William DeGrado, PhD

Title(s)Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address555 Mission Bay Blvd South
San Francisco CA 94158
Phone415-476-9679
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    Collapse Biography 
    Collapse Awards and Honors
    1988Du Vigneaud Award for Young Investigators in Peptide Research
    1989Protein Society Young Investigator Award
    1992Eli Lilly Award in Biological Chemistry
    1993DuPont Merck Summit Award
    1995Fellow, American Association for the Advancement of Science
    1998Fellow, AAAS
    1999Member, National Academy of Sciences (U.S.A.)
    2003Merrifield Award, Peptide Society
    2008Ralph F. Hirschmann Award in Peptide Chemistry (American Chemical Society)
    2009Makineni Award (APS)
    The Protein Society2015The Stein and Moore Award
    Weizmann Institute2016Max Perutz Memorial Lecture
    American Chemical Society2018Cope Scholar Award
    American Chemical Society2018M. Goodman Memorial Prize
    Franklin Institute & City Council of Philadelphia2020John C. Scott Award

    Collapse Overview 
    Collapse Overview
    One research interest is in the de novo design, in which one designs proteins or drugs beginning from first principles. This approach critically tests our understanding of protein folding and function, while also laying the groundwork for the design of molecules with properties unprecedented in nature.

    Collapse Research 
    Collapse Research Activities and Funding
    Relationships between conformational strains of tau and amyloid-beta, TREM2 and APOE variants, and phenotypic variations of Alzheimer's Disease
    NIH RF1AG061874Sep 30, 2018 - Mar 31, 2023
    Role: Co-Principal Investigator
    Deciphering the relationship between structure, dynamics and function in helical bundle proteins
    NIH R35GM122603May 1, 2017 - Apr 30, 2022
    Role: Principal Investigator
    Treatment of pulmonary fibrosis with inhibitors of integrin alphavbeta1.
    NIH UH3HL123423Sep 1, 2014 - Jun 30, 2019
    Role: Co-Principal Investigator
    Treatment of pulmonary fibrosis with inhibitors of integrin alphavbeta1.
    NIH UH2HL123423Sep 1, 2014 - Jul 14, 2016
    Role: Co-Principal Investigator
    Vaccines that Replicate the Neutralization-Competent Structure of the gp41 MPER
    NIH R01AI097051Mar 1, 2012 - Feb 28, 2018
    Role: Co-Principal Investigator
    Development of drugs that target the M2 proton channel from the influenza A Virus
    NIH U01AI074571May 15, 2008 - Apr 30, 2014
    Role: Principal Investigator
    Design and mechanistic studies of mimics of antimicrobial peptides
    NIH R56AI074866Apr 15, 2008 - Jul 31, 2014
    Role: Principal Investigator
    Design and mechanistic studies of mimics of antimicrobial peptides
    NIH R01AI074866Apr 15, 2008 - Jul 31, 2013
    Role: Principal Investigator
    Proteomics to Biomimetic Polymers: Engineering Principle
    NIH R01EB002048Sep 24, 2002 - Aug 31, 2007
    Role: Principal Investigator
    Proteomics to Biomimetic Polymers: Engineering Principle
    NIH R01GM065803Sep 24, 2002 - Aug 31, 2006
    Role: Principal Investigator
    An Undulator Resource for Structural Biology
    NIH P41RR015301Jun 15, 2001 - Mar 31, 2013
    Role: Co-Investigator
    Bioorganic models for transmembrane proteins
    NIH R01GM060610Dec 1, 1999 - Apr 30, 2010
    Role: Principal Investigator
    Structure of M2 Proton Channel from Influenza A Virus
    NIH R01GM056423Aug 1, 1997 - Apr 30, 2017
    Role: Principal Investigator
    Degenerative and Dementing Diseases of Aging
    NIH P01AG002132Apr 1, 1997 - Mar 31, 2025
    Role: Co-Investigator
    PURCHASE OF ANALYTICAL ULTRACENTRIFUGE
    NIH S10RR011854Mar 18, 1997 - Mar 17, 1998
    Role: Principal Investigator
    De Novo Design of Alpha-Helical Bundles
    NIH R01GM054616Aug 1, 1996 - Jun 30, 2018
    Role: Principal Investigator
    De novo design of alpha-helical bundles
    NIH R37GM054616Aug 1, 1996 - Jul 31, 2014
    Role: Principal Investigator
    Principles of Energy Transduction in Proteins
    NIH P01GM048130Aug 1, 1993 - Jul 31, 2010
    Role: Co-Investigator
    High Performance Computing for Biomedical Research
    NIH P41RR006009Sep 1, 1990 - Jul 31, 2013
    Role: Co-Investigator
    National Biomedical NMR Resource at Madison
    NIH P41RR002301Jul 1, 1985 - Feb 28, 2015
    Role: Co-Investigator
    ULTRAFAST OPTICAL PROCESSES LABORATORY
    NIH P41RR001348Aug 1, 1982 - May 31, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Academic Senate

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Elucidation of the molecular interactions that enable stable assembly and structural diversity in multicomponent immune receptors. Proc Natl Acad Sci U S A. 2021 Jun 29; 118(26). Fong LK, Chalkley MJ, Tan SK, Grabe M, DeGrado WF. PMID: 34155106.
