like structures.

Nature chemical biology

Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF

Structure and Function of the Transmembrane Domain of NsaS, an Antibiotic Sensing Histidine Kinase in Staphylococcus aureus.

Journal of the American Chemical Society

Bhate MP, Lemmin T, Kuenze G, Mensa B, Ganguly S, Peters JM, Schmidt N, Pelton JG, Gross CA, Meiler J, DeGrado WF

Peptide-Programmable Nanoparticle Superstructures with Tailored Electrocatalytic Activity.

ACS nano

Kang ES, Kim YT, Ko YS, Kim NH, Cho G, Huh YH, Kim JH, Nam J, Thach TT, Youn D, Kim YD, Yun WS, DeGrado WF, Kim SY, Hammond PT, Lee J, Kwon YU, Ha DH, Kim YH

De novo designed transmembrane peptides activating the α5β1 integrin.

Protein engineering, design & selection : PEDS

Mravic M, Hu H, Lu Z, Bennett JS, Sanders CR, Orr AW, DeGrado WF

Design of a Short Thermally Stable α-Helix Embedded in a Macrocycle.

Chembiochem : a European journal of chemical biology

Wu H, Acharyya A, Wu Y, Liu L, Jo H, Gai F, DeGrado WF

De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles.

Journal of the American Chemical Society

Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A

A long-lived Aβ oligomer resistant to fibrillization.

Biopolymers

Nick M, Wu Y, Schmidt NW, Prusiner SB, Stöhr J, DeGrado WF

Structural heterogeneity and intersubject variability of Aβ in familial and sporadic Alzheimer's disease.

Proceedings of the National Academy of Sciences of the United States of America

Condello C, Lemmin T, Stöhr J, Nick M, Wu Y, Maxwell AM, Watts JC, Caro CD, Oehler A, Keene CD, Bird TD, van Duinen SG, Lannfelt L, Ingelsson M, Graff C, Giles K, DeGrado WF, Prusiner SB

Spontaneous and specific chemical cross-linking in live cells to capture and identify protein interactions.

Nature communications

Yang B, Tang S, Ma C, Li ST, Shao GC, Dang B, DeGrado WF, Dong MQ, Wang PG, Ding S, Wang L

Self-assembling dipeptide antibacterial nanostructures with membrane disrupting activity.

Nature communications

Schnaider L, Brahmachari S, Schmidt NW, Mensa B, Shaham-Niv S, Bychenko D, Adler-Abramovich L, Shimon LJW, Kolusheva S, DeGrado WF, Gazit E

De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures.

Proceedings of the National Academy of Sciences of the United States of America

Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva DA, Baker D, DeGrado WF

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.

Proceedings of the National Academy of Sciences of the United States of America

Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF

De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy.

Nature chemistry

Polizzi NF, Wu Y, Lemmin T, Maxwell AM, Zhang SQ, Rawson J, Beratan DN, Therien MJ, DeGrado WF

Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Joh NH, Grigoryan G, Wu Y, DeGrado WF

Zinc-binding structure of a catalytic amyloid from solid-state NMR.

Proceedings of the National Academy of Sciences of the United States of America

Lee M, Wang T, Makhlynets OV, Wu Y, Polizzi NF, Wu H, Gosavi PM, Stöhr J, Korendovych IV, DeGrado WF, Hong M

Blue fluorescent amino acid for biological spectroscopy and microscopy.

Proceedings of the National Academy of Sciences of the United States of America

Hilaire MR, Ahmed IA, Lin CW, Jo H, DeGrado WF, Gai F

Water Distribution, Dynamics, and Interactions with Alzheimer's β-Amyloid Fibrils Investigated by Solid-State NMR.

Journal of the American Chemical Society

Wang T, Jo H, DeGrado WF, Hong M

Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy.

Angewandte Chemie (International ed. in English)

Lin CW, Mensa B, Barniol-Xicota M, DeGrado WF, Gai F

A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells.

Nature chemistry

Stöhr J, Wu H, Nick M, Wu Y, Bhate M, Condello C, Johnson N, Rodgers J, Lemmin T, Acharya S, Becker J, Robinson K, Kelly MJS, Gai F, Stubbs G, Prusiner SB, DeGrado WF

Stapled Voltage-Gated Calcium Channel (CaV) α-Interaction Domain (AID) Peptides Act As Selective Protein-Protein Interaction Inhibitors of CaV Function.

ACS chemical neuroscience

Findeisen F, Campiglio M, Jo H, Abderemane-Ali F, Rumpf CH, Pope L, Rossen ND, Flucher BE, DeGrado WF, Minor DL

The accommodation index measures the perturbation associated with insertions and deletions in coiled-coils: Application to understand signaling in histidine kinases.

Protein science : a publication of the Protein Society

Schmidt NW, Grigoryan G, DeGrado WF

Pharmacologic Blockade of αvβ1 Integrin Ameliorates Renal Failure and Fibrosis In Vivo.

Journal of the American Society of Nephrology : JASN

Chang Y, Lau WL, Jo H, Tsujino K, Gewin L, Reed NI, Atakilit A, Nunes ACF, DeGrado WF, Sheppard D

An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses.

Antiviral research

Hu Y, Musharrafieh R, Ma C, Zhang J, Smee DF, DeGrado WF, Wang J

Targeting integrin α5β1 ameliorates severe airway hyperresponsiveness in experimental asthma.

The Journal of clinical investigation

Sundaram A, Chen C, Khalifeh-Soltani A, Atakilit A, Ren X, Qiu W, Jo H, DeGrado W, Huang X, Sheppard D

Acid activation mechanism of the influenza A M2 proton channel.

Proceedings of the National Academy of Sciences of the United States of America

Liang R, Swanson JMJ, Madsen JJ, Hong M, DeGrado WF, Voth GA

Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel.

Physical chemistry chemical physics : PCCP

Markiewicz BN, Lemmin T, Zhang W, Ahmed IA, Jo H, Fiorin G, Troxler T, DeGrado WF, Gai F

Exploring N-Arylsulfonyl-l-proline Scaffold as a Platform for Potent and Selective αvβ1 Integrin Inhibitors.

ACS medicinal chemistry letters

Reed NI, Tang YZ, McIntosh J, Wu Y, Molnar KS, Civitavecchia A, Sheppard D, DeGrado WF, Jo H

Structural Polymorphism of Alzheimer's β-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study.

Journal of the American Chemical Society

Elkins MR, Wang T, Nick M, Jo H, Lemmin T, Prusiner SB, DeGrado WF, Stöhr J, Hong M

Graphene Symmetry Amplified by Designed Peptide Self-Assembly.

Biophysical Journal

Mustata GM, Kim YH, Zhang J, DeGrado WF, Grigoryan G, Wanunu M

Crystal structure of the drug-resistant S31N influenza M2 proton channel.

Protein science : a publication of the Protein Society

Thomaston JL, DeGrado WF

Photoactivatable protein labeling by singlet oxygen mediated reactions.

Bioorganic & medicinal chemistry letters

To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X

Protein-directed self-assembly of a fullerene crystal.

Nature communications

Kim KH, Ko DK, Kim YT, Kim NH, Paul J, Zhang SQ, Murray CB, Acharya R, DeGrado WF, Kim YH, Grigoryan G

Directly Activating the Integrin αIIbβ3 Initiates Outside-In Signaling by Causing αIIbβ3 Clustering.

The Journal of biological chemistry

Fong KP, Zhu H, Span LM, Moore DT, Yoon K, Tamura R, Yin H, DeGrado WF, Bennett JS

Designed metalloprotein stabilizes a semiquinone radical.

