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William Degrado, PhD

Title(s)Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
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

    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/NIA RF1AG061874Sep 30, 2018 - Jun 30, 2023
    Role: Co-Principal Investigator
    Deciphering the relationship between structure, dynamics and function in helical bundle proteins
    NIH/NIGMS R35GM122603Apr 1, 2017 - Apr 30, 2022
    Role: Principal Investigator
    Treatment of pulmonary fibrosis with inhibitors of integrin alphavbeta1.
    NIH/NHLBI UH2HL123423Sep 1, 2014 - Jun 30, 2019
    Role: Co-Principal Investigator
    Treatment of pulmonary fibrosis with inhibitors of integrin alphavbeta1.
    NIH/NHLBI UH3HL123423Sep 1, 2014 - Jun 30, 2019
    Role: Co-Principal Investigator
    Vaccines that Replicate the Neutralization-Competent Structure of the gp41 MPER
    NIH/NIAID R01AI097051Mar 1, 2012 - Feb 29, 2016
    Role: Co-Principal Investigator
    Development of drugs that target the M2 proton channel from the influenza A Virus
    NIH/NIAID U01AI074571May 15, 2008 - Apr 30, 2014
    Role: Principal Investigator
    Design and mechanistic studies of mimics of antimicrobial peptides
    NIH/NIAID R56AI074866Apr 15, 2008 - Jul 31, 2014
    Role: Principal Investigator
    Design and mechanistic studies of mimics of antimicrobial peptides
    NIH/NIAID R01AI074866Apr 15, 2008 - Mar 31, 2014
    Role: Principal Investigator
    Proteomics to Biomimetic Polymers: Engineering Principle
    NIH/NIBIB R01EB002048Sep 24, 2002 - Aug 31, 2007
    Role: Principal Investigator
    Proteomics to Biomimetic Polymers: Engineering Principle
    NIH/NIGMS 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/NIGMS R01GM060610Dec 1, 1999 - Apr 30, 2010
    Role: Principal Investigator
    Structure of M2 Proton Channel from Influenza A Virus
    NIH/NIGMS R01GM056423Aug 1, 1997 - Apr 30, 2017
    Role: Principal Investigator
    PURCHASE OF ANALYTICAL ULTRACENTRIFUGE
    NIH/NCRR S10RR011854Mar 18, 1997 - Mar 17, 1998
    Role: Principal Investigator
    De Novo Design of Alpha-Helical Bundles
    NIH/NIGMS R01GM054616Aug 1, 1996 - Jun 30, 2018
    Role: Principal Investigator
    De novo design of alpha-helical bundles
    NIH/NIGMS 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
    Degenerative and Dementing Diseases of Aging
    NIH/NIA P01AG002132Jan 1, 1981 - Mar 31, 2020
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Websites

    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.
    List All   |   Timeline
    1. Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. 4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules. 2019 Feb 08; 24(3). PMID: 30744004.
      View in: PubMed
    2. Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F. Exposing the Nucleation Site in a-Helix Folding: A Joint Experimental and Simulation Study. J Phys Chem B. 2019 Jan 29. PMID: 30694671.
      View in: PubMed
    3. 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. Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations. Cancer Cell. 2018 Nov 12; 34(5):792-806.e5. PMID: 30449325.
      View in: PubMed
    4. Yang B, Wu H, Schnier PD, Liu Y, Liu J, Wang N, DeGrado WF, Wang L. 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. PMID: 30322930.
      View in: PubMed
    5. Thomaston JL, Polizzi NF, Konstantinidi A, Wang J, Kolocouris A, DeGrado WF. Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters. J Am Chem Soc. 2018 Nov 14; 140(45):15219-15226. PMID: 30165017.
      View in: PubMed
    6. Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF. Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster. Biopolymers. 2018 Aug; 109(10):e23339. PMID: 30203532.
      View in: PubMed
    7. Liu J, Cheng R, Wu H, Li S, Wang PG, DeGrado WF, Rozovsky S, Wang L. Building and Breaking Bonds via a Compact S-Propargyl-Cysteine to Chemically Control Enzymes and Modify Proteins. Angew Chem Int Ed Engl. 2018 Sep 24; 57(39):12702-12706. PMID: 30118570.
      View in: PubMed
    8. Bokoch MP, Jo H, Valcourt JR, Srinivasan Y, Pan AC, Capponi S, Grabe M, Dror RO, Shaw DE, DeGrado WF, Coughlin SR. Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule. Biochemistry. 2018 Oct 02; 57(39):5748-5758. PMID: 30102523.
      View in: PubMed
    9. Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. Designed peptides that assemble into cross-a amyloid-like structures. Nat Chem Biol. 2018 Sep; 14(9):870-875. PMID: 30061717.
      View in: PubMed
    10. Bhate MP, Lemmin T, Kuenze G, Mensa B, Ganguly S, Peters JM, Schmidt N, Pelton JG, Gross CA, Meiler J, DeGrado WF. 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. PMID: 29771498.
      View in: PubMed
    11. 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. Peptide-Programmable Nanoparticle Superstructures with Tailored Electrocatalytic Activity. ACS Nano. 2018 Jul 24; 12(7):6554-6562. PMID: 29842775.
      View in: PubMed
    12. Mravic M, Hu H, Lu Z, Bennett JS, Sanders CR, Orr AW, DeGrado WF. De novo designed transmembrane peptides activating the a5ß1 integrin. Protein Eng Des Sel. 2018 05 01; 31(5):181-190. PMID: 29992271.
      View in: PubMed
    13. Wu H, Acharyya A, Wu Y, Liu L, Jo H, Gai F, DeGrado WF. Design of a Short Thermally Stable a-Helix Embedded in a Macrocycle. Chembiochem. 2018 May 04; 19(9):902-906. PMID: 29417711.
      View in: PubMed
    14. Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A. 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. PMID: 29249157.
      View in: PubMed
    15. Nick M, Wu Y, Schmidt NW, Prusiner SB, Stöhr J, DeGrado WF. A long-lived Aß oligomer resistant to fibrillization. Biopolymers. 2018 Aug; 109(8):e23096. PMID: 29319162.
      View in: PubMed
    16. 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. 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. PMID: 29311311.
      View in: PubMed
    17. Yang B, Tang S, Ma C, Li ST, Shao GC, Dang B, DeGrado WF, Dong MQ, Wang PG, Ding S, Wang L. Spontaneous and specific chemical cross-linking in live cells to capture and identify protein interactions. Nat Commun. 2017 12 21; 8(1):2240. PMID: 29269770.
      View in: PubMed
    18. Schnaider L, Brahmachari S, Schmidt NW, Mensa B, Shaham-Niv S, Bychenko D, Adler-Abramovich L, Shimon LJW, Kolusheva S, DeGrado WF, Gazit E. Self-assembling dipeptide antibacterial nanostructures with membrane disrupting activity. Nat Commun. 2017 11 08; 8(1):1365. PMID: 29118336.
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    19. Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva DA, Baker D, DeGrado WF. 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. PMID: 28973862.
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    20. 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. 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. PMID: 28835537.
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    21. Polizzi NF, Wu Y, Lemmin T, Maxwell AM, Zhang SQ, Rawson J, Beratan DN, Therien MJ, DeGrado WF. De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy. Nat Chem. 2017 Dec; 9(12):1157-1164. PMID: 29168496.
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    22. Joh NH, Grigoryan G, Wu Y, DeGrado WF. 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 Aug 05; 372(1726). PMID: 28630154.
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    23. Lee M, Wang T, Makhlynets OV, Wu Y, Polizzi NF, Wu H, Gosavi PM, Stöhr J, Korendovych IV, DeGrado WF, Hong M. 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. PMID: 28566494.