      View in: PubMed   Mentions:    Fields:    
    2. Visualization of Platelet Integrins via Two-Photon Microscopy Using Anti-transmembrane Domain Peptides Containing a Blue Fluorescent Amino Acid. Biochemistry. 2021 May 19. Fong KP, Ahmed IA, Mravic M, Jo H, Kim OV, Litvinov RI, Weisel JW, DeGrado WF, Gai F, Bennett JS. PMID: 34010565.
      View in: PubMed   Mentions:    Fields:    
    3. Inclusion of the C-Terminal Domain in the ß-Sheet Core of Heparin-Fibrillized Three-Repeat Tau Protein Revealed by Solid-State Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc. 2021 May 13. Dregni AJ, Wang HK, Wu H, Duan P, Jin J, DeGrado WF, Hong M. PMID: 33983722.
      View in: PubMed   Mentions:    Fields:    
    4. Constructing ion channels from water-soluble a-helical barrels. Nat Chem. 2021 May 10. 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. PMID: 33972753.
      View in: PubMed   Mentions:    Fields:    
    5. Integrin a2ß1 regulates collagen I tethering to modulate hyperresponsiveness in reactive airway disease models. J Clin Invest. 2021 May 06. Liu S, Ngo U, Tang XZ, Ren X, Qiu W, Huang X, DeGrado W, Allen CD, Jo H, Sheppard D, Sundaram AB. PMID: 33956668.
      View in: PubMed   Mentions:    Fields:    
    6. Protein design-scapes generated by microfluidic DNA assembly elucidate domain coupling in the bacterial histidine kinase CpxA. Proc Natl Acad Sci U S A. 2021 Mar 23; 118(12). Clark IC, Mensa B, Ochs CJ, Schmidt NW, Mravic M, Quintana FJ, DeGrado WF, Abate AR. PMID: 33723045.
      View in: PubMed   Mentions: 1     Fields:    
    7. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of a-Helix As Oxyanion-Binding Site. J Am Chem Soc. 2021 Mar 10; 143(9):3330-3339. Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. PMID: 33635059.
      View in: PubMed   Mentions: 1     Fields:    
    8. De Novo Design, Solution Characterization, and Crystallographic Structure of an Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing a Mn(V) Species. J Am Chem Soc. 2021 01 13; 143(1):252-259. Mann SI, Nayak A, Gassner GT, Therien MJ, DeGrado WF. PMID: 33373215.