Nature chemistry

Ulas G, Lemmin T, Wu Y, Gassner GT, DeGrado WF

Discovery of Highly Potent Inhibitors Targeting the Predominant Drug-Resistant S31N Mutant of the Influenza A Virus M2 Proton Channel.

Journal of medicinal chemistry

Li F, Ma C, DeGrado WF, Wang J

High-density grids for efficient data collection from multiple crystals.

Acta crystallographica. Section D, Structural biology

Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, Bonagura CA, Brehmer W, Brunger AT, Calero G, Caradoc-Davies TT, Chatterjee R, Degrado WF, Fraser JS, Ibrahim M, Kern J, Kobilka BK, Kruse AC, Larsson KM, Lemke HT, Lyubimov AY, Manglik A, McPhillips SE, Norgren E, Pang SS, Soltis SM, Song J, Thomaston J, Tsai Y, Weis WI, Woldeyes RA, Yachandra V, Yano J, Zouni A, Cohen AE

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.

Proceedings of the National Academy of Sciences of the United States of America

Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF

Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins.

Biochemistry

Snyder RA, Betzu J, Butch SE, Reig AJ, DeGrado WF, Solomon EI

Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins.

Journal of the American Chemical Society

Snyder RA, Butch SE, Reig AJ, DeGrado WF, Solomon EI

Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure.

European journal of inorganic chemistry

Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A

The αvβ1 integrin plays a critical in vivo role in tissue fibrosis.

Science translational medicine

Reed NI, Jo H, Chen C, Tsujino K, Arnold TD, DeGrado WF, Sheppard D

Signal transduction in histidine kinases: insights from new structures.

Structure (London, England : 1993)

Bhate MP, Molnar KS, Goulian M, DeGrado WF

The Tyrosine Kinase c-Src Specifically Binds to the Active Integrin αIIbβ3 to Initiate Outside-in Signaling in Platelets.

The Journal of biological chemistry

Wu Y, Span LM, Nygren P, Zhu H, Moore DT, Cheng H, Roder H, DeGrado WF, Bennett JS

The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

Structure (London, England : 1993)

Zhang SQ, Kulp DW, Schramm CA, Mravic M, Samish I, DeGrado WF

Computational design and experimental characterization of peptides intended for pH-dependent membrane insertion and pore formation.

ACS chemical biology

Zhang Y, Bartz R, Grigoryan G, Bryant M, Aaronson J, Beck S, Innocent N, Klein L, Procopio W, Tucker T, Jadhav V, Tellers DM, DeGrado WF

C-terminal juxtamembrane region of full-length M2 protein forms a membrane surface associated amphipathic helix.

Protein science : a publication of the Protein Society

Huang S, Green B, Thompson M, Chen R, Thomaston J, DeGrado WF, Howard KP

De novo design of a transmembrane Zn²⁺-transporting four-helix bundle.

Science (New York, N.Y.)

Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF

Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel.

Journal of the American Chemical Society

Wu Y, Canturk B, Jo H, Ma C, Gianti E, Klein ML, Pinto LH, Lamb RA, Fiorin G, Wang J, DeGrado WF

Specific aromatic foldamers potently inhibit spontaneous and seeded Aβ42 and Aβ43 fibril assembly.

The Biochemical journal

Seither KM, McMahon HA, Singh N, Wang H, Cushman-Nick M, Montalvo GL, DeGrado WF, Shorter J

Hydrogen-bonded water molecules in the M2 channel of the influenza A virus guide the binding preferences of ammonium-based inhibitors.

The journal of physical chemistry. B

Gianti E, Carnevale V, DeGrado WF, Klein ML, Fiorin G

Proton release from the histidine-tetrad in the M2 channel of the influenza A virus.

The journal of physical chemistry. B

Dong H, Fiorin G, DeGrado WF, Klein ML

A real-time all-atom structural search engine for proteins.

PLoS computational biology

Gonzalez G, Hannigan B, DeGrado WF

Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.

Structure (London, England : 1993)

Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF

Catalytic efficiency of designed catalytic proteins.

Current opinion in structural biology

Korendovych IV, DeGrado WF

Distinct synthetic Aβ prion strains producing different amyloid deposits in bigenic mice.

Proceedings of the National Academy of Sciences of the United States of America

Stöhr J, Condello C, Watts JC, Bloch L, Oehler A, Nick M, DeArmond SJ, Giles K, DeGrado WF, Prusiner SB

Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus.

Journal of medicinal chemistry

Rey-Carrizo M, Barniol-Xicota M, Ma C, Frigolé-Vivas M, Torres E, Naesens L, Llabrés S, Juárez-Jiménez J, Luque FJ, DeGrado WF, Lamb RA, Pinto LH, Vázquez S

2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel.

The Journal of chemical physics

Ghosh A, Wang J, Moroz YS, Korendovych IV, Zanni M, DeGrado WF, Gai F, Hochstrasser RM

Comparative mechanistic studies of brilacidin, daptomycin, and the antimicrobial peptide LL16.

Antimicrobial agents and chemotherapy

Mensa B, Howell GL, Scott R, DeGrado WF

Crystal structure of an amphiphilic foldamer reveals a 48-mer assembly comprising a hollow truncated octahedron.

Nature communications

Pavone V, Zhang SQ, Merlino A, Lombardi A, Wu Y, DeGrado WF

Short peptides self-assemble to produce catalytic amyloids.

Nature chemistry

Rufo CM, Moroz YS, Moroz OV, Stöhr J, Smith TA, Hu X, DeGrado WF, Korendovych IV

De novo design of self-assembling foldamers that inhibit heparin-protein interactions.

ACS chemical biology

Montalvo GL, Zhang Y, Young TM, Costanzo MJ, Freeman KB, Wang J, Clements DJ, Magavern E, Kavash RW, Scott RW, Liu D, Degrado WF

Structural Stability and Binding Strength of a Designed Peptide-Carbon Nanotube Hybrid.

The journal of physical chemistry. C, Nanomaterials and interfaces

Roxbury D, Zhang SQ, Mittal J, Degrado WF, Jagota A

Mechanistic insights from functional characterization of an unnatural His37 mutant of the influenza A/M2 protein.

Biochimica et biophysica acta

Polishchuk AL, Cristian L, Pinto LH, Lear JD, DeGrado WF

Slow folding-unfolding kinetics of an octameric β-peptide bundle.

ACS chemical biology

Montalvo GL, Gai F, Roder H, DeGrado WF

Assessment of local friction in protein folding dynamics using a helix cross-linker.

The journal of physical chemistry. B

Markiewicz BN, Jo H, Culik RM, DeGrado WF, Gai F

3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant.

Journal of medicinal chemistry

Rey-Carrizo M, Torres E, Ma C, Barniol-Xicota M, Wang J, Wu Y, Naesens L, DeGrado WF, Lamb RA, Pinto LH, Vázquez S

Template-constrained cyclic sulfopeptide HIV-1 entry inhibitors.

Organic & biomolecular chemistry

Rudick JG, Laakso MM, Schloss AC, DeGrado WF

Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus.

Structure (London, England : 1993)

Ma C, Fiorin G, Carnevale V, Wang J, Lamb RA, Klein ML, Wu Y, Pinto LH, DeGrado WF

Influenza virus A M2 protein generates negative Gaussian membrane curvature necessary for budding and scission.

Journal of the American Chemical Society

Schmidt NW, Mishra A, Wang J, DeGrado WF, Wong GC

Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore.

Journal of the American Chemical Society

Fry HC, Lehmann A, Sinks LE, Asselberghs I, Tronin A, Krishnan V, Blasie JK, Clays K, DeGrado WF, Saven JG, Therien MJ

Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan.

Chemical physics

Nanda V, Cristian L, Toptygin D, Brand L, Degrado WF

Exploring Histidine Conformations in the M2 Channel Lumen of the Influenza A Virus at Neutral pH via Molecular Simulations.