      View in: PubMed
    24. Hilaire MR, Ahmed IA, Lin CW, Jo H, DeGrado WF, Gai F. Blue fluorescent amino acid for biological spectroscopy and microscopy. Proc Natl Acad Sci U S A. 2017 06 06; 114(23):6005-6009. PMID: 28533371.
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    25. Wang T, Jo H, DeGrado WF, Hong M. Water Distribution, Dynamics, and Interactions with Alzheimer's ß-Amyloid Fibrils Investigated by Solid-State NMR. J Am Chem Soc. 2017 05 03; 139(17):6242-6252. PMID: 28406028.
      View in: PubMed
    26. Lin CW, Mensa B, Barniol-Xicota M, DeGrado WF, Gai F. Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl. 2017 05 02; 56(19):5283-5287. PMID: 28374543.
      View in: PubMed
    27. 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. A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells. Nat Chem. 2017 Sep; 9(9):874-881. PMID: 28837163.
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    28. Findeisen F, Campiglio M, Jo H, Abderemane-Ali F, Rumpf CH, Pope L, Rossen ND, Flucher BE, DeGrado WF, Minor DL. Stapled Voltage-Gated Calcium Channel (CaV) a-Interaction Domain (AID) Peptides Act As Selective Protein-Protein Interaction Inhibitors of CaV Function. ACS Chem Neurosci. 2017 06 21; 8(6):1313-1326. PMID: 28278376.
      View in: PubMed
    29. Schmidt NW, Grigoryan G, DeGrado WF. The accommodation index measures the perturbation associated with insertions and deletions in coiled-coils: Application to understand signaling in histidine kinases. Protein Sci. 2017 03; 26(3):414-435. PMID: 27977891.
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    30. Chang Y, Lau WL, Jo H, Tsujino K, Gewin L, Reed NI, Atakilit A, Nunes ACF, DeGrado WF, Sheppard D. Pharmacologic Blockade of avß1 Integrin Ameliorates Renal Failure and Fibrosis In Vivo. J Am Soc Nephrol. 2017 Jul; 28(7):1998-2005. PMID: 28220032.
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    31. Hu Y, Musharrafieh R, Ma C, Zhang J, Smee DF, DeGrado WF, Wang J. An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Antiviral Res. 2017 04; 140:45-54. PMID: 28087313.
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    32. Sundaram A, Chen C, Khalifeh-Soltani A, Atakilit A, Ren X, Qiu W, Jo H, DeGrado W, Huang X, Sheppard D. Targeting integrin a5ß1 ameliorates severe airway hyperresponsiveness in experimental asthma. J Clin Invest. 2017 01 03; 127(1):365-374. PMID: 27918306.
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    33. Liang R, Swanson JMJ, Madsen JJ, Hong M, DeGrado WF, Voth GA. Acid activation mechanism of the influenza A M2 proton channel. Proc Natl Acad Sci U S A. 2016 Nov 08; 113(45):E6955-E6964. PMID: 27791184.
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    34. Markiewicz BN, Lemmin T, Zhang W, Ahmed IA, Jo H, Fiorin G, Troxler T, DeGrado WF, Gai F. Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel. Phys Chem Chem Phys. 2016 Oct 19; 18(41):28939-28950. PMID: 27725984.
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    35. Reed NI, Tang YZ, McIntosh J, Wu Y, Molnar KS, Civitavecchia A, Sheppard D, DeGrado WF, Jo H. Exploring N-Arylsulfonyl-l-proline Scaffold as a Platform for Potent and Selective avß1 Integrin Inhibitors. ACS Med Chem Lett. 2016 Oct 13; 7(10):902-907. PMID: 27774126.
      View in: PubMed
    36. Elkins MR, Wang T, Nick M, Jo H, Lemmin T, Prusiner SB, DeGrado WF, Stöhr J, Hong M. Structural Polymorphism of Alzheimer's ß-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study. J Am Chem Soc. 2016 08 10; 138(31):9840-52. PMID: 27414264.
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    37. Mustata GM, Kim YH, Zhang J, DeGrado WF, Grigoryan G, Wanunu M. Graphene Symmetry Amplified by Designed Peptide Self-Assembly. Biophys J. 2016 06 07; 110(11):2507-2516. PMID: 27276268.
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    38. Thomaston JL, DeGrado WF. Crystal structure of the drug-resistant S31N influenza M2 proton channel. Protein Sci. 2016 08; 25(8):1551-4. PMID: 27082171; PMCID: PMC4972211 [Available on 08/01/17].
    39. To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. Photoactivatable protein labeling by singlet oxygen mediated reactions. Bioorg Med Chem Lett. 2016 07 15; 26(14):3359-3363. PMID: 27220724; PMCID: PMC4903891 [Available on 07/15/17].
    40. Kim KH, Ko DK, Kim YT, Kim NH, Paul J, Zhang SQ, Murray CB, Acharya R, DeGrado WF, Kim YH, Grigoryan G. Protein-directed self-assembly of a fullerene crystal. Nat Commun. 2016 Apr 26; 7:11429. PMID: 27113637.
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    41. Fong KP, Zhu H, Span LM, Moore DT, Yoon K, Tamura R, Yin H, DeGrado WF, Bennett JS. Directly Activating the Integrin aIIbß3 Initiates Outside-In Signaling by Causing aIIbß3 Clustering. J Biol Chem. 2016 May 27; 291(22):11706-16. PMID: 27056329; PMCID: PMC4882439 [Available on 05/27/17].
    42. Ulas G, Lemmin T, Wu Y, Gassner GT, DeGrado WF. Designed metalloprotein stabilizes a semiquinone radical. Nat Chem. 2016 Apr; 8(4):354-9. PMID: 27001731; PMCID: PMC4857601.
    43. Li F, Ma C, DeGrado WF, Wang J. Discovery of Highly Potent Inhibitors Targeting the Predominant Drug-Resistant S31N Mutant of the Influenza A Virus M2 Proton Channel. J Med Chem. 2016 Feb 11; 59(3):1207-16. PMID: 26771709; PMCID: PMC4829348.
    44. 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-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Struct Biol. 2016 Jan; 72(Pt 1):2-11. PMID: 26894529.
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    45. Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF. High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction. Proc Natl Acad Sci U S A. 2015 Nov 17; 112(46):14260-5. PMID: 26578770.
      View in: PubMed
    46. Snyder RA, Betzu J, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Systematic Perturbations of Binuclear Non-heme Iron Sites: Structure and Dioxygen Reactivity of de Novo Due Ferri Proteins. Biochemistry. 2015 Aug 04; 54(30):4637-51. PMID: 26154739; PMCID: PMC4857603.
    47. Snyder RA, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. J Am Chem Soc. 2015 Jul 29; 137(29):9302-14. PMID: 26090726.
      View in: PubMed
    48. Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem. 2015 Jul; 2015(21):3371-3390. PMID: 27630532.
      View in: PubMed
    49. Reed NI, Jo H, Chen C, Tsujino K, Arnold TD, DeGrado WF, Sheppard D. The avß1 integrin plays a critical in vivo role in tissue fibrosis. Sci Transl Med. 2015 May 20; 7(288):288ra79. PMID: 25995225; PMCID: PMC4461057.
    50. Bhate MP, Molnar KS, Goulian M, DeGrado WF. Signal transduction in histidine kinases: insights from new structures. Structure. 2015 Jun 02; 23(6):981-94. PMID: 25982528; PMCID: PMC4456306.
    51. Wu Y, Span LM, Nygren P, Zhu H, Moore DT, Cheng H, Roder H, DeGrado WF, Bennett JS. The Tyrosine Kinase c-Src Specifically Binds to the Active Integrin aIIbß3 to Initiate Outside-in Signaling in Platelets. J Biol Chem. 2015 Jun 19; 290(25):15825-34. PMID: 25947380; PMCID: PMC4505490.
    52. Zhang SQ, Kulp DW, Schramm CA, Mravic M, Samish I, DeGrado WF. The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions. Structure. 2015 Mar 03; 23(3):527-541. PMID: 25703378.