      View in: PubMed   Mentions:    Fields:    
    9. Allosteric cooperation in a de novo-designed two-domain protein. Proc Natl Acad Sci U S A. 2020 12 29; 117(52):33246-33253. Pirro F, Schmidt N, Lincoff J, Widel ZX, Polizzi NF, Liu L, Therien MJ, Grabe M, Chino M, Lombardi A, DeGrado WF. PMID: 33318174.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    10. Platform to Discover Protease-Activated Antibiotics and Application to Siderophore-Antibiotic Conjugates. J Am Chem Soc. 2020 12 23; 142(51):21310-21321. Boyce JH, Dang B, Ary B, Edmondson Q, Craik CS, DeGrado WF, Seiple IB. PMID: 33301681.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    11. Dual antagonists of a5ß1/avß1 integrin for airway hyperresponsiveness. Bioorg Med Chem Lett. 2020 11 15; 30(22):127578. 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. PMID: 33007395.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    12. Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics. J Am Chem Soc. 2020 10 14; 142(41):17425-17433. Watkins LC, DeGrado WF, Voth GA. PMID: 32933245.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    13. Prion biology: implications for Alzheimer's disease therapeutics. Lancet Neurol. 2020 10; 19(10):802-803. Condello C, DeGrado WF, Prusiner SB. PMID: 32949533.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. A defined structural unit enables de novo design of small-molecule-binding proteins. Science. 2020 09 04; 369(6508):1227-1233. Polizzi NF, DeGrado WF. PMID: 32883865.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    15. Robust Sequence Determinants of a-Synuclein Toxicity in Yeast Implicate Membrane Binding. ACS Chem Biol. 2020 08 21; 15(8):2137-2153. 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. PMID: 32786289.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    16. Deep mutational scanning reveals the structural basis for a-synuclein activity. Nat Chem Biol. 2020 06; 16(6):653-659. Newberry RW, Leong JT, Chow ED, Kampmann M, DeGrado WF. PMID: 32152544.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    17. De novo protein design, a retrospective. Q Rev Biophys. 2020 02 11; 53:e3. Korendovych IV, DeGrado WF. PMID: 32041676.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    18. 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. 2020 02 04; 59(4):627-634. Thomaston JL, Konstantinidi A, Liu L, Lambrinidis G, Tan J, Caffrey M, Wang J, Degrado WF, Kolocouris A. PMID: 31894969.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    19. De novo design of a homo-trimeric amantadine-binding protein. Elife. 2019 12 19; 8. Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D. PMID: 31854299.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    20. A disease-associated mutation in fibrillin-1 differentially regulates integrin-mediated cell adhesion. J Biol Chem. 2019 11 29; 294(48):18232-18243. Del Cid JS, Reed NI, Molnar K, Liu S, Dang B, Jensen SA, DeGrado W, Handford PA, Sheppard D, Sundaram AB. PMID: 31640988.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    21. In vitro 0N4R tau fibrils contain a monomorphic ß-sheet core enclosed by dynamically heterogeneous fuzzy coat segments. Proc Natl Acad Sci U S A. 2019 08 13; 116(33):16357-16366. Dregni AJ, Mandala VS, Wu H, Elkins MR, Wang HK, Hung I, DeGrado WF, Hong M. PMID: 31358628.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    22. Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. J Am Chem Soc. 2019 07 24; 141(29):11667-11676. Watkins LC, Liang R, Swanson JMJ, DeGrado WF, Voth GA. PMID: 31264413.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    23. Modulating Integrin aIIbß3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts. Biochemistry. 2019 07 30; 58(30):3251-3259. Tan SK, Fong KP, Polizzi NF, Sternisha A, Slusky JSG, Yoon K, DeGrado WF, Bennett JS. PMID: 31264850.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    24. X-ray Crystal Structure of the Influenza A M2 Proton Channel S31N Mutant in Two Conformational States: An Open and Shut Case. J Am Chem Soc. 2019 07 24; 141(29):11481-11488. Thomaston JL, Wu Y, Polizzi N, Liu L, Wang J, DeGrado WF. PMID: 31184871.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    25. Unique transmembrane domain interactions differentially modulate integrin avß3 and aIIbß3 function. Proc Natl Acad Sci U S A. 2019 06 18; 116(25):12295-12300. Litvinov RI, Mravic M, Zhu H, Weisel JW, DeGrado WF, Bennett JS. PMID: 31160446.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    26. Genetically Introducing Biochemically Reactive Amino Acids Dehydroalanine and Dehydrobutyrine in Proteins. J Am Chem Soc. 2019 05 15; 141(19):7698-7703. Yang B, Wang N, Schnier PD, Zheng F, Zhu H, Polizzi NF, Ittuveetil A, Saikam V, DeGrado WF, Wang Q, Wang PG, Wang L. PMID: 31038942.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    27. Aß and tau prion-like activities decline with longevity in the Alzheimer's disease human brain. Sci Transl Med. 2019 05 01; 11(490). 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. PMID: 31043574.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    28. Synthesis and application of the blue fluorescent amino acid l-4-cyanotryptophan to assess peptide-membrane interactions. Chem Commun (Camb). 2019 Apr 25; 55(35):5095-5098. Zhang K, Ahmed IA, Kratochvil HT, DeGrado WF, Gai F, Jo H. PMID: 30957824.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    29. Glutamine Side Chain 13C-18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc. 2019 05 08; 141(18):7320-7326. Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. PMID: 30998340.