The journal of physical chemistry letters

Dong H, Fiorin G, Degrado WF, Klein ML

Nature-inspired design of motif-specific antibody scaffolds.

Nature biotechnology

Koerber JT, Thomsen ND, Hannigan BT, Degrado WF, Wells JA

Drug-induced conformational and dynamical changes of the S31N mutant of the influenza M2 proton channel investigated by solid-state NMR.

Journal of the American Chemical Society

Williams JK, Tietze D, Wang J, Wu Y, DeGrado WF, Hong M

Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus.

Journal of medicinal chemistry

Wang J, Ma C, Wang J, Jo H, Canturk B, Fiorin G, Pinto LH, Lamb RA, Klein ML, DeGrado WF

Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay.

PloS one

Balgi AD, Wang J, Cheng DY, Ma C, Pfeifer TA, Shimizu Y, Anderson HJ, Pinto LH, Lamb RA, DeGrado WF, Roberge M

Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations.

PLoS computational biology

Lemmin T, Soto CS, Clinthorne G, DeGrado WF, Dal Peraro M

An assay suitable for high throughput screening of anti-influenza drugs.

PloS one

Mao L, Wang J, DeGrado WF, Inouye M

Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus.

Proceedings of the National Academy of Sciences of the United States of America

Wang J, Wu Y, Ma C, Fiorin G, Wang J, Pinto LH, Lamb RA, Klein ML, Degrado WF

Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals.

Proceedings of the National Academy of Sciences of the United States of America

Hu X, Zhao J, DeGrado WF, Binns AN

Platelet factor 4 activity against P. falciparum and its translation to nonpeptidic mimics as antimalarials.

Cell host & microbe

Love MS, Millholland MG, Mishra S, Kulkarni S, Freeman KB, Pan W, Kavash RW, Costanzo MJ, Jo H, Daly TM, Williams DR, Kowalska MA, Bergman LW, Poncz M, DeGrado WF, Sinnis P, Scott RW, Greenbaum DC

Detection of drug-induced conformational change of a transmembrane protein in lipid bilayers using site-directed spin labeling.

Protein science : a publication of the Protein Society

Thomaston JL, Nguyen PA, Brown EC, Upshur MA, Wang J, DeGrado WF, Howard KP

Development of α-helical calpain probes by mimicking a natural protein-protein interaction.

Journal of the American Chemical Society

Jo H, Meinhardt N, Wu Y, Kulkarni S, Hu X, Low KE, Davies PL, DeGrado WF, Greenbaum DC

Structural basis for proton conduction and inhibition by the influenza M2 protein.

Protein science : a publication of the Protein Society

Hong M, DeGrado WF

Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins.

Nature chemistry

Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF

Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions.

Structure (London, England : 1993)

Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, Degrado WF, Samish I

Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding.

Journal of the American Chemical Society

Culik RM, Jo H, DeGrado WF, Gai F

Computational design of a protein crystal.

Proceedings of the National Academy of Sciences of the United States of America

Lanci CJ, MacDermaid CM, Kang SG, Acharya R, North B, Yang X, Qiu XJ, DeGrado WF, Saven JG

Inhibition of integrin α2β1 ameliorates glomerular injury.

Journal of the American Society of Nephrology : JASN

Borza CM, Su Y, Chen X, Yu L, Mont S, Chetyrkin S, Voziyan P, Hudson BG, Billings PC, Jo H, Bennett JS, Degrado WF, Eckes B, Zent R, Pozzi A

Neutralizing epitopes in the membrane-proximal external region of HIV-1 gp41 are influenced by the transmembrane domain and the plasma membrane.

Journal of virology

Montero M, Gulzar N, Klaric KA, Donald JE, Lepik C, Wu S, Tsai S, Julien JP, Hessell AJ, Wang S, Lu S, Burton DR, Pai EF, Degrado WF, Scott JK

Affinity of talin-1 for the β3-integrin cytosolic domain is modulated by its phospholipid bilayer environment.

Proceedings of the National Academy of Sciences of the United States of America

Moore DT, Nygren P, Jo H, Boesze-Battaglia K, Bennett JS, DeGrado WF

Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5.

Proceedings of the National Academy of Sciences of the United States of America

Kim YH, Donald JE, Grigoryan G, Leser GP, Fadeev AY, Lamb RA, DeGrado WF

A photon-free approach to transmembrane protein structure determination.

Journal of molecular biology

Soto CS, Hannigan BT, DeGrado WF

Antibacterial mechanism of action of arylamide foldamers.

Antimicrobial agents and chemotherapy

Mensa B, Kim YH, Choi S, Scott R, Caputo GA, DeGrado WF

Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel.

Journal of the American Chemical Society

Wang J, Ma C, Wu Y, Lamb RA, Pinto LH, DeGrado WF

Computational design of a β-peptide that targets transmembrane helices.

Journal of the American Chemical Society

Shandler SJ, Korendovych IV, Moore DT, Smith-Dupont KB, Streu CN, Litvinov RI, Billings PC, Gai F, Bennett JS, DeGrado WF

Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2.

Journal of the American Chemical Society

Wang J, Ma C, Fiorin G, Carnevale V, Wang T, Hu F, Lamb RA, Pinto LH, Hong M, Klein ML, DeGrado WF

Environment- and sequence-dependence of helical type in membrane-spanning peptides composed of β3-amino acids.

Organic letters

Korendovych IV, Shandler SJ, Montalvo GL, DeGrado WF

Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer.

Science (New York, N.Y.)

Remorino A, Korendovych IV, Wu Y, DeGrado WF, Hochstrasser RM

Computational design of virus-like protein assemblies on carbon nanotube surfaces.

Science (New York, N.Y.)

Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF

Exploring the Requirements for the Hydrophobic Scaffold and Polar Amine in inhibitors of M2 from Influenza A Virus.

ACS medicinal chemistry letters

Wang J, Ma C, Balannik V, Pinto LH, Lamb RA, Degrado WF

Design of a switchable eliminase.

Proceedings of the National Academy of Sciences of the United States of America

Korendovych IV, Kulp DW, Wu Y, Cheng H, Roder H, DeGrado WF

Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus.

Journal of medicinal chemistry

Duque MD, Ma C, Torres E, Wang J, Naesens L, Juárez-Jiménez J, Camps P, Luque FJ, DeGrado WF, Lamb RA, Pinto LH, Vázquez S

Tidal surge in the M2 proton channel, sensed by 2D IR spectroscopy.

Proceedings of the National Academy of Sciences of the United States of America

Ghosh A, Qiu J, DeGrado WF, Hochstrasser RM

Photoinduced electron transfer and fluorophore motion as a probe of the conformational dynamics of membrane proteins: application to the influenza a M2 proton channel.

Langmuir : the ACS journal of surfaces and colloids

Rogers JM, Polishchuk AL, Guo L, Wang J, DeGrado WF, Gai F

Specific binding of adamantane drugs and direction of their polar amines in the pore of the influenza M2 transmembrane domain in lipid bilayers and dodecylphosphocholine micelles determined by NMR spectroscopy.

Journal of the American Chemical Society

Cady SD, Wang J, Wu Y, DeGrado WF, Hong M

Design of a three-helix bundle capable of binding heavy metals in a triscysteine environment.

Angewandte Chemie (International ed. in English)

Chakraborty S, Kravitz JY, Thulstrup PW, Hemmingsen L, DeGrado WF, Pecoraro VL

Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion.

Proceedings of the National Academy of Sciences of the United States of America

Donald JE, Zhang Y, Fiorin G, Carnevale V, Slochower DR, Gai F, Klein ML, DeGrado WF

Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus.