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    53. 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. Computational design and experimental characterization of peptides intended for pH-dependent membrane insertion and pore formation. ACS Chem Biol. 2015 Apr 17; 10(4):1082-93. PMID: 25630033; PMCID: PMC4843813.
    54. Huang S, Green B, Thompson M, Chen R, Thomaston J, DeGrado WF, Howard KP. C-terminal juxtamembrane region of full-length M2 protein forms a membrane surface associated amphipathic helix. Protein Sci. 2015 Mar; 24(3):426-9. PMID: 25545360; PMCID: PMC4353368.
    55. Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF. De novo design of a transmembrane Zn²?-transporting four-helix bundle. Science. 2014 Dec 19; 346(6216):1520-4. PMID: 25525248; PMCID: PMC4400864.
    56. Wu Y, Canturk B, Jo H, Ma C, Gianti E, Klein ML, Pinto LH, Lamb RA, Fiorin G, Wang J, 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. J Am Chem Soc. 2014 Dec 31; 136(52):17987-95. PMID: 25470189; PMCID: PMC4286326.
    57. Seither KM, McMahon HA, Singh N, Wang H, Cushman-Nick M, Montalvo GL, DeGrado WF, Shorter J. Specific aromatic foldamers potently inhibit spontaneous and seeded Aß42 and Aß43 fibril assembly. Biochem J. 2014 Nov 15; 464(1):85-98. PMID: 25142005.
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    58. Gianti E, Carnevale V, DeGrado WF, Klein ML, Fiorin G. Hydrogen-bonded water molecules in the M2 channel of the influenza A virus guide the binding preferences of ammonium-based inhibitors. J Phys Chem B. 2015 Jan 22; 119(3):1173-83. PMID: 25353315; PMCID: PMC4386636.
    59. Dong H, Fiorin G, DeGrado WF, Klein ML. Proton release from the histidine-tetrad in the M2 channel of the influenza A virus. J Phys Chem B. 2014 Nov 06; 118(44):12644-51. PMID: 25317959; PMCID: PMC4226308.
    60. Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ. Structure. 2014 Sep 02; 22(9):1239-1251. PMID: 25087511; PMCID: PMC4322757.
    61. Gonzalez G, Hannigan B, DeGrado WF. A real-time all-atom structural search engine for proteins. PLoS Comput Biol. 2014 Jul; 10(7):e1003750. PMID: 25079944.
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    62. Korendovych IV, DeGrado WF. Catalytic efficiency of designed catalytic proteins. Curr Opin Struct Biol. 2014 Aug; 27:113-21. PMID: 25048695; PMCID: PMC4182119.
    63. Stöhr J, Condello C, Watts JC, Bloch L, Oehler A, Nick M, DeArmond SJ, Giles K, DeGrado WF, Prusiner SB. Distinct synthetic Aß prion strains producing different amyloid deposits in bigenic mice. Proc Natl Acad Sci U S A. 2014 Jul 15; 111(28):10329-34. PMID: 24982137; PMCID: PMC4104853.
    64. 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. Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. J Med Chem. 2014 Jul 10; 57(13):5738-47. PMID: 24941437; PMCID: PMC4096222.
    65. Ghosh A, Wang J, Moroz YS, Korendovych IV, Zanni M, DeGrado WF, Gai F, Hochstrasser RM. 2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel. J Chem Phys. 2014 Jun 21; 140(23):235105. PMID: 24952572; PMCID: PMC4098053.
    66. Mensa B, Howell GL, Scott R, DeGrado WF. Comparative mechanistic studies of brilacidin, daptomycin, and the antimicrobial peptide LL16. Antimicrob Agents Chemother. 2014 Sep; 58(9):5136-45. PMID: 24936592.
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    67. Pavone V, Zhang SQ, Merlino A, Lombardi A, Wu Y, DeGrado WF. Crystal structure of an amphiphilic foldamer reveals a 48-mer assembly comprising a hollow truncated octahedron. Nat Commun. 2014 Apr 07; 5:3581. PMID: 24705140; PMCID: PMC4013780.
    68. Rufo CM, Moroz YS, Moroz OV, Stöhr J, Smith TA, Hu X, DeGrado WF, Korendovych IV. Short peptides self-assemble to produce catalytic amyloids. Nat Chem. 2014 Apr; 6(4):303-9. PMID: 24651196; PMCID: PMC3996680.
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    72. Montalvo GL, Gai F, Roder H, DeGrado WF. Slow folding-unfolding kinetics of an octameric ß-peptide bundle. ACS Chem Biol. 2014 Jan 17; 9(1):276-81. PMID: 24164344; PMCID: PMC3947042.
    73. Markiewicz BN, Jo H, Culik RM, DeGrado WF, Gai F. Assessment of local friction in protein folding dynamics using a helix cross-linker. J Phys Chem B. 2013 Nov 27; 117(47):14688-96. PMID: 24205975; PMCID: PMC3904762.
    74. Rey-Carrizo M, Torres E, Ma C, Barniol-Xicota M, Wang J, Wu Y, Naesens L, DeGrado WF, Lamb RA, Pinto LH, Vázquez S. 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. J Med Chem. 2013 Nov 27; 56(22):9265-74. PMID: 24237039; PMCID: PMC3889466.
    75. Rudick JG, Laakso MM, Schloss AC, DeGrado WF. Template-constrained cyclic sulfopeptide HIV-1 entry inhibitors. Org Biomol Chem. 2013 Nov 07; 11(41):7096-100. PMID: 24065278; PMCID: PMC3889485.
    76. Ma C, Fiorin G, Carnevale V, Wang J, Lamb RA, Klein ML, Wu Y, Pinto LH, DeGrado WF. Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Structure. 2013 Nov 05; 21(11):2033-41. PMID: 24139991; PMCID: PMC3927992.
    77. Schmidt NW, Mishra A, Wang J, DeGrado WF, Wong GC. Influenza virus A M2 protein generates negative Gaussian membrane curvature necessary for budding and scission. J Am Chem Soc. 2013 Sep 18; 135(37):13710-9. PMID: 23962302; PMCID: PMC4000230.
    78. Fry HC, Lehmann A, Sinks LE, Asselberghs I, Tronin A, Krishnan V, Blasie JK, Clays K, DeGrado WF, Saven JG, Therien MJ. Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore. J Am Chem Soc. 2013 Sep 18; 135(37):13914-26. PMID: 23931685.
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    83. Wang J, Ma C, Wang J, Jo H, Canturk B, Fiorin G, Pinto LH, Lamb RA, Klein ML, DeGrado WF. 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. J Med Chem. 2013 Apr 11; 56(7):2804-12. PMID: 23437766; PMCID: PMC4036227.
    84. Balgi AD, Wang J, Cheng DY, Ma C, Pfeifer TA, Shimizu Y, Anderson HJ, Pinto LH, Lamb RA, DeGrado WF, Roberge M. Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. PLoS One. 2013; 8(2):e55271. PMID: 23383318; PMCID: PMC3562233.
    85. Lemmin T, Soto CS, Clinthorne G, DeGrado WF, Dal Peraro M. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations. PLoS Comput Biol. 2013; 9(1):e1002878. PMID: 23359663; PMCID: PMC3554529.
    86. Mao L, Wang J, DeGrado WF, Inouye M. An assay suitable for high throughput screening of anti-influenza drugs. PLoS One. 2013; 8(1):e54070. PMID: 23326573; PMCID: PMC3542334.
    87. Wang J, Wu Y, Ma C, Fiorin G, Wang J, Pinto LH, Lamb RA, Klein ML, Degrado WF. Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. Proc Natl Acad Sci U S A. 2013 Jan 22; 110(4):1315-20. PMID: 23302696; PMCID: PMC3557100.