      View in: PubMed   Mentions: 3     Fields:    
    30. De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities. Acc Chem Res. 2019 05 21; 52(5):1148-1159. Lombardi A, Pirro F, Maglio O, Chino M, DeGrado WF. PMID: 30973707.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    31. Packing of apolar side chains enables accurate design of highly stable membrane proteins. Science. 2019 03 29; 363(6434):1418-1423. Mravic M, Thomaston JL, Tucker M, Solomon PE, Liu L, DeGrado WF. PMID: 30923216.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    32. SNAC-tag for sequence-specific chemical protein cleavage. Nat Methods. 2019 04; 16(4):319-322. Dang B, Mravic M, Hu H, Schmidt N, Mensa B, DeGrado WF. PMID: 30923372.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    33. Exposing the Nucleation Site in a-Helix Folding: A Joint Experimental and Simulation Study. J Phys Chem B. 2019 02 28; 123(8):1797-1807. Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F. PMID: 30694671.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    34. 4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules. 2019 Feb 08; 24(3). Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. PMID: 30744004.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    35. Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations. Cancer Cell. 2018 11 12; 34(5):792-806.e5. 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. PMID: 30449325.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    36. Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry. Proc Natl Acad Sci U S A. 2018 10 30; 115(44):11162-11167. Yang B, Wu H, Schnier PD, Liu Y, Liu J, Wang N, DeGrado WF, Wang L. PMID: 30322930.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    37. Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters. J Am Chem Soc. 2018 11 14; 140(45):15219-15226. Thomaston JL, Polizzi NF, Konstantinidi A, Wang J, Kolocouris A, DeGrado WF. PMID: 30165017.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    38. Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster. Biopolymers. 2018 Aug; 109(10):e23339. Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF. PMID: 30203532.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    39. Building and Breaking Bonds via a Compact S-Propargyl-Cysteine to Chemically Control Enzymes and Modify Proteins. Angew Chem Int Ed Engl. 2018 09 24; 57(39):12702-12706. Liu J, Cheng R, Wu H, Li S, Wang PG, DeGrado WF, Rozovsky S, Wang L. PMID: 30118570.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    40. Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule. Biochemistry. 2018 10 02; 57(39):5748-5758. Bokoch MP, Jo H, Valcourt JR, Srinivasan Y, Pan AC, Capponi S, Grabe M, Dror RO, Shaw DE, DeGrado WF, Coughlin SR. PMID: 30102523.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    41. Designed peptides that assemble into cross-a amyloid-like structures. Nat Chem Biol. 2018 09; 14(9):870-875. Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. PMID: 30061717.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    42. Structure and Function of the Transmembrane Domain of NsaS, an Antibiotic Sensing Histidine Kinase in Staphylococcus aureus. J Am Chem Soc. 2018 06 20; 140(24):7471-7485. Bhate MP, Lemmin T, Kuenze G, Mensa B, Ganguly S, Peters JM, Schmidt N, Pelton JG, Gross CA, Meiler J, DeGrado WF. PMID: 29771498.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    43. Peptide-Programmable Nanoparticle Superstructures with Tailored Electrocatalytic Activity. ACS Nano. 2018 07 24; 12(7):6554-6562. 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. PMID: 29842775.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    44. De novo designed transmembrane peptides activating the a5ß1 integrin. Protein Eng Des Sel. 2018 05 01; 31(5):181-190. Mravic M, Hu H, Lu Z, Bennett JS, Sanders CR, Orr AW, DeGrado WF. PMID: 29992271.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    45. Design of a Short Thermally Stable a-Helix Embedded in a Macrocycle. Chembiochem. 2018 05 04; 19(9):902-906. Wu H, Acharyya A, Wu Y, Liu L, Jo H, Gai F, DeGrado WF. PMID: 29417711.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    46. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles. J Am Chem Soc. 2018 01 31; 140(4):1294-1304. Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A. PMID: 29249157.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    47. A long-lived Aß oligomer resistant to fibrillization. Biopolymers. 2018 Aug; 109(8):e23096. Nick M, Wu Y, Schmidt NW, Prusiner SB, Stöhr J, DeGrado WF. PMID: 29319162.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    48. Structural heterogeneity and intersubject variability of Aß in familial and sporadic Alzheimer's disease. Proc Natl Acad Sci U S A. 2018 01 23; 115(4):E782-E791. 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. PMID: 29311311.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    49. Spontaneous and specific chemical cross-linking in live cells to capture and identify protein interactions. Nat Commun. 2017 12 21; 8(1):2240. Yang B, Tang S, Ma C, Li ST, Shao GC, Dang B, DeGrado WF, Dong MQ, Wang PG, Ding S, Wang L. PMID: 29269770.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    50. Self-assembling dipeptide antibacterial nanostructures with membrane disrupting activity. Nat Commun. 2017 11 08; 8(1):1365. Schnaider L, Brahmachari S, Schmidt NW, Mensa B, Shaham-Niv S, Bychenko D, Adler-Abramovich L, Shimon LJW, Kolusheva S, DeGrado WF, Gazit E. PMID: 29118336.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    51. De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Proc Natl Acad Sci U S A. 2017 10 10; 114(41):10852-10857. Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva DA, Baker D, DeGrado WF. PMID: 28973862.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    52. XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proc Natl Acad Sci U S A. 2017 12 19; 114(51):13357-13362. 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. PMID: 28835537.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    53. De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy. Nat Chem. 2017 12; 9(12):1157-1164. Polizzi NF, Wu Y, Lemmin T, Maxwell AM, Zhang SQ, Rawson J, Beratan DN, Therien MJ, DeGrado WF. PMID: 29168496.