Current opinion in structural biology

Wang J, Qiu JX, Soto C, DeGrado WF

Salt bridges: geometrically specific, designable interactions.

Proteins

Donald JE, Kulp DW, DeGrado WF

Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K⁺ channels, and integrin receptors.

Annual review of biochemistry

Grigoryan G, Moore DT, DeGrado WF

NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation.

Proceedings of the National Academy of Sciences of the United States of America

Metcalf DG, Moore DT, Wu Y, Kielec JM, Molnar K, Valentine KG, Wand AJ, Bennett JS, DeGrado WF

Lipid membranes supported on optically transparent nanosilicas: synthesis and application in characterization of protein-membrane interactions.

Journal of colloid and interface science

Fadeev AY, DeGrado WF

Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation.

Biochemistry

Jo H, Culik RM, Korendovych IV, Degrado WF, Gai F

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.

Journal of the American Chemical Society

Korendovych IV, Senes A, Kim YH, Lear JD, Fry HC, Therien MJ, Blasie JK, Walker FA, Degrado WF

A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein.

Biochemistry

Polishchuk AL, Lear JD, Ma C, Lamb RA, Pinto LH, Degrado WF

Role of the conformational rigidity in the design of biomimetic antimicrobial compounds.

Angewandte Chemie (International ed. in English)

Ivankin A, Livne L, Mor A, Caputo GA, Degrado WF, Meron M, Lin B, Gidalevitz D

Structural biology. The flu's proton escort.

Science (New York, N.Y.)

Fiorin G, Carnevale V, DeGrado WF

Multiple Proton Confinement in the M2 Channel from the Influenza A Virus.

The journal of physical chemistry. C, Nanomaterials and interfaces

Carnevale V, Fiorin G, Levine BG, Degrado WF, Klein ML

Computational design of a self-assembling β-peptide oligomer.

Organic letters

Korendovych IV, Kim YH, Ryan AH, Lear JD, Degrado WF, Shandler SJ

Identification of interacting hot spots in the beta3 integrin stalk using comprehensive interface design.

The Journal of biological chemistry

Donald JE, Zhu H, Litvinov RI, DeGrado WF, Bennett JS

Probing designability via a generalized model of helical bundle geometry.

Journal of molecular biology

Grigoryan G, Degrado WF

The effects of pK(a) tuning on the thermodynamics and kinetics of folding: design of a solvent-shielded carboxylate pair at the a-position of a coiled-coil.

Biophysical Journal

Lau WL, Degrado WF, Roder H

Proton and cation transport activity of the M2 proton channel from influenza A virus.

Proceedings of the National Academy of Sciences of the United States of America

Leiding T, Wang J, Martinsson J, DeGrado WF, Arsköld SP

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus.

Proceedings of the National Academy of Sciences of the United States of America

Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF, Klein ML

Orientation, dynamics, and lipid interaction of an antimicrobial arylamide investigated by 19F and 31P solid-state NMR spectroscopy.

Journal of the American Chemical Society

Su Y, DeGrado WF, Hong M

Specificity for homooligomer versus heterooligomer formation in integrin transmembrane helices.

Journal of molecular biology

Zhu H, Metcalf DG, Streu CN, Billings PC, Degrado WF, Bennett JS

Discovery of potent small-molecule inhibitors of multidrug-resistant Plasmodium falciparum using a novel miniaturized high-throughput luciferase-based assay.

Antimicrobial agents and chemotherapy

Lucumi E, Darling C, Jo H, Napper AD, Chandramohanadas R, Fisher N, Shone AE, Jing H, Ward SA, Biagini GA, DeGrado WF, Diamond SL, Greenbaum DC

Development of a rotamer library for use in beta-peptide foldamer computational design.

Journal of the American Chemical Society

Shandler SJ, Shapovalov MV, Dunbrack RL, DeGrado WF

Infrared signature and folding dynamics of a helical beta-peptide.

Journal of the American Chemical Society

Montalvo G, Waegele MM, Shandler S, Gai F, DeGrado WF

Transmembrane polar interactions are required for signaling in the Escherichia coli sensor kinase PhoQ.

Proceedings of the National Academy of Sciences of the United States of America

Goldberg SD, Clinthorne GD, Goulian M, DeGrado WF

Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore.

Journal of the American Chemical Society

Fry HC, Lehmann A, Saven JG, DeGrado WF, Therien MJ

Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers.

Nature

Cady SD, Schmidt-Rohr K, Wang J, Soto CS, Degrado WF, Hong M

Functional studies and modeling of pore-lining residue mutants of the influenza a virus M2 ion channel.

Biochemistry

Balannik V, Carnevale V, Fiorin G, Levine BG, Lamb RA, Klein ML, Degrado WF, Pinto LH

De novo design of antimicrobial polymers, foldamers, and small molecules: from discovery to practical applications.

Accounts of chemical research

Tew GN, Scott RW, Klein ML, Degrado WF

Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus.

Biochemistry

Balannik V, Wang J, Ohigashi Y, Jing X, Magavern E, Lamb RA, Degrado WF, Pinto LH

Consensus motif for integrin transmembrane helix association.

Proceedings of the National Academy of Sciences of the United States of America

Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF

Solid-supported membrane technology for the investigation of the influenza A virus M2 channel activity.

Pflugers Archiv : European journal of physiology

Balannik V, Obrdlik P, Inayat S, Steensen C, Wang J, Rausch JM, DeGrado WF, Kelety B, Pinto LH

An artificial di-iron oxo-protein with phenol oxidase activity.

Nature chemical biology

Faiella M, Andreozzi C, de Rosales RT, Pavone V, Maglio O, Nastri F, DeGrado WF, Lombardi A

A key role for the integrin alpha2beta1 in experimental and developmental angiogenesis.

The American journal of pathology

San Antonio JD, Zoeller JJ, Habursky K, Turner K, Pimtong W, Burrows M, Choi S, Basra S, Bennett JS, DeGrado WF, Iozzo RV

Experimental and computational evaluation of forces directing the association of transmembrane helices.

Journal of the American Chemical Society

Zhang Y, Kulp DW, Lear JD, DeGrado WF

Engineering and design: editorial overview.

Current opinion in structural biology

Kuhlman B, DeGrado WF

Molecular basis of ChvE function in sugar binding, sugar utilization, and virulence in Agrobacterium tumefaciens.

Journal of bacteriology

He F, Nair GR, Soto CS, Chang Y, Hsu L, Ronzone E, DeGrado WF, Binns AN

Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel.

Proceedings of the National Academy of Sciences of the United States of America

Ma C, Polishchuk AL, Ohigashi Y, Stouffer AL, Schön A, Magavern E, Jing X, Lear JD, Freire E, Lamb RA, DeGrado WF, Pinto LH

Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus.

Journal of the American Chemical Society

Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF, Hong M

Engineered single- and multi-cell chemotaxis pathways in E. coli.

Molecular systems biology

Goldberg SD, Derr P, DeGrado WF, Goulian M

Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer.

Journal of molecular biology

Metcalf DG, Kulp DW, Bennett JS, DeGrado WF

De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers.

Proceedings of the National Academy of Sciences of the United States of America

Choi S, Isaacs A, Clements D, Liu D, Kim H, Scott RW, Winkler JD, DeGrado WF

Using two fluorescent probes to dissect the binding, insertion, and dimerization kinetics of a model membrane peptide.

Journal of the American Chemical Society

Tang J, Yin H, Qiu J, Tucker MJ, DeGrado WF, Gai F

Metal-binding dependent disruption of membranes by designed helices.

Journal of the American Chemical Society

Signarvic RS, Degrado WF

A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha(3)D.