    88. Hu X, Zhao J, DeGrado WF, Binns AN. Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals. Proc Natl Acad Sci U S A. 2013 Jan 08; 110(2):678-83. PMID: 23267119; PMCID: PMC3545744.
    89. 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. Platelet factor 4 activity against P. falciparum and its translation to nonpeptidic mimics as antimalarials. Cell Host Microbe. 2012 Dec 13; 12(6):815-23. PMID: 23245326; PMCID: PMC3638032.
    90. Thomaston JL, Nguyen PA, Brown EC, Upshur MA, Wang J, DeGrado WF, Howard KP. Detection of drug-induced conformational change of a transmembrane protein in lipid bilayers using site-directed spin labeling. Protein Sci. 2013 Jan; 22(1):65-73. PMID: 23139077; PMCID: PMC3575861.
    91. Jo H, Meinhardt N, Wu Y, Kulkarni S, Hu X, Low KE, Davies PL, DeGrado WF, Greenbaum DC. Development of a-helical calpain probes by mimicking a natural protein-protein interaction. J Am Chem Soc. 2012 Oct 24; 134(42):17704-13. PMID: 22998171.
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    93. Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF. Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem. 2012 Nov; 4(11):900-6. PMID: 23089864; PMCID: PMC3568993.
    94. Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, Degrado WF, Samish I. Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Structure. 2012 May 09; 20(5):924-35. PMID: 22579257; PMCID: PMC3366090.
    95. Culik RM, Jo H, DeGrado WF, Gai F. Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in ß-sheet folding. J Am Chem Soc. 2012 May 16; 134(19):8026-9. PMID: 22540162; PMCID: PMC3354031.
    96. Lanci CJ, MacDermaid CM, Kang SG, Acharya R, North B, Yang X, Qiu XJ, DeGrado WF, Saven JG. Computational design of a protein crystal. Proc Natl Acad Sci U S A. 2012 May 08; 109(19):7304-9. PMID: 22538812; PMCID: PMC3358839.
    97. 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. Inhibition of integrin a2ß1 ameliorates glomerular injury. J Am Soc Nephrol. 2012 Jun; 23(6):1027-38. PMID: 22440900; PMCID: PMC3358756.
    98. 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. Neutralizing epitopes in the membrane-proximal external region of HIV-1 gp41 are influenced by the transmembrane domain and the plasma membrane. J Virol. 2012 Mar; 86(6):2930-41. PMID: 22238313.
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    99. Moore DT, Nygren P, Jo H, Boesze-Battaglia K, Bennett JS, DeGrado WF. Affinity of talin-1 for the ß3-integrin cytosolic domain is modulated by its phospholipid bilayer environment. Proc Natl Acad Sci U S A. 2012 Jan 17; 109(3):793-8. PMID: 22210111; PMCID: PMC3271903.
    100. Kim YH, Donald JE, Grigoryan G, Leser GP, Fadeev AY, Lamb RA, DeGrado WF. Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5. Proc Natl Acad Sci U S A. 2011 Dec 27; 108(52):20992-7. PMID: 22178759; PMCID: PMC3248524.
    101. Soto CS, Hannigan BT, DeGrado WF. A photon-free approach to transmembrane protein structure determination. J Mol Biol. 2011 Dec 09; 414(4):596-610. PMID: 22024595; PMCID: PMC3808161.
    102. Mensa B, Kim YH, Choi S, Scott R, Caputo GA, DeGrado WF. Antibacterial mechanism of action of arylamide foldamers. Antimicrob Agents Chemother. 2011 Nov; 55(11):5043-53. PMID: 21844313; PMCID: PMC3195038.
    103. Wang J, Ma C, Wu Y, Lamb RA, Pinto LH, DeGrado WF. Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. J Am Chem Soc. 2011 Sep 07; 133(35):13844-7. PMID: 21819109.
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    104. Shandler SJ, Korendovych IV, Moore DT, Smith-Dupont KB, Streu CN, Litvinov RI, Billings PC, Gai F, Bennett JS, DeGrado WF. Computational design of a ß-peptide that targets transmembrane helices. J Am Chem Soc. 2011 Aug 17; 133(32):12378-81. PMID: 21780757; PMCID: PMC3155016.
    105. Wang J, Ma C, Fiorin G, Carnevale V, Wang T, Hu F, Lamb RA, Pinto LH, Hong M, Klein ML, DeGrado WF. Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. J Am Chem Soc. 2011 Aug 17; 133(32):12834-41. PMID: 21744829; PMCID: PMC3354620.
    106. Korendovych IV, Shandler SJ, Montalvo GL, DeGrado WF. Environment- and sequence-dependence of helical type in membrane-spanning peptides composed of ß3-amino acids. Org Lett. 2011 Jul 01; 13(13):3474-7. PMID: 21651308; PMCID: PMC3124938.
    107. Remorino A, Korendovych IV, Wu Y, DeGrado WF, Hochstrasser RM. Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer. Science. 2011 Jun 03; 332(6034):1206-9. PMID: 21636774; PMCID: PMC3295544.
    108. Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science. 2011 May 27; 332(6033):1071-6. PMID: 21617073; PMCID: PMC3264056.
    109. Wang J, Ma C, Balannik V, Pinto LH, Lamb RA, Degrado WF. Exploring the Requirements for the Hydrophobic Scaffold and Polar Amine in inhibitors of M2 from Influenza A Virus. ACS Med Chem Lett. 2011 Apr 14; 2(4):307-312. PMID: 21691418.
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    111. 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. Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. J Med Chem. 2011 Apr 28; 54(8):2646-57. PMID: 21466220; PMCID: PMC3174104.
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    113. Rogers JM, Polishchuk AL, Guo L, Wang J, DeGrado WF, Gai F. 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. 2011 Apr 05; 27(7):3815-21. PMID: 21401044; PMCID: PMC3068240.
    114. Cady SD, Wang J, Wu Y, DeGrado WF, Hong M. 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. J Am Chem Soc. 2011 Mar 30; 133(12):4274-84. PMID: 21381693; PMCID: PMC3078525.
    115. Chakraborty S, Kravitz JY, Thulstrup PW, Hemmingsen L, DeGrado WF, Pecoraro VL. Design of a three-helix bundle capable of binding heavy metals in a triscysteine environment. Angew Chem Int Ed Engl. 2011 Feb 25; 50(9):2049-53. PMID: 21344549; PMCID: PMC3058785.
    116. Donald JE, Zhang Y, Fiorin G, Carnevale V, Slochower DR, Gai F, Klein ML, DeGrado WF. Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion. Proc Natl Acad Sci U S A. 2011 Mar 08; 108(10):3958-63. PMID: 21321234; PMCID: PMC3054033.
    117. Wang J, Qiu JX, Soto C, DeGrado WF. Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus. Curr Opin Struct Biol. 2011 Feb; 21(1):68-80. PMID: 21247754; PMCID: PMC3039100.
    118. Donald JE, Kulp DW, DeGrado WF. Salt bridges: geometrically specific, designable interactions. Proteins. 2011 Mar; 79(3):898-915. PMID: 21287621; PMCID: PMC3069487.
    119. Grigoryan G, Moore DT, DeGrado WF. Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K? channels, and integrin receptors. Annu Rev Biochem. 2011; 80:211-37. PMID: 21548783; PMCID: PMC3767166.
    120. Metcalf DG, Moore DT, Wu Y, Kielec JM, Molnar K, Valentine KG, Wand AJ, Bennett JS, DeGrado WF. NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation. Proc Natl Acad Sci U S A. 2010 Dec 28; 107(52):22481-6. PMID: 21156831; PMCID: PMC3012518.
    121. Fadeev AY, DeGrado WF. Lipid membranes supported on optically transparent nanosilicas: synthesis and application in characterization of protein-membrane interactions. J Colloid Interface Sci. 2011 Mar 01; 355(1):265-8. PMID: 21193202; PMCID: PMC4123449.