      View in: PubMed   Mentions: 21     Fields:    
    54. Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport. Philos Trans R Soc Lond B Biol Sci. 2017 08 05; 372(1726). Joh NH, Grigoryan G, Wu Y, DeGrado WF. PMID: 28630154.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    55. Zinc-binding structure of a catalytic amyloid from solid-state NMR. Proc Natl Acad Sci U S A. 2017 06 13; 114(24):6191-6196. Lee M, Wang T, Makhlynets OV, Wu Y, Polizzi NF, Wu H, Gosavi PM, Stöhr J, Korendovych IV, DeGrado WF, Hong M. PMID: 28566494.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    56. Blue fluorescent amino acid for biological spectroscopy and microscopy. Proc Natl Acad Sci U S A. 2017 06 06; 114(23):6005-6009. Hilaire MR, Ahmed IA, Lin CW, Jo H, DeGrado WF, Gai F. PMID: 28533371.
      View in: PubMed   Mentions: 12     Fields:    
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    214. Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy. J Am Chem Soc. 2007 Oct 24; 129(42):12801-8. Balakrishnan G, Hu Y, Bender GM, Getahun Z, DeGrado WF, Spiro TG. PMID: 17910449.
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    216. De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc. 2007 Sep 05; 129(35):10732-40. Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, DeGrado WF. PMID: 17691729.
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    217. Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores. J Phys Chem A. 2007 Aug 02; 111(30):6977-90. Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM, Vinogradov SA. PMID: 17608457.
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    218. Mutagenesis data in the automated prediction of transmembrane helix dimers. Proteins. 2007 May 01; 67(2):375-84. Metcalf DG, Law PB, DeGrado WF. PMID: 17311347.
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    219. Foldamers as versatile frameworks for the design and evolution of function. Nat Chem Biol. 2007 May; 3(5):252-62. Goodman CM, Choi S, Shandler S, DeGrado WF. PMID: 17438550.
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    220. 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. J Am Chem Soc. 2007 May 02; 129(17):5719-29. Cady SD, Goodman C, Tatko CD, DeGrado WF, Hong M. PMID: 17417850.
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    221. Adhesion of MC3T3-E1 cells to RGD peptides of different flanking residues: detachment strength and correlation with long-term cellular function. J Biomed Mater Res A. 2007 Apr; 81(1):150-60. Lee MH, Adams CS, Boettiger D, Degrado WF, Shapiro IM, Composto RJ, Ducheyne P. PMID: 17111408.
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    223. Interactions of ADP-stimulated human platelets with PEGylated polystyrene substrates prepared by surface amidation. Colloids Surf B Biointerfaces. 2007 Aug 01; 58(2):225-30. Wang PC, Vilaire G, DeGrado WF, Bennett JS. PMID: 17499487.
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    224. The leech product saratin is a potent inhibitor of platelet integrin alpha2beta1 and von Willebrand factor binding to collagen. FEBS J. 2007 Mar; 274(6):1481-91. White TC, Berny MA, Robinson DK, Yin H, DeGrado WF, Hanson SR, McCarty OJ. PMID: 17489103.