The Journal of chemical physics

Liu F, Dumont C, Zhu Y, DeGrado WF, Gai F, Gruebele M

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus.

Proceedings of the National Academy of Sciences of the United States of America

Khurana E, Dal Peraro M, DeVane R, Vemparala S, DeGrado WF, Klein ML

Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism.

Proceedings of the National Academy of Sciences of the United States of America

Miller MW, Basra S, Kulp DW, Billings PC, Choi S, Beavers MP, McCarty OJ, Zou Z, Kahn ML, Bennett JS, DeGrado WF

Spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle DFsc peptides: implications for O2 reactivity of binuclear non-heme iron enzymes.

Biochemistry

Bell CB, Calhoun JR, Bobyr E, Wei PP, Hedman B, Hodgson KO, Degrado WF, Solomon EI

The role of hydrophobicity in the antimicrobial and hemolytic activities of polymethacrylate derivatives.

Chemistry (Weinheim an der Bergstrasse, Germany)

Kuroda K, Caputo GA, DeGrado WF

Functional analysis of the transmembrane domain in paramyxovirus F protein-mediated membrane fusion.

Journal of molecular biology

Bissonnette ML, Donald JE, DeGrado WF, Jardetzky TS, Lamb RA

De novo designed synthetic mimics of antimicrobial peptides.

Current opinion in biotechnology

Scott RW, DeGrado WF, Tew GN

Species differences in small molecule binding to alpha IIb beta 3 are the result of sequence differences in 2 loops of the alpha IIb beta propeller.

Blood

Basani RB, Zhu H, Thornton MA, Soto CS, Degrado WF, Kowalska MA, Bennett JS, Poncz M

Investigation of an unnatural amino acid for use as a resonance Raman probe: Detection limits, solvent and temperature dependence of the νC≡N band of 4-cyanophenylalanine.

Journal of Raman spectroscopy : JRS

Weeks CL, Polishchuk A, Getahun Z, Degrado WF, Spiro TG

pH-induced conformational change of the influenza M2 protein C-terminal domain.

Biochemistry

Nguyen PA, Soto CS, Polishchuk A, Caputo GA, Tatko CD, Ma C, Ohigashi Y, Pinto LH, DeGrado WF, Howard KP

Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays.

Journal of the American Chemical Society

McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF

Computationally designed peptide inhibitors of protein-protein interactions in membranes.

Biochemistry

Caputo GA, Litvinov RI, Li W, Bennett JS, Degrado WF, Yin H

New design of helix bundle peptide-polymer conjugates.

Biomacromolecules

Shu JY, Tan C, DeGrado WF, Xu T

Modest membrane hydrogen bonds deliver rich results.

Nature chemical biology

Grigoryan G, Degrado WF

Protein-protein interactions in the membrane: sequence, structural, and biological motifs.

Structure (London, England : 1993)

Moore DT, Berger BW, DeGrado WF

The interplay of functional tuning, drug resistance, and thermodynamic stability in the evolution of the M2 proton channel from the influenza A virus.

Structure (London, England : 1993)

Stouffer AL, Ma C, Cristian L, Ohigashi Y, Lamb RA, Lear JD, Pinto LH, DeGrado WF

Oxygen reactivity of the biferrous site in the de novo designed four helix bundle peptide DFsc: nature of the "intermediate" and reaction mechanism.

Journal of the American Chemical Society

Calhoun JR, Bell CB, Smith TJ, Thamann TJ, DeGrado WF, Solomon EI

Determination of the physiological dimer interface of the PhoQ sensor domain.

Journal of molecular biology

Goldberg SD, Soto CS, Waldburger CD, Degrado WF

Identification of the pore-lining residues of the BM2 ion channel protein of influenza B virus.

The Journal of biological chemistry

Ma C, Soto CS, Ohigashi Y, Taylor A, Bournas V, Glawe B, Udo MK, Degrado WF, Lamb RA, Pinto LH

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

Structure (London, England : 1993)

Calhoun JR, Liu W, Spiegel K, Dal Peraro M, Klein ML, Valentine KG, Wand AJ, DeGrado WF

Structural basis for the function and inhibition of an influenza virus proton channel.

Nature

Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF

Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers.

Biochemistry

Tang J, Signarvic RS, DeGrado WF, Gai F

Small molecule inhibitors of integrin alpha2beta1.

Journal of medicinal chemistry

Choi S, Vilaire G, Marcinkiewicz C, Winkler JD, Bennett JS, DeGrado WF

Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy.

Journal of the American Chemical Society

Balakrishnan G, Hu Y, Bender GM, Getahun Z, DeGrado WF, Spiro TG

Site-specific hydration status of an amphipathic peptide in AOT reverse micelles.

Langmuir : the ACS journal of surfaces and colloids

Mukherjee S, Chowdhury P, DeGrado WF, Gai F

De novo design of a single-chain diphenylporphyrin metalloprotein.

Journal of the American Chemical Society

Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, DeGrado WF

Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores.

The journal of physical chemistry. A

Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM, Vinogradov SA

Foldamers as versatile frameworks for the design and evolution of function.

Nature chemical biology

Goodman CM, Choi S, Shandler S, DeGrado WF

Mutagenesis data in the automated prediction of transmembrane helix dimers.

Proteins

Metcalf DG, Law PB, DeGrado WF

Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle.

Journal of the American Chemical Society

Cady SD, Goodman C, Tatko CD, DeGrado WF, Hong M

Adhesion of MC3T3-E1 cells to RGD peptides of different flanking residues: detachment strength and correlation with long-term cellular function.

Journal of biomedical materials research. Part A

Lee MH, Adams CS, Boettiger D, Degrado WF, Shapiro IM, Composto RJ, Ducheyne P

Computational design of peptides that target transmembrane helices.

Science (New York, N.Y.)

Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, DeGrado WF

Interactions of ADP-stimulated human platelets with PEGylated polystyrene substrates prepared by surface amidation.

Colloids and surfaces. B, Biointerfaces

Wang PC, Vilaire G, DeGrado WF, Bennett JS

The leech product saratin is a potent inhibitor of platelet integrin alpha2beta1 and von Willebrand factor binding to collagen.

The FEBS journal

White TC, Berny MA, Robinson DK, Yin H, DeGrado WF, Hanson SR, McCarty OJ

Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer.

Proceedings of the National Academy of Sciences of the United States of America

Fang C, Senes A, Cristian L, DeGrado WF, Hochstrasser RM

Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations.

Journal of structural biology

Dal Peraro M, Spiegel K, Lamoureux G, De Vivo M, DeGrado WF, Klein ML

Activation of platelet alphaIIbbeta3 by an exogenous peptide corresponding to the transmembrane domain of alphaIIb.

The Journal of biological chemistry

Yin H, Litvinov RI, Vilaire G, Zhu H, Li W, Caputo GA, Moore DT, Lear JD, Weisel JW, Degrado WF, Bennett JS

E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices.

Journal of molecular biology

Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF

Truncation of a cross-linked GCN4-p1 coiled coil leads to ultrafast folding.

Biochemistry

Bunagan MR, Cristian L, DeGrado WF, Gai F

Helix-packing motifs in membrane proteins.

Proceedings of the National Academy of Sciences of the United States of America

Walters RF, DeGrado WF

The structure of a designed diiron(III) protein: implications for cofactor stabilization and catalysis.

Angewandte Chemie (International ed. in English)

Wade H, Stayrook SE, Degrado WF

Arylamide derivatives as allosteric inhibitors of the integrin alpha2beta1/type I collagen interaction.

Bioorganic & medicinal chemistry letters

Yin H, Gerlach LO, Miller MW, Moore DT, Liu D, Vilaire G, Bennett JS, DeGrado WF

Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics.