    122. Jo H, Culik RM, Korendovych IV, Degrado WF, Gai F. Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation. Biochemistry. 2010 Dec 14; 49(49):10354-6. PMID: 21077670; PMCID: PMC2999665.
    123. Korendovych IV, Senes A, Kim YH, Lear JD, Fry HC, Therien MJ, Blasie JK, Walker FA, Degrado WF. De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex. J Am Chem Soc. 2010 Nov 10; 132(44):15516-8. PMID: 20945900; PMCID: PMC3016712.
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    126. Fiorin G, Carnevale V, DeGrado WF. Structural biology. The flu's proton escort. Science. 2010 Oct 22; 330(6003):456-8. PMID: 20966238; PMCID: PMC3771513.
    127. Carnevale V, Fiorin G, Levine BG, Degrado WF, Klein ML. Multiple Proton Confinement in the M2 Channel from the Influenza A Virus. J Phys Chem C Nanomater Interfaces. 2010 Oct 21; 114(48):20856-20863. PMID: 21359105.
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    129. Donald JE, Zhu H, Litvinov RI, DeGrado WF, Bennett JS. Identification of interacting hot spots in the beta3 integrin stalk using comprehensive interface design. J Biol Chem. 2010 Dec 03; 285(49):38658-65. PMID: 20929856; PMCID: PMC2992298.
    130. Grigoryan G, Degrado WF. Probing designability via a generalized model of helical bundle geometry. J Mol Biol. 2011 Jan 28; 405(4):1079-100. PMID: 20932976; PMCID: PMC3052747.
    131. Lau WL, Degrado WF, Roder H. 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. Biophys J. 2010 Oct 06; 99(7):2299-308. PMID: 20923665; PMCID: PMC3042555.
    132. Leiding T, Wang J, Martinsson J, DeGrado WF, Arsköld SP. Proton and cation transport activity of the M2 proton channel from influenza A virus. Proc Natl Acad Sci U S A. 2010 Aug 31; 107(35):15409-14. PMID: 20713739; PMCID: PMC2932607.
    133. Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF, Klein ML. Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. Proc Natl Acad Sci U S A. 2010 Aug 24; 107(34):15075-80. PMID: 20689043; PMCID: PMC2930543.
    134. Su Y, DeGrado WF, Hong M. Orientation, dynamics, and lipid interaction of an antimicrobial arylamide investigated by 19F and 31P solid-state NMR spectroscopy. J Am Chem Soc. 2010 Jul 07; 132(26):9197-205. PMID: 20536141; PMCID: PMC2904348.
    135. Zhu H, Metcalf DG, Streu CN, Billings PC, Degrado WF, Bennett JS. Specificity for homooligomer versus heterooligomer formation in integrin transmembrane helices. J Mol Biol. 2010 Sep 03; 401(5):882-91. PMID: 20615419; PMCID: PMC2935666.
    136. 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. Discovery of potent small-molecule inhibitors of multidrug-resistant Plasmodium falciparum using a novel miniaturized high-throughput luciferase-based assay. Antimicrob Agents Chemother. 2010 Sep; 54(9):3597-604. PMID: 20547797; PMCID: PMC2934977.
    137. Shandler SJ, Shapovalov MV, Dunbrack RL, DeGrado WF. Development of a rotamer library for use in beta-peptide foldamer computational design. J Am Chem Soc. 2010 Jun 02; 132(21):7312-20. PMID: 20446685.
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    139. Goldberg SD, Clinthorne GD, Goulian M, DeGrado WF. Transmembrane polar interactions are required for signaling in the Escherichia coli sensor kinase PhoQ. Proc Natl Acad Sci U S A. 2010 May 04; 107(18):8141-6. PMID: 20404199; PMCID: PMC2889538.
    140. Fry HC, Lehmann A, Saven JG, DeGrado WF, Therien MJ. Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore. J Am Chem Soc. 2010 Mar 24; 132(11):3997-4005. PMID: 20192195; PMCID: PMC2856663.
    141. Cady SD, Schmidt-Rohr K, Wang J, Soto CS, Degrado WF, Hong M. Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature. 2010 Feb 04; 463(7281):689-92. PMID: 20130653; PMCID: PMC2818718.
    142. Balannik V, Carnevale V, Fiorin G, Levine BG, Lamb RA, Klein ML, Degrado WF, Pinto LH. Functional studies and modeling of pore-lining residue mutants of the influenza a virus M2 ion channel. Biochemistry. 2010 Feb 02; 49(4):696-708. PMID: 20028125; PMCID: PMC4924815.
    143. Tew GN, Scott RW, Klein ML, Degrado WF. De novo design of antimicrobial polymers, foldamers, and small molecules: from discovery to practical applications. Acc Chem Res. 2010 Jan 19; 43(1):30-9. PMID: 19813703; PMCID: PMC2808429.
    144. Balannik V, Wang J, Ohigashi Y, Jing X, Magavern E, Lamb RA, Degrado WF, Pinto LH. Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Biochemistry. 2009 Dec 22; 48(50):11872-82. PMID: 19905033; PMCID: PMC2794939.
    145. Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF. Consensus motif for integrin transmembrane helix association. Proc Natl Acad Sci U S A. 2010 Jan 12; 107(2):703-8. PMID: 20080739; PMCID: PMC2818961.
    146. Balannik V, Obrdlik P, Inayat S, Steensen C, Wang J, Rausch JM, DeGrado WF, Kelety B, Pinto LH. Solid-supported membrane technology for the investigation of the influenza A virus M2 channel activity. Pflugers Arch. 2010 Mar; 459(4):593-605. PMID: 19946785; PMCID: PMC3428792.
    147. Faiella M, Andreozzi C, de Rosales RT, Pavone V, Maglio O, Nastri F, DeGrado WF, Lombardi A. An artificial di-iron oxo-protein with phenol oxidase activity. Nat Chem Biol. 2009 Dec; 5(12):882-4. PMID: 19915535; PMCID: PMC3808167.
    148. San Antonio JD, Zoeller JJ, Habursky K, Turner K, Pimtong W, Burrows M, Choi S, Basra S, Bennett JS, DeGrado WF, Iozzo RV. A key role for the integrin alpha2beta1 in experimental and developmental angiogenesis. Am J Pathol. 2009 Sep; 175(3):1338-47. PMID: 19700757; PMCID: PMC2731151.
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    151. He F, Nair GR, Soto CS, Chang Y, Hsu L, Ronzone E, DeGrado WF, Binns AN. Molecular basis of ChvE function in sugar binding, sugar utilization, and virulence in Agrobacterium tumefaciens. J Bacteriol. 2009 Sep; 191(18):5802-13. PMID: 19633083; PMCID: PMC2737963.
    152. Ma C, Polishchuk AL, Ohigashi Y, Stouffer AL, Schön A, Magavern E, Jing X, Lear JD, Freire E, Lamb RA, DeGrado WF, Pinto LH. Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 2009 Jul 28; 106(30):12283-8. PMID: 19590009; PMCID: PMC2718339.
    153. Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF, Hong M. Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus. J Am Chem Soc. 2009 Jun 17; 131(23):8066-76. PMID: 19469531; PMCID: PMC3807247.
    154. Goldberg SD, Derr P, DeGrado WF, Goulian M. Engineered single- and multi-cell chemotaxis pathways in E. coli. Mol Syst Biol. 2009; 5:283. PMID: 19536206; PMCID: PMC2710872.
    155. Metcalf DG, Kulp DW, Bennett JS, DeGrado WF. Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer. J Mol Biol. 2009 Oct 02; 392(4):1087-101. PMID: 19527732; PMCID: PMC3856686.
    156. Choi S, Isaacs A, Clements D, Liu D, Kim H, Scott RW, Winkler JD, DeGrado WF. De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers. Proc Natl Acad Sci U S A. 2009 Apr 28; 106(17):6968-73. PMID: 19359494.