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    225. Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer. Proc Natl Acad Sci U S A. 2006 Nov 07; 103(45):16740-5. Fang C, Senes A, Cristian L, DeGrado WF, Hochstrasser RM. PMID: 17075037.
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    226. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J Struct Biol. 2007 Mar; 157(3):444-53. Dal Peraro M, Spiegel K, Lamoureux G, De Vivo M, DeGrado WF, Klein ML. PMID: 17188512.
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    227. Activation of platelet alphaIIbbeta3 by an exogenous peptide corresponding to the transmembrane domain of alphaIIb. J Biol Chem. 2006 Dec 01; 281(48):36732-41. Yin H, Litvinov RI, Vilaire G, Zhu H, Li W, Caputo GA, Moore DT, Lear JD, Weisel JW, Degrado WF, Bennett JS. PMID: 17032655.
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    229. Truncation of a cross-linked GCN4-p1 coiled coil leads to ultrafast folding. Biochemistry. 2006 Sep 12; 45(36):10981-6. Bunagan MR, Cristian L, DeGrado WF, Gai F. PMID: 16953584.
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    230. The structure of a designed diiron(III) protein: implications for cofactor stabilization and catalysis. Angew Chem Int Ed Engl. 2006 Jul 24; 45(30):4951-4. Wade H, Stayrook SE, Degrado WF. PMID: 16819737.
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    231. Arylamide derivatives as allosteric inhibitors of the integrin alpha2beta1/type I collagen interaction. Bioorg Med Chem Lett. 2006 Jul 01; 16(13):3380-2. Yin H, Gerlach LO, Miller MW, Moore DT, Liu D, Vilaire G, Bennett JS, DeGrado WF. PMID: 16678410.
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    232. Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics. J Chem Theory Comput. 2006 May; 2(3):649-655. Lopez CF, Nielsen SO, Srinivas G, Degrado WF, Klein ML. PMID: 18985168.
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    234. Activation of individual alphaIIbbeta3 integrin molecules by disruption of transmembrane domain interactions in the absence of clustering. Biochemistry. 2006 Apr 18; 45(15):4957-64. Litvinov RI, Vilaire G, Li W, DeGrado WF, Weisel JW, Bennett JS. PMID: 16605263.
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    235. Polar networks control oligomeric assembly in membranes. J Am Chem Soc. 2006 Apr 05; 128(13):4170-1. Tatko CD, Nanda V, Lear JD, Degrado WF. PMID: 16568959.
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    236. Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study. J Phys Chem B. 2006 Mar 02; 110(8):3517-26. Pophristic V, Vemparala S, Ivanov I, Liu Z, Klein ML, DeGrado WF. PMID: 16494407.
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    237. Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics. J Am Chem Soc. 2006 Feb 15; 128(6):1778-9. Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML. PMID: 16464062.
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    238. Arsenite pre-conditioning reduces UVB-induced apoptosis in corneal epithelial cells through the anti-apoptotic activity of 27 kDa heat shock protein (HSP27). J Cell Physiol. 2006 Feb; 206(2):301-8. Shi B, Isseroff RR. PMID: 16150962.
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    239. Computational design of heterochiral peptides against a helical target. J Am Chem Soc. 2006 Jan 25; 128(3):809-16. Nanda V, DeGrado WF. PMID: 16417370.
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    240. Arylamide derivatives as peptidomimetic inhibitors of calmodulin. Org Lett. 2006 Jan 19; 8(2):223-5. Yin H, Frederick KK, Liu D, Wand AJ, Degrado WF. PMID: 16408880.
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    241. Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography. J Am Chem Soc. 2005 Dec 14; 127(49):17266-76. Geremia S, Di Costanzo L, Randaccio L, Engel DE, Lombardi A, Nastri F, DeGrado WF. PMID: 16332076.
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    242. 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. J Am Chem Soc. 2005 Nov 23; 127(46):16098-106. Wei PP, Skulan AJ, Wade H, DeGrado WF, Solomon EI. PMID: 16287296.
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    243. Alpha-alpha linking motifs and interhelical orientations. Proteins. 2005 Nov 01; 61(2):325-37. Engel DE, DeGrado WF. PMID: 16104016.
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    244. The design and evaluation of heparin-binding foldamers. Angew Chem Int Ed Engl. 2005 Oct 21; 44(41):6685-9. Choi S, Clements DJ, Pophristic V, Ivanov I, Vemparala S, Bennett JS, Klein ML, Winkler JD, DeGrado WF. PMID: 16094685.