Journal of chemical theory and computation

Lopez CF, Nielsen SO, Srinivas G, Degrado WF, Klein ML

Characterization of a membrane protein folding motif, the Ser zipper, using designed peptides.

Journal of molecular biology

North B, Cristian L, Fu Stowell X, Lear JD, Saven JG, Degrado WF

Activation of individual alphaIIbbeta3 integrin molecules by disruption of transmembrane domain interactions in the absence of clustering.

Biochemistry

Litvinov RI, Vilaire G, Li W, DeGrado WF, Weisel JW, Bennett JS

Polar networks control oligomeric assembly in membranes.

Journal of the American Chemical Society

Tatko CD, Nanda V, Lear JD, Degrado WF

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study.

The journal of physical chemistry. B

Pophristic V, Vemparala S, Ivanov I, Liu Z, Klein ML, DeGrado WF

Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics.

Journal of the American Chemical Society

Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML

Computational design of heterochiral peptides against a helical target.

Journal of the American Chemical Society

Nanda V, DeGrado WF

Arylamide derivatives as peptidomimetic inhibitors of calmodulin.

Organic letters

Yin H, Frederick KK, Liu D, Wand AJ, Degrado WF

Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.

Journal of the American Chemical Society

Geremia S, Di Costanzo L, Randaccio L, Engel DE, Lombardi A, Nastri F, DeGrado WF

Spectroscopic and computational studies of the de novo designed protein DF2t: correlation to the biferrous active site of ribonucleotide reductase and factors that affect O2 reactivity.

Journal of the American Chemical Society

Wei PP, Skulan AJ, Wade H, DeGrado WF, Solomon EI

Alpha-alpha linking motifs and interhelical orientations.

Proteins

Engel DE, DeGrado WF

The design and evaluation of heparin-binding foldamers.

Angewandte Chemie (International ed. in English)

Choi S, Clements DJ, Pophristic V, Ivanov I, Vemparala S, Bennett JS, Klein ML, Winkler JD, DeGrado WF

An atomic environment potential for use in protein structure prediction.

Journal of molecular biology

Summa CM, Levitt M, Degrado WF

Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops.

Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry

Maglio O, Nastri F, Calhoun JR, Lahr S, Wade H, Pavone V, DeGrado WF, Lombardi A

T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1.

Biophysical Journal

Wang T, Lau WL, DeGrado WF, Gai F

Dynamic heterodimer-functionalized surfaces for endothelial cell adhesion.

Biomaterials

Willcox PJ, Reinhart-King CA, Lahr SJ, DeGrado WF, Hammer DA

Structural organization and interactions of transmembrane domains in tetraspanin proteins.

BMC structural biology

Kovalenko OV, Metcalf DG, DeGrado WF, Hemler ME

Automated use of mutagenesis data in structure prediction.

Proteins

Nanda V, DeGrado WF

Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins.

Proteins

Adamian L, Nanda V, DeGrado WF, Liang J

X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils.

Journal of molecular biology

Slovic AM, Stayrook SE, North B, Degrado WF

De novo design of a redox-active minimal rubredoxin mimic.

Journal of the American Chemical Society

Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, Degrado WF

Synergistic interactions between aqueous and membrane domains of a designed protein determine its fold and stability.

Journal of molecular biology

Cristian L, Nanda V, Lear JD, DeGrado WF

Amphiphilic polymethacrylate derivatives as antimicrobial agents.

Journal of the American Chemical Society

Kuroda K, DeGrado WF

De novo design of a pentameric coiled-coil: decoding the motif for tetramer versus pentamer formation in water-soluble phospholamban.

The journal of peptide research : official journal of the American Peptide Society

Slovic AM, Lear JD, DeGrado WF

Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle.

Protein science : a publication of the Protein Society

Howard KP, Liu W, Crocker E, Nanda V, Lear J, Degrado WF, Smith SO

The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment.

Protein science : a publication of the Protein Society

Duong-Ly KC, Nanda V, Degrado WF, Howard KP

Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor.

Journal of the American Chemical Society

Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF

A push-pull mechanism for regulating integrin function.

Proceedings of the National Academy of Sciences of the United States of America

Li W, Metcalf DG, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, Degrado WF, Bennett JS

Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function.

Journal of molecular biology

Stouffer AL, Nanda V, Lear JD, DeGrado WF

Analysis and design of turns in alpha-helical hairpins.

Journal of molecular biology

Lahr SJ, Engel DE, Stayrook SE, Maglio O, North B, Geremia S, Lombardi A, DeGrado WF

Artificial diiron proteins: from structure to function.

Biopolymers

Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, DeGrado WF

Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide.

FEBS letters

Ghirlanda G, Hilcove SA, Pidikiti R, Johansson JS, Lear JD, Degrado WF, Eckenhoff RG

Simulated evolution of emergent chiral structures in polyalanine.

Journal of the American Chemical Society

Nanda V, Degrado WF

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers.

Chemistry (Weinheim an der Bergstrasse, Germany)

Doerksen RJ, Chen B, Liu D, Tew GN, Degrado WF, Klein ML

Length Dependent Helix-Coil Transition Kinetics of Nine Alanine-Based Peptides.

The journal of physical chemistry. B

Wang T, Zhu Y, Getahun Z, Du D, Huang CY, Degrado WF, Gai F

Association of a model transmembrane peptide containing gly in a heptad sequence motif.

Biophysical Journal

Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF

De novo design of catalytic proteins.

Proceedings of the National Academy of Sciences of the United States of America

Kaplan J, DeGrado WF

Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs.

Current opinion in structural biology

Senes A, Engel DE, DeGrado WF

De novo design of a D2-symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc1.

Journal of the American Chemical Society

Ghirlanda G, Osyczka A, Liu W, Antolovich M, Smith KM, Dutton PL, Wand AJ, DeGrado WF

Structural basis for integrin alphaIIbbeta3 clustering.

Biochemical Society transactions

Li R, Bennett JS, Degrado WF

A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides.

Journal of the American Chemical Society

Tucker MJ, Getahun Z, Nanda V, DeGrado WF, Gai F

Amino acid propensities are position-dependent throughout the length of alpha-helices.

Journal of molecular biology

Engel DE, DeGrado WF

Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes.

The Journal of biological chemistry

Li R, Gorelik R, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS

Nontoxic membrane-active antimicrobial arylamide oligomers.

Angewandte Chemie (International ed. in English)

Liu D, Choi S, Chen B, Doerksen RJ, Clements DJ, Winkler JD, Klein ML, DeGrado WF

Computational design of water-soluble analogues of the potassium channel KcsA.

Proceedings of the National Academy of Sciences of the United States of America

Slovic AM, Kono H, Lear JD, Saven JG, DeGrado WF

Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization.

Biophysical Journal

Lau WL, Ege DS, Lear JD, Hammer DA, DeGrado WF

Computational design and characterization of a monomeric helical dinuclear metalloprotein.

Journal of molecular biology

Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, Saven JG

Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein.

Proceedings of the National Academy of Sciences of the United States of America

Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF, Gai F

Use of thiol-disulfide equilibria to measure the energetics of assembly of transmembrane helices in phospholipid bilayers.

Proceedings of the National Academy of Sciences of the United States of America

Cristian L, Lear JD, DeGrado WF

De novo design of a molecular switch: phosphorylation-dependent association of designed peptides.

Journal of molecular biology

Signarvic RS, DeGrado WF

Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange.

Protein science : a publication of the Protein Society

Cristian L, Lear JD, DeGrado WF

Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles.

Biochemistry

Lear JD, Gratkowski H, Adamian L, Liang J, DeGrado WF

Computational biology: Biosensor design.

Nature

DeGrado WF

Activation of integrin alphaIIbbeta3 by modulation of transmembrane helix associations.