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    158. Signarvic RS, Degrado WF. Metal-binding dependent disruption of membranes by designed helices. J Am Chem Soc. 2009 Mar 11; 131(9):3377-84. PMID: 19209932; PMCID: PMC3774282.
    159. Liu F, Dumont C, Zhu Y, DeGrado WF, Gai F, Gruebele M. A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha(3)D. J Chem Phys. 2009 Feb 14; 130(6):061101. PMID: 19222256; PMCID: PMC2671193.
    160. Khurana E, Dal Peraro M, DeVane R, Vemparala S, DeGrado WF, Klein ML. Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus. Proc Natl Acad Sci U S A. 2009 Jan 27; 106(4):1069-74. PMID: 19144924; PMCID: PMC2626606.
    161. Miller MW, Basra S, Kulp DW, Billings PC, Choi S, Beavers MP, McCarty OJ, Zou Z, Kahn ML, Bennett JS, DeGrado WF. Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism. Proc Natl Acad Sci U S A. 2009 Jan 20; 106(3):719-24. PMID: 19141632; PMCID: PMC2625282.
    162. Bell CB, Calhoun JR, Bobyr E, Wei PP, Hedman B, Hodgson KO, Degrado WF, Solomon EI. 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. 2009 Jan 13; 48(1):59-73. PMID: 19090676; PMCID: PMC2660568.
    163. Kuroda K, Caputo GA, DeGrado WF. The role of hydrophobicity in the antimicrobial and hemolytic activities of polymethacrylate derivatives. Chemistry. 2009; 15(5):1123-33. PMID: 19072946; PMCID: PMC3814040.
    164. Bissonnette ML, Donald JE, DeGrado WF, Jardetzky TS, Lamb RA. Functional analysis of the transmembrane domain in paramyxovirus F protein-mediated membrane fusion. J Mol Biol. 2009 Feb 13; 386(1):14-36. PMID: 19121325.
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    165. Scott RW, DeGrado WF, Tew GN. De novo designed synthetic mimics of antimicrobial peptides. Curr Opin Biotechnol. 2008 Dec; 19(6):620-7. PMID: 18996193; PMCID: PMC2646611.
    166. Basani RB, Zhu H, Thornton MA, Soto CS, Degrado WF, Kowalska MA, Bennett JS, Poncz M. 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. 2009 Jan 22; 113(4):902-10. PMID: 18987357; PMCID: PMC2630275.
    167. Weeks CL, Polishchuk A, Getahun Z, Degrado WF, Spiro TG. Investigation of an unnatural amino acid for use as a resonance Raman probe: Detection limits, solvent and temperature dependence of the ?C=N band of 4-cyanophenylalanine. J Raman Spectrosc. 2008 Nov; 39(11):1606-1613. PMID: 20648227.
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    168. Nguyen PA, Soto CS, Polishchuk A, Caputo GA, Tatko CD, Ma C, Ohigashi Y, Pinto LH, DeGrado WF, Howard KP. pH-induced conformational change of the influenza M2 protein C-terminal domain. Biochemistry. 2008 Sep 23; 47(38):9934-6. PMID: 18754675; PMCID: PMC2746938.
    169. 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. Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. J Am Chem Soc. 2008 Sep 10; 130(36):11921-7. PMID: 18710226; PMCID: PMC3663296.
    170. Caputo GA, Litvinov RI, Li W, Bennett JS, Degrado WF, Yin H. Computationally designed peptide inhibitors of protein-protein interactions in membranes. Biochemistry. 2008 Aug 19; 47(33):8600-6. PMID: 18642886; PMCID: PMC2719017.
    171. Shu JY, Tan C, DeGrado WF, Xu T. New design of helix bundle peptide-polymer conjugates. Biomacromolecules. 2008 Aug; 9(8):2111-7. PMID: 18627200; PMCID: PMC3815612.
    172. Stouffer AL, Ma C, Cristian L, Ohigashi Y, Lamb RA, Lear JD, Pinto LH, 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. 2008 Jul; 16(7):1067-76. PMID: 18611380; PMCID: PMC2594009.
    173. Grigoryan G, Degrado WF. Modest membrane hydrogen bonds deliver rich results. Nat Chem Biol. 2008 Jul; 4(7):393-4. PMID: 18560430; PMCID: PMC2721465.
    174. Moore DT, Berger BW, DeGrado WF. Protein-protein interactions in the membrane: sequence, structural, and biological motifs. Structure. 2008 Jul; 16(7):991-1001. PMID: 18611372; PMCID: PMC3771515.
    175. Calhoun JR, Bell CB, Smith TJ, Thamann TJ, DeGrado WF, Solomon EI. Oxygen reactivity of the biferrous site in the de novo designed four helix bundle peptide DFsc: nature of the "intermediate" and reaction mechanism. J Am Chem Soc. 2008 Jul 23; 130(29):9188-9. PMID: 18572936.
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    176. Goldberg SD, Soto CS, Waldburger CD, Degrado WF. Determination of the physiological dimer interface of the PhoQ sensor domain. J Mol Biol. 2008 Jun 13; 379(4):656-65. PMID: 18468622; PMCID: PMC2542651.
    177. Ma C, Soto CS, Ohigashi Y, Taylor A, Bournas V, Glawe B, Udo MK, Degrado WF, Lamb RA, Pinto LH. Identification of the pore-lining residues of the BM2 ion channel protein of influenza B virus. J Biol Chem. 2008 Jun 06; 283(23):15921-31. PMID: 18408016; PMCID: PMC2414288.
    178. Calhoun JR, Liu W, Spiegel K, Dal Peraro M, Klein ML, Valentine KG, Wand AJ, DeGrado WF. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement. Structure. 2008 Feb; 16(2):210-5. PMID: 18275812; PMCID: PMC3814030.
    179. Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. Structural basis for the function and inhibition of an influenza virus proton channel. Nature. 2008 Jan 31; 451(7178):596-9. PMID: 18235504.
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    180. Tang J, Signarvic RS, DeGrado WF, Gai F. Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers. Biochemistry. 2007 Dec 04; 46(48):13856-63. PMID: 17994771.
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    181. Choi S, Vilaire G, Marcinkiewicz C, Winkler JD, Bennett JS, DeGrado WF. Small molecule inhibitors of integrin alpha2beta1. J Med Chem. 2007 Nov 01; 50(22):5457-62. PMID: 17915848.
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    182. Mukherjee S, Chowdhury P, DeGrado WF, Gai F. Site-specific hydration status of an amphipathic peptide in AOT reverse micelles. Langmuir. 2007 Oct 23; 23(22):11174-9. PMID: 17910485.
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    183. Balakrishnan G, Hu Y, Bender GM, Getahun Z, DeGrado WF, Spiro TG. 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. PMID: 17910449; PMCID: PMC2887291.
    184. Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, DeGrado WF. De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc. 2007 Sep 05; 129(35):10732-40. PMID: 17691729; PMCID: PMC2542652.
    185. Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM, Vinogradov SA. Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores. J Phys Chem A. 2007 Aug 02; 111(30):6977-90. PMID: 17608457; PMCID: PMC2441487.
    186. Metcalf DG, Law PB, DeGrado WF. Mutagenesis data in the automated prediction of transmembrane helix dimers. Proteins. 2007 May 01; 67(2):375-84. PMID: 17311347.
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    187. Goodman CM, Choi S, Shandler S, DeGrado WF. Foldamers as versatile frameworks for the design and evolution of function. Nat Chem Biol. 2007 May; 3(5):252-62. PMID: 17438550.
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    188. Cady SD, Goodman C, Tatko CD, DeGrado WF, Hong M. 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. PMID: 17417850.
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    189. Lee MH, Adams CS, Boettiger D, Degrado WF, Shapiro IM, Composto RJ, Ducheyne P. 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. PMID: 17111408.