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    245. An atomic environment potential for use in protein structure prediction. J Mol Biol. 2005 Sep 30; 352(4):986-1001. Summa CM, Levitt M, Degrado WF. PMID: 16126228.
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    246. Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops. J Biol Inorg Chem. 2005 Aug; 10(5):539-49. Maglio O, Nastri F, Calhoun JR, Lahr S, Wade H, Pavone V, DeGrado WF, Lombardi A. PMID: 16091937.
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    247. Dynamic heterodimer-functionalized surfaces for endothelial cell adhesion. Biomaterials. 2005 Aug; 26(23):4757-66. Willcox PJ, Reinhart-King CA, Lahr SJ, DeGrado WF, Hammer DA. PMID: 15763255.
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    248. Structural organization and interactions of transmembrane domains in tetraspanin proteins. BMC Struct Biol. 2005 Jun 28; 5:11. Kovalenko OV, Metcalf DG, DeGrado WF, Hemler ME. PMID: 15985154.
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    249. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins. 2005 May 15; 59(3):496-509. Adamian L, Nanda V, DeGrado WF, Liang J. PMID: 15789404.
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    251. X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils. J Mol Biol. 2005 May 06; 348(3):777-87. Slovic AM, Stayrook SE, North B, Degrado WF. PMID: 15826670.
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    252. De novo design of a redox-active minimal rubredoxin mimic. J Am Chem Soc. 2005 Apr 27; 127(16):5804-5. Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, Degrado WF. PMID: 15839675.
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    253. Synergistic interactions between aqueous and membrane domains of a designed protein determine its fold and stability. J Mol Biol. 2005 May 20; 348(5):1225-33. Cristian L, Nanda V, Lear JD, DeGrado WF. PMID: 15854657.
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    254. Amphiphilic polymethacrylate derivatives as antimicrobial agents. J Am Chem Soc. 2005 Mar 30; 127(12):4128-9. Kuroda K, DeGrado WF. PMID: 15783168.
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    255. The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Sci. 2005 Apr; 14(4):856-61. Duong-Ly KC, Nanda V, Degrado WF, Howard KP. PMID: 15741338.
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    256. Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle. Protein Sci. 2005 Apr; 14(4):1019-24. Howard KP, Liu W, Crocker E, Nanda V, Lear J, Degrado WF, Smith SO. PMID: 15741331.
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    257. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J Am Chem Soc. 2005 Feb 09; 127(5):1346-7. Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. PMID: 15686346.
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    258. A push-pull mechanism for regulating integrin function. Proc Natl Acad Sci U S A. 2005 Feb 01; 102(5):1424-9. Li W, Metcalf DG, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, Degrado WF, Bennett JS. PMID: 15671157.
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    259. Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function. J Mol Biol. 2005 Mar 18; 347(1):169-79. Stouffer AL, Nanda V, Lear JD, DeGrado WF. PMID: 15733926.
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    261. Artificial diiron proteins: from structure to function. Biopolymers. 2005; 80(2-3):264-78. Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, DeGrado WF. PMID: 15700297.
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    262. Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide. FEBS Lett. 2004 Dec 03; 578(1-2):140-4. Ghirlanda G, Hilcove SA, Pidikiti R, Johansson JS, Lear JD, Degrado WF, Eckenhoff RG. PMID: 15581631.
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    263. Simulated evolution of emergent chiral structures in polyalanine. J Am Chem Soc. 2004 Nov 10; 126(44):14459-67. Nanda V, Degrado WF. PMID: 15521766.
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    264. Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers. Chemistry. 2004 Oct 11; 10(20):5008-16. Doerksen RJ, Chen B, Liu D, Tew GN, Degrado WF, Klein ML. PMID: 15372664.
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    265. Length Dependent Helix-Coil Transition Kinetics of Nine Alanine-Based Peptides. J Phys Chem B. 2004 Sep 30; 108(39). Wang T, Zhu Y, Getahun Z, Du D, Huang CY, Degrado WF, Gai F. PMID: 24307864.
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    267. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol. 2004 Aug; 14(4):465-79. Senes A, Engel DE, DeGrado WF. PMID: 15313242.
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    268. De novo design of a D2-symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc1. J Am Chem Soc. 2004 Jul 07; 126(26):8141-7. Ghirlanda G, Osyczka A, Liu W, Antolovich M, Smith KM, Dutton PL, Wand AJ, DeGrado WF. PMID: 15225055.