Science (New York, N.Y.)

Li R, Mitra N, Gratkowski H, Vilaire G, Litvinov R, Nagasami C, Weisel JW, Lear JD, DeGrado WF, Bennett JS

How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles.

Protein science : a publication of the Protein Society

DeGrado WF, Gratkowski H, Lear JD

Preorganization of molecular binding sites in designed diiron proteins.

Proceedings of the National Academy of Sciences of the United States of America

Maglio O, Nastri F, Pavone V, Lombardi A, DeGrado WF

The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.

Protein science : a publication of the Protein Society

Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF

Computational design of a water-soluble analog of phospholamban.

Protein science : a publication of the Protein Society

Slovic AM, Summa CM, Lear JD, DeGrado WF

Sliding helix and change of coordination geometry in a model di-MnII protein.

Angewandte Chemie (International ed. in English)

DeGrado WF, Di Costanzo L, Geremia S, Lombardi A, Pavone V, Randaccio L

Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor.

Journal of the American Chemical Society

Papoian GA, DeGrado WF, Klein ML

Using nitrile-derivatized amino acids as infrared probes of local environment.

Journal of the American Chemical Society

Getahun Z, Huang CY, Wang T, De León B, DeGrado WF, Gai F

Use of phage display to probe the evolution of binding specificity and affinity in integrins.

Protein engineering

Li R, Hoess RH, Bennett JS, DeGrado WF

Characterization of the monomeric form of the transmembrane and cytoplasmic domains of the integrin beta 3 subunit by NMR spectroscopy.

Biochemistry

Li R, Babu CR, Valentine K, Lear JD, Wand AJ, Bennett JS, DeGrado WF

Light-induced helix formation.

Journal of the American Chemical Society

Huang CY, He S, DeGrado WF, McCafferty DG, Gai F

Long-range interactions stabilize the fold of a non-natural oligomer.

Journal of the American Chemical Society

Cheng RP, DeGrado WF

Cooperativity and specificity of association of a designed transmembrane peptide.

Biophysical Journal

Gratkowski H, Dai QH, Wand AJ, DeGrado WF, Lear JD

Computational de novo design, and characterization of an A(2)B(2) diiron protein.

Journal of molecular biology

Summa CM, Rosenblatt MM, Hong JK, Lear JD, DeGrado WF

Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein.

Proceedings of the National Academy of Sciences of the United States of America

Howard KP, Lear JD, DeGrado WF

A hierarchic approach to the design of hexameric helical barrels.

Journal of molecular biology

Ghirlanda G, Lear JD, Ogihara NL, Eisenberg D, DeGrado WF

De novo design of biomimetic antimicrobial polymers.

Proceedings of the National Academy of Sciences of the United States of America

Tew GN, Liu D, Chen B, Doerksen RJ, Kaplan J, Carroll PJ, Klein ML, DeGrado WF

Noncovalent self-assembly of a heterotetrameric diiron protein.

Proceedings of the National Academy of Sciences of the United States of America

Marsh EN, DeGrado WF

Helix formation via conformation diffusion search.

Proceedings of the National Academy of Sciences of the United States of America

Huang CY, Getahun Z, Zhu Y, Klemke JW, DeGrado WF, Gai F

Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center.

Journal of the American Chemical Society

Di Costanzo L, Wade H, Geremia S, Randaccio L, Pavone V, DeGrado WF, Lombardi A

Template-constrained somatostatin analogues: a biphenyl linker induces a type-V' turn.

Journal of the American Chemical Society

Cheng RP, Suich DJ, Cheng H, Roder H, DeGrado WF

Time-resolved infrared study of the helix-coil transition using (13)C-labeled helical peptides.

Journal of the American Chemical Society

Huang CY, Getahun Z, Wang T, DeGrado WF, Gai F

Oligomerization of the integrin alphaIIbbeta3: roles of the transmembrane and cytoplasmic domains.

Proceedings of the National Academy of Sciences of the United States of America

Li R, Babu CR, Lear JD, Wand AJ, Bennett JS, DeGrado WF

Introduction: protein design.

Chemical reviews

DeGrado WF

beta-Peptides: from structure to function.

Chemical reviews

Cheng RP, Gellman SH, DeGrado WF

Temperature-dependent helix-coil transition of an alanine based peptide.

Journal of the American Chemical Society

Huang CY, Klemke JW, Getahun Z, DeGrado WF, Gai F

D(n)-symmetrical tertiary templates for the design of tubular proteins.

Journal of molecular biology

North B, Summa CM, Ghirlanda G, DeGrado WF

Dynamics of a de novo designed three-helix bundle protein studied by 15N, 13C, and 2H NMR relaxation methods.

Biochemistry

Walsh ST, Lee AL, DeGrado WF, Wand AJ

De novo design, synthesis, and characterization of antimicrobial beta-peptides.

Journal of the American Chemical Society

Liu D, DeGrado WF

De novo design, synthesis and characterization of membrane-active peptides.

Biochemical Society transactions

Lear JD, Gratkowski H, DeGrado WF

De novo design of a monomeric helical beta-peptide stabilized by electrostatic interactions.

Journal of the American Chemical Society

Cheng RP, DeGrado WF

Proton and metal ion-dependent assembly of a model diiron protein.

Protein science : a publication of the Protein Society

Pasternak A, Kaplan J, Lear JD, Degrado WF

Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability This work was supported by a grant from the U.S. Army Research Office. Y. Tang is supported by a Whitaker Graduate Research Fellowship. We thank Dr. Gary Hat

Angewandte Chemie (International ed. in English)

Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF, Tirrell DA

Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability.

Angewandte Chemie (International ed. in English)

Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF, Tirrell DA

Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine.

Biochemistry

Tang Y, Ghirlanda G, Vaidehi N, Kua J, Mainz DT, Goddard III WA, DeGrado WF, Tirrell DA

Design of three-dimensional domain-swapped dimers and fibrous oligomers.

Proceedings of the National Academy of Sciences of the United States of America

Ogihara NL, Ghirlanda G, Bryson JW, Gingery M, DeGrado WF, Eisenberg D

Polar side chains drive the association of model transmembrane peptides.

Proceedings of the National Academy of Sciences of the United States of America

Gratkowski H, Lear JD, DeGrado WF

Hydrophobic core malleability of a de novo designed three-helix bundle protein.

Journal of molecular biology

Walsh ST, Sukharev VI, Betz SF, Vekshin NL, DeGrado WF

Evolution of binding affinity in a WW domain probed by phage display.

Protein science : a publication of the Protein Society

Dalby PA, Hoess RH, DeGrado WF

Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy.

Proceedings of the National Academy of Sciences of the United States of America

Talaga DS, Lau WL, Roder H, Tang J, Jia Y, DeGrado WF, Hochstrasser RM

pH-dependent tetramerization and amantadine binding of the transmembrane helix of M2 from the influenza A virus.

Biochemistry

Salom D, Hill BR, Lear JD, DeGrado WF

Structural consequences of an amino acid deletion in the B1 domain of protein G.

Proteins

O'Neil KT, Bach AC, DeGrado WF

De novo design of helical bundles as models for understanding protein folding and function.

Accounts of chemical research

Hill RB, Raleigh DP, Lombardi A, DeGrado WF

Template-constrained cyclic peptide analogues of somatostatin: subtype-selective binding to somatostatin receptors and antiangiogenic activity.

Bioorganic & medicinal chemistry

Suich DJ, Mousa SA, Singh G, Liapakis G, Reisine T, DeGrado WF

The activation state of alphavbeta 3 regulates platelet and lymphocyte adhesion to intact and thrombin-cleaved osteopontin.