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    190. Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, DeGrado WF. Computational design of peptides that target transmembrane helices. Science. 2007 Mar 30; 315(5820):1817-22. PMID: 17395823.
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    191. Wang PC, Vilaire G, DeGrado WF, Bennett JS. 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. PMID: 17499487.
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    192. White TC, Berny MA, Robinson DK, Yin H, DeGrado WF, Hanson SR, McCarty OJ. 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. PMID: 17489103.
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    193. Fang C, Senes A, Cristian L, DeGrado WF, Hochstrasser RM. 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. PMID: 17075037; PMCID: PMC1636525.
    194. Dal Peraro M, Spiegel K, Lamoureux G, De Vivo M, DeGrado WF, Klein ML. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J Struct Biol. 2007 Mar; 157(3):444-53. PMID: 17188512.
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    195. Yin H, Litvinov RI, Vilaire G, Zhu H, Li W, Caputo GA, Moore DT, Lear JD, Weisel JW, Degrado WF, Bennett JS. 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. PMID: 17032655.
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    196. Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF. 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. J Mol Biol. 2007 Feb 16; 366(2):436-48. PMID: 17174324.
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    197. Bunagan MR, Cristian L, DeGrado WF, Gai F. Truncation of a cross-linked GCN4-p1 coiled coil leads to ultrafast folding. Biochemistry. 2006 Sep 12; 45(36):10981-6. PMID: 16953584.
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    198. Wade H, Stayrook SE, Degrado WF. 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. PMID: 16819737.
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    199. Yin H, Gerlach LO, Miller MW, Moore DT, Liu D, Vilaire G, Bennett JS, DeGrado WF. Arylamide derivatives as allosteric inhibitors of the integrin alpha2beta1/type I collagen interaction. Bioorg Med Chem Lett. 2006 Jul 01; 16(13):3380-2. PMID: 16678410.
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    200. Lopez CF, Nielsen SO, Srinivas G, Degrado WF, Klein ML. Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-grain Molecular Dynamics. J Chem Theory Comput. 2006 May; 2(3):649-655. PMID: 18985168.
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    201. North B, Cristian L, Fu Stowell X, Lear JD, Saven JG, Degrado WF. Characterization of a membrane protein folding motif, the Ser zipper, using designed peptides. J Mol Biol. 2006 Jun 16; 359(4):930-9. PMID: 16697010.
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    202. Litvinov RI, Vilaire G, Li W, DeGrado WF, Weisel JW, Bennett JS. 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. PMID: 16605263.
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    203. Tatko CD, Nanda V, Lear JD, Degrado WF. Polar networks control oligomeric assembly in membranes. J Am Chem Soc. 2006 Apr 05; 128(13):4170-1. PMID: 16568959.
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    204. Pophristic V, Vemparala S, Ivanov I, Liu Z, Klein ML, DeGrado WF. 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. PMID: 16494407.
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    205. Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA, Klein ML. 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. PMID: 16464062.
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    206. Nanda V, DeGrado WF. Computational design of heterochiral peptides against a helical target. J Am Chem Soc. 2006 Jan 25; 128(3):809-16. PMID: 16417370.
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    207. Yin H, Frederick KK, Liu D, Wand AJ, Degrado WF. Arylamide derivatives as peptidomimetic inhibitors of calmodulin. Org Lett. 2006 Jan 19; 8(2):223-5. PMID: 16408880.
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    208. Geremia S, Di Costanzo L, Randaccio L, Engel DE, Lombardi A, Nastri F, DeGrado WF. 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. PMID: 16332076.
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    209. Wei PP, Skulan AJ, Wade H, DeGrado WF, Solomon EI. 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. PMID: 16287296.
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    210. Engel DE, DeGrado WF. Alpha-alpha linking motifs and interhelical orientations. Proteins. 2005 Nov 01; 61(2):325-37. PMID: 16104016.
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    211. Choi S, Clements DJ, Pophristic V, Ivanov I, Vemparala S, Bennett JS, Klein ML, Winkler JD, DeGrado WF. The design and evaluation of heparin-binding foldamers. Angew Chem Int Ed Engl. 2005 Oct 21; 44(41):6685-9. PMID: 16094685.
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    212. Summa CM, Levitt M, Degrado WF. An atomic environment potential for use in protein structure prediction. J Mol Biol. 2005 Sep 30; 352(4):986-1001. PMID: 16126228.
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    213. Maglio O, Nastri F, Calhoun JR, Lahr S, Wade H, Pavone V, DeGrado WF, Lombardi A. 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. PMID: 16091937.
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    214. Wang T, Lau WL, DeGrado WF, Gai F. T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1. Biophys J. 2005 Dec; 89(6):4180-7. PMID: 16150962; PMCID: PMC1366983.
    215. Willcox PJ, Reinhart-King CA, Lahr SJ, DeGrado WF, Hammer DA. Dynamic heterodimer-functionalized surfaces for endothelial cell adhesion. Biomaterials. 2005 Aug; 26(23):4757-66. PMID: 15763255.
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    216. Kovalenko OV, Metcalf DG, DeGrado WF, Hemler ME. Structural organization and interactions of transmembrane domains in tetraspanin proteins. BMC Struct Biol. 2005 Jun 28; 5:11. PMID: 15985154; PMCID: PMC1190194.
    217. Adamian L, Nanda V, DeGrado WF, Liang J. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins. 2005 May 15; 59(3):496-509. PMID: 15789404.
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    218. Nanda V, DeGrado WF. Automated use of mutagenesis data in structure prediction. Proteins. 2005 May 15; 59(3):454-66. PMID: 15768404.
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    219. Slovic AM, Stayrook SE, North B, Degrado WF. 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. PMID: 15826670.
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    220. Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, Degrado WF. De novo design of a redox-active minimal rubredoxin mimic. J Am Chem Soc. 2005 Apr 27; 127(16):5804-5. PMID: 15839675.
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    221. Cristian L, Nanda V, Lear JD, DeGrado WF. 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. PMID: 15854657.
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    222. Kuroda K, DeGrado WF. Amphiphilic polymethacrylate derivatives as antimicrobial agents. J Am Chem Soc. 2005 Mar 30; 127(12):4128-9. PMID: 15783168.
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    223. Duong-Ly KC, Nanda V, Degrado WF, Howard KP. The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Sci. 2005 Apr; 14(4):856-61. PMID: 15741338; PMCID: PMC2253456.
    224. Howard KP, Liu W, Crocker E, Nanda V, Lear J, Degrado WF, Smith SO. Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle. Protein Sci. 2005 Apr; 14(4):1019-24. PMID: 15741331; PMCID: PMC2253437.
    225. Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. 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. PMID: 15686346.
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    226. Li W, Metcalf DG, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, Degrado WF, Bennett JS. A push-pull mechanism for regulating integrin function. Proc Natl Acad Sci U S A. 2005 Feb 01; 102(5):1424-9. PMID: 15671157; PMCID: PMC547819.
    227. Stouffer AL, Nanda V, Lear JD, DeGrado WF. Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function. J Mol Biol. 2005 Mar 18; 347(1):169-79. PMID: 15733926.
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    228. Lahr SJ, Engel DE, Stayrook SE, Maglio O, North B, Geremia S, Lombardi A, DeGrado WF. Analysis and design of turns in alpha-helical hairpins. J Mol Biol. 2005 Mar 11; 346(5):1441-54. PMID: 15713492.
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    229. Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, DeGrado WF. Artificial diiron proteins: from structure to function. Biopolymers. 2005; 80(2-3):264-78. PMID: 15700297.
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    230. Ghirlanda G, Hilcove SA, Pidikiti R, Johansson JS, Lear JD, Degrado WF, Eckenhoff RG. Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide. FEBS Lett. 2004 Dec 03; 578(1-2):140-4. PMID: 15581631.