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    269. A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides. J Am Chem Soc. 2004 Apr 28; 126(16):5078-9. Tucker MJ, Getahun Z, Nanda V, DeGrado WF, Gai F. PMID: 15099085.
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    270. Amino acid propensities are position-dependent throughout the length of alpha-helices. J Mol Biol. 2004 Apr 09; 337(5):1195-205. Engel DE, DeGrado WF. PMID: 15046987.
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    272. Nontoxic membrane-active antimicrobial arylamide oligomers. Angew Chem Int Ed Engl. 2004 Feb 20; 43(9):1158-62. Liu D, Choi S, Chen B, Doerksen RJ, Clements DJ, Winkler JD, Klein ML, DeGrado WF. PMID: 14983462.
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    274. Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization. Biophys J. 2004 Jan; 86(1 Pt 1):272-84. Lau WL, Ege DS, Lear JD, Hammer DA, DeGrado WF. PMID: 14695269.
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    275. Computational design and characterization of a monomeric helical dinuclear metalloprotein. J Mol Biol. 2003 Dec 12; 334(5):1101-15. Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, Saven JG. PMID: 14643669.
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    276. Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein. Proc Natl Acad Sci U S A. 2003 Dec 23; 100(26):15486-91. Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF, Gai F. PMID: 14671331.
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    277. Use of thiol-disulfide equilibria to measure the energetics of assembly of transmembrane helices in phospholipid bilayers. Proc Natl Acad Sci U S A. 2003 Dec 09; 100(25):14772-7. Cristian L, Lear JD, DeGrado WF. PMID: 14657351.
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    281. Computational biology: Biosensor design. Nature. 2003 May 08; 423(6936):132-3. DeGrado WF. PMID: 12736670.
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    288. Using nitrile-derivatized amino acids as infrared probes of local environment. J Am Chem Soc. 2003 Jan 15; 125(2):405-11. Getahun Z, Huang CY, Wang T, De León B, DeGrado WF, Gai F. PMID: 12517152.
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    289. Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor. J Am Chem Soc. 2003 Jan 15; 125(2):560-9. Papoian GA, DeGrado WF, Klein ML. PMID: 12517172.
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    292. Light-induced helix formation. J Am Chem Soc. 2002 Oct 30; 124(43):12674-5. Huang CY, He S, DeGrado WF, McCafferty DG, Gai F. PMID: 12392410.
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    294. Cooperativity and specificity of association of a designed transmembrane peptide. Biophys J. 2002 Sep; 83(3):1613-9. Gratkowski H, Dai QH, Wand AJ, DeGrado WF, Lear JD. PMID: 12202385.
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    295. Computational de novo design, and characterization of an A(2)B(2) diiron protein. J Mol Biol. 2002 Aug 30; 321(5):923-38. Summa CM, Rosenblatt MM, Hong JK, Lear JD, DeGrado WF. PMID: 12206771.
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    296. Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein. Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13):8568-72. Howard KP, Lear JD, DeGrado WF. PMID: 12084917.
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    297. A hierarchic approach to the design of hexameric helical barrels. J Mol Biol. 2002 May 24; 319(1):243-53. Ghirlanda G, Lear JD, Ogihara NL, Eisenberg D, DeGrado WF. PMID: 12051949.
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    298. De novo design of biomimetic antimicrobial polymers. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5110-4. Tew GN, Liu D, Chen B, Doerksen RJ, Kaplan J, Carroll PJ, Klein ML, DeGrado WF. PMID: 11959961.
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    299. Noncovalent self-assembly of a heterotetrameric diiron protein. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5150-4. Marsh EN, DeGrado WF. PMID: 11959963.
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    300. Helix formation via conformation diffusion search. Proc Natl Acad Sci U S A. 2002 Mar 05; 99(5):2788-93. Huang CY, Getahun Z, Zhu Y, Klemke JW, DeGrado WF, Gai F. PMID: 11867741.
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    301. 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 Hathaway for performing matrix-assisted laser desorption/ionization analyses. Angew Chem Int Ed Engl. 2001 Apr 17; 40(8):1494-1496. Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF, Tirrell DA. PMID: 11317312.
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    302. Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability. Angew Chem Int Ed Engl. 2001 Apr 17; 40(8):1494-1496. Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF, Tirrell DA. PMID: 29712367.
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