The Journal of biological chemistry

Helluin O, Chan C, Vilaire G, Mousa S, DeGrado WF, Bennett JS

Retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.

Proceedings of the National Academy of Sciences of the United States of America

Lombardi A, Summa CM, Geremia S, Randaccio L, Pavone V, DeGrado WF

A polar, solvent-exposed residue can be essential for native protein structure.

Structure (London, England : 1993)

Hill RB, DeGrado WF

Asparagine-mediated self-association of a model transmembrane helix.

Nature structural biology

Choma C, Gratkowski H, Lear JD, DeGrado WF

Total chemical synthesis of the integral membrane protein influenza A virus M2: role of its C-terminal domain in tetramer assembly.

Biochemistry

Kochendoerfer GG, Salom D, Lear JD, Wilk-Orescan R, Kent SB, DeGrado WF

The twists and turns of beta-peptides.

The journal of peptide research : official journal of the American Peptide Society

DeGrado WF, Schneider JP, Hamuro Y

Tertiary templates for the design of diiron proteins.

Current opinion in structural biology

Summa CM, Lombardi A, Lewis M, DeGrado WF

Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.

Protein science : a publication of the Protein Society

Patterson WR, Anderson DH, DeGrado WF, Cascio D, Eisenberg D

Solution structure and dynamics of a de novo designed three-helix bundle protein.

Proceedings of the National Academy of Sciences of the United States of America

Walsh ST, Cheng H, Bryson JW, Roder H, DeGrado WF

Rapid synthesis of RGD mimetics with isoxazoline scaffolds on solid phase: identification of alphavbeta3 antagonists lead compounds.

Bioorganic & medicinal chemistry letters

Rockwell AL, Rafalski M, Pitts WJ, Batt DG, Petraitis JJ, DeGrado WF, Mousa S, Jadhav PK

The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in relation to its three-dimensional structure.

Proceedings of the National Academy of Sciences of the United States of America

Hamm P, Lim M, DeGrado WF, Hochstrasser RM

Cu(II) inhibition of the proton translocation machinery of the influenza A virus M2 protein.

The Journal of biological chemistry

Gandhi CS, Shuck K, Lear JD, Dieckmann GR, DeGrado WF, Lamb RA, Pinto LH

Exploration of the structural features defining the conduction properties of a synthetic ion channel.

Biophysical Journal

Dieckmann GR, Lear JD, Zhong Q, Klein ML, DeGrado WF, Sharp KA

De novo design and structural characterization of proteins and metalloproteins.

Annual review of biochemistry

DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A

Synthesis and antiplatelet effects of an isoxazole series of glycoprotein IIb/IIIa antagonists.

Bioorganic & medicinal chemistry letters

Xue CB, Roderick J, Mousa S, Olson RE, DeGrado WF

From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin.

Journal of molecular biology

Ghirlanda G, Lear JD, Lombardi A, DeGrado WF

The role of protonation and metal chelation preferences in defining the properties of mercury-binding coiled coils.

Journal of molecular biology

Dieckmann GR, McRorie DK, Lear JD, Sharp KA, DeGrado WF, Pecoraro VL

From coiled coils to small globular proteins: design of a native-like three-helix bundle.

Protein science : a publication of the Protein Society

Bryson JW, Desjarlais JR, Handel TM, DeGrado WF

Design and synthesis of cyclic inhibitors of matrix metalloproteinases and TNF-alpha production.

Journal of medicinal chemistry

Xue CB, He X, Roderick J, DeGrado WF, Cherney RJ, Hardman KD, Nelson DJ, Copeland RA, Jaffee BD, Decicco CP

Macrocyclic amino carboxylates as selective MMP-8 inhibitors.

Journal of medicinal chemistry

Cherney RJ, Wang L, Meyer DT, Xue CB, Wasserman ZR, Hardman KD, Welch PK, Covington MB, Copeland RA, Arner EC, DeGrado WF, Decicco CP

Analysis and design of three-stranded coiled coils and three-helix bundles.

Folding & design

Schneider JP, Lombardi A, DeGrado WF

Two models of the influenza A M2 channel domain: verification by comparison.

Folding & design

Forrest LR, DeGrado WF, Dieckmann GR, Sansom MS

A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity.

Proceedings of the National Academy of Sciences of the United States of America

Pinto LH, Dieckmann GR, Gandhi CS, Papworth CG, Braman J, Shaughnessy MA, Lear JD, Lamb RA, DeGrado WF

Proteins from scratch.

Science (New York, N.Y.)

DeGrado WF

Modeling transmembrane helical oligomers.

Current opinion in structural biology

Dieckmann GR, DeGrado WF

Design, synthesis, and in vitro activities of benzamide-core glycoprotein IIb/IIIa antagonists: 2,3-diaminopropionic acid derivatives as surrogates of aspartic acid.

Bioorganic & medicinal chemistry

Xue CB, Roderick J, Jackson S, Rafalski M, Rockwell A, Mousa S, Olson RE, DeGrado WF

Agonist-activated alphavbeta3 on platelets and lymphocytes binds to the matrix protein osteopontin.

The Journal of biological chemistry

Bennett JS, Chan C, Vilaire G, Mousa SA, DeGrado WF

De novo design of native proteins: characterization of proteins intended to fold into antiparallel, rop-like, four-helix bundles.

Biochemistry

Betz SF, Liebman PA, DeGrado WF

The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies.

Protein science : a publication of the Protein Society

Ogihara NL, Weiss MS, Degrado WF, Eisenberg D

Thermodynamic analysis of a designed three-stranded coiled coil.

Biochemistry

Boice JA, Dieckmann GR, DeGrado WF, Fairman R

Novel nonpeptide antiplatelet glycoprotein IIb/IIIa receptor antagonist, DMP754: receptor binding affinity and specificity.

Coronary artery disease

Mousa SA, Forsythe M, Lorelli W, Bozarth J, Xue CB, Wityak J, Sielecki TM, Olson RE, DeGrado W, Kapil R, Hussain M, Wexler R, Thoolen MJ, Reilly TM

Expression of de novo designed alpha-helical bundles.

Acta chemica Scandinavica (Copenhagen, Denmark : 1989)

Betz SF, Bryson JW, Passador MC, Brown RJ, O'Neil KT, DeGrado WF

Protein minimization: downsizing through mutation.

Proceedings of the National Academy of Sciences of the United States of America

DeGrado WF, Sosnick TR

Controlling topology and native-like behavior of de novo-designed peptides: design and characterization of antiparallel four-stranded coiled coils.

Biochemistry

Betz SF, DeGrado WF

Membrane fusion activity of the influenza virus hemagglutinin: interaction of HA2 N-terminal peptides with phospholipid vesicles.

Biochemistry

Rafalski M, Ortiz A, Rockwell A, van Ginkel LC, Lear JD, DeGrado WF, Wilschut J

The interaction of calmodulin with fluorescent and photoreactive model peptides: evidence for a short interdomain separation.

Proteins

O'Neil KT, DeGrado WF

p-Benzoyl-L-phenylalanine, a new photoreactive amino acid. Photolabeling of calmodulin with a synthetic calmodulin-binding peptide.

The Journal of biological chemistry

Kauer JC, Erickson-Viitanen S, Wolfe HR, DeGrado WF

Antibodies to human c-myc oncogene product: evidence of an evolutionarily conserved protein induced during cell proliferation.

Science (New York, N.Y.)

Persson H, Hennighausen L, Taub R, DeGrado W, Leder P

Purification and properties of thiol beta-lactamase. A mutant of pBR322 beta-lactamase in which the active site serine has been replaced with cysteine.

The Journal of biological chemistry

Sigal IS, DeGrado WF, Thomas BJ, Petteway SR

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William Degrado, PhD