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    231. Nanda V, Degrado WF. Simulated evolution of emergent chiral structures in polyalanine. J Am Chem Soc. 2004 Nov 10; 126(44):14459-67. PMID: 15521766.
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    232. Doerksen RJ, Chen B, Liu D, Tew GN, Degrado WF, Klein ML. 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. PMID: 15372664.
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    233. Wang T, Zhu Y, Getahun Z, Du D, Huang CY, Degrado WF, Gai F. Length Dependent Helix-Coil Transition Kinetics of Nine Alanine-Based Peptides. J Phys Chem B. 2004 Sep 30; 108(39). PMID: 24307864.
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    234. Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF. Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophys J. 2004 Nov; 87(5):3421-9. PMID: 15315956; PMCID: PMC1304808.
    235. Senes A, Engel DE, DeGrado WF. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol. 2004 Aug; 14(4):465-79. PMID: 15313242.
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    236. Ghirlanda G, Osyczka A, Liu W, Antolovich M, Smith KM, Dutton PL, Wand AJ, DeGrado WF. 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. PMID: 15225055.
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    237. Tucker MJ, Getahun Z, Nanda V, DeGrado WF, Gai F. 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. PMID: 15099085.
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    238. Engel DE, DeGrado WF. Amino acid propensities are position-dependent throughout the length of alpha-helices. J Mol Biol. 2004 Apr 09; 337(5):1195-205. PMID: 15046987.
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    239. Li R, Gorelik R, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS. Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes. J Biol Chem. 2004 Jun 18; 279(25):26666-73. PMID: 15067009.
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    240. Liu D, Choi S, Chen B, Doerksen RJ, Clements DJ, Winkler JD, Klein ML, DeGrado WF. Nontoxic membrane-active antimicrobial arylamide oligomers. Angew Chem Int Ed Engl. 2004 Feb 20; 43(9):1158-62. PMID: 14983462.
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    241. Slovic AM, Kono H, Lear JD, Saven JG, DeGrado WF. Computational design of water-soluble analogues of the potassium channel KcsA. Proc Natl Acad Sci U S A. 2004 Feb 17; 101(7):1828-33. PMID: 14766985; PMCID: PMC357012.
    242. Lau WL, Ege DS, Lear JD, Hammer DA, DeGrado WF. Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization. Biophys J. 2004 Jan; 86(1 Pt 1):272-84. PMID: 14695269; PMCID: PMC1303790.
    243. Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, Saven JG. Computational design and characterization of a monomeric helical dinuclear metalloprotein. J Mol Biol. 2003 Dec 12; 334(5):1101-15. PMID: 14643669.
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    244. Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF, Gai F. 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. PMID: 14671331; PMCID: PMC307594.
    245. Cristian L, Lear JD, DeGrado WF. 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. PMID: 14657351; PMCID: PMC299801.
    246. Signarvic RS, DeGrado WF. De novo design of a molecular switch: phosphorylation-dependent association of designed peptides. J Mol Biol. 2003 Nov 14; 334(1):1-12. PMID: 14596795.
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    247. Cristian L, Lear JD, DeGrado WF. Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange. Protein Sci. 2003 Aug; 12(8):1732-40. PMID: 12876322; PMCID: PMC2323959.
    248. Lear JD, Gratkowski H, Adamian L, Liang J, DeGrado WF. Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry. 2003 Jun 03; 42(21):6400-7. PMID: 12767221.
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    249. DeGrado WF. Computational biology: Biosensor design. Nature. 2003 May 08; 423(6936):132-3. PMID: 12736670.
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    250. Li R, Mitra N, Gratkowski H, Vilaire G, Litvinov R, Nagasami C, Weisel JW, Lear JD, DeGrado WF, Bennett JS. Activation of integrin alphaIIbbeta3 by modulation of transmembrane helix associations. Science. 2003 May 02; 300(5620):795-8. PMID: 12730600.
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    251. DeGrado WF, Gratkowski H, Lear JD. How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci. 2003 Apr; 12(4):647-65. PMID: 12649422; PMCID: PMC2323850.
    252. Maglio O, Nastri F, Pavone V, Lombardi A, DeGrado WF. Preorganization of molecular binding sites in designed diiron proteins. Proc Natl Acad Sci U S A. 2003 Apr 01; 100(7):3772-7. PMID: 12655072.
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    253. Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF. The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR. Protein Sci. 2003 Mar; 12(3):520-31. PMID: 12592022; PMCID: PMC2312439.
    254. Slovic AM, Summa CM, Lear JD, DeGrado WF. Computational design of a water-soluble analog of phospholamban. Protein Sci. 2003 Feb; 12(2):337-48. PMID: 12538897; PMCID: PMC2312418.
    255. DeGrado WF, Di Costanzo L, Geremia S, Lombardi A, Pavone V, Randaccio L. Sliding helix and change of coordination geometry in a model di-MnII protein. Angew Chem Int Ed Engl. 2003 Jan 27; 42(4):417-20. PMID: 12569505.
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    256. Papoian GA, DeGrado WF, Klein ML. 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. PMID: 12517172.
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    257. Getahun Z, Huang CY, Wang T, De León B, DeGrado WF, Gai F. Using nitrile-derivatized amino acids as infrared probes of local environment. J Am Chem Soc. 2003 Jan 15; 125(2):405-11. PMID: 12517152.
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    258. Li R, Hoess RH, Bennett JS, DeGrado WF. Use of phage display to probe the evolution of binding specificity and affinity in integrins. Protein Eng. 2003 Jan; 16(1):65-72. PMID: 12646694.
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    259. Li R, Babu CR, Valentine K, Lear JD, Wand AJ, 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. 2002 Dec 31; 41(52):15618-24. PMID: 12501190.
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    260. Huang CY, He S, DeGrado WF, McCafferty DG, Gai F. Light-induced helix formation. J Am Chem Soc. 2002 Oct 30; 124(43):12674-5. PMID: 12392410.
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    261. Cheng RP, DeGrado WF. Long-range interactions stabilize the fold of a non-natural oligomer. J Am Chem Soc. 2002 Oct 02; 124(39):11564-5. PMID: 12296699.
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    262. Gratkowski H, Dai QH, Wand AJ, DeGrado WF, Lear JD. Cooperativity and specificity of association of a designed transmembrane peptide. Biophys J. 2002 Sep; 83(3):1613-9. PMID: 12202385; PMCID: PMC1302258.
    263. Summa CM, Rosenblatt MM, Hong JK, Lear JD, DeGrado WF. Computational de novo design, and characterization of an A(2)B(2) diiron protein. J Mol Biol. 2002 Aug 30; 321(5):923-38. PMID: 12206771.
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    264. Howard KP, Lear JD, DeGrado WF. 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. PMID: 12084917; PMCID: PMC124313.
    265. Ghirlanda G, Lear JD, Ogihara NL, Eisenberg D, DeGrado WF. A hierarchic approach to the design of hexameric helical barrels. J Mol Biol. 2002 May 24; 319(1):243-53. PMID: 12051949.
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    266. Tew GN, Liu D, Chen B, Doerksen RJ, Kaplan J, Carroll PJ, Klein ML, DeGrado WF. De novo design of biomimetic antimicrobial polymers. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5110-4. PMID: 11959961; PMCID: PMC122730.
    267. Marsh EN, DeGrado WF. Noncovalent self-assembly of a heterotetrameric diiron protein. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5150-4. PMID: 11959963; PMCID: PMC122737.
    268. Huang CY, Getahun Z, Zhu Y, Klemke JW, DeGrado WF, Gai F. Helix formation via conformation diffusion search. Proc Natl Acad Sci U S A. 2002 Mar 05; 99(5):2788-93. PMID: 11867741; PMCID: PMC122426.
    269. 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 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. PMID: 11317312.
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    270. 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. Angew Chem Int Ed Engl. 2001 Apr 17; 40(8):1494-1496. PMID: 29712367.
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