Publications

Culik RM, Jo H, Degrado WF & Gai F.. (2012). Using Thioamides To Site-Specifically Interrogate the Dynamics of Hydrogen Bond Formation in - Sheet Folding. J Am Chem Soc 16, 8026-9. [PubMed]

Lanci CJ, Macdermaid CM, Kang SG, Acharya R, North B, Yang X, Qiu XJ, Degrado WF & Saven JG. (2012). Computational design of a protein crystal. Proc Natl Acad Sci U S A 8, 7304-9. [PubMed]

Korendovych IV, Shandler SJ, L Montalvo G & Degrado WF. (2012). Environment- and Sequence-Dependence of Helical Type in Membrane-Spanning Peptides Composed of (3)-Amino Acids . Org Lett 0, [Epub ahead of print]. [PubMed]

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. (2012). Neutralizing epitopes in the membrane-proximal external region of HIV-1 gp41 are influenced by the transmembrane domain and the plasma membrane. . J Virol. 86, 2930-41. [PubMed]

Moore DT, Nygren P, Jo H, Boesze-Battaglia K, Bennett JS & DeGrado WF. (2012). Affinity of talin-1 for the 3-integrin cytosolic domain is modulated by its phospholipid bilayer environment. Proc Natl Acad Sci U S A 17, 793-8. [PubMed]

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. (2012). Inhibition of Integrin 21 Ameliorates Glomerular Injury. JASN 23, 1027-38. [PubMed]

Soto CS, Hannigan BT & DeGrado WF. (2011). A Photon-Free Approach to Transmembrane Protein Structure Determination . JMB 414, 596-610. [PubMed]

Kim YH, Donald JE, Grigoryan G, Leser GP, Fadeev AY, Lamb RA & DeGrado WF. (2011). Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5.. Proc Natl Acad Sci U S A 27, 20992-7. [PubMed]

Mensa B, Kim YH, Choi S, Scott R, Caputo GA & DeGrado WF. (2011). Antibacterial mechanism of action of arylamide foldamers. . Antimicrob Agents Chemother. 55, 5043-53. [PubMed]

Wang J, Ma C, Wu Y, Lamb RA, Pinto LH & DeGrado WF. (2011). Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel.. J Am Chem Soc 7, 13844-7. [PubMed]

Shandler SJ, Korendovych IV, Moore DT, Smith-Dupont KB, Streu CN, Litvinov RI, Billings PC, Gai F, Bennett JS & DeGrado WF. (2011). Computational design of a -peptide that targets transmembrane helices. J Am Chem Soc 17, 12378-81. [PubMed]

Wang J, Ma C, Fiorin G, Carnevale V, Wang T, Hu F, Lamb RA, Pinto LH, Hong M, Klein ML & DeGrado WF. (2011). Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. J Am Chem Soc 17, 12834-41. [PubMed]

Wang J, Ma C, Balannik V, Pinto LH, Lamb RA & Degrado WF. (2011). Exploring the Requirements for the Hydrophobic Scaffold and Polar Amine in inhibitors of M2 from Influenza A Virus. ACS Med Chem Lett 14, 307-312. [PubMed]

Korendovych IV, Shandler SJ, Montalvo GL & DeGrado WF. (2011). Environment- and sequence-dependence of helical type in membrane-spanning peptides composed of 3-amino acids. Org Lett 1, 3474-7. [PubMed]

Remorino A, Korendovych IV, Wu Y, DeGrado WF & Hochstrasser RM. (2011). Residue-specific vibrational echoes yield 3D structures ofa transmembrane helix dimer. Science 3, 1206-9. [PubMed]

Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM & DeGrado WF. (2011). Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 27, 1071-6. [PubMed]

Grigoryan G, Moore DT & DeGrado WF. (2011). Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K+ channels, and integrin receptors. Annu Rev Biochem 7, 211-37. [PubMed]

Korendovych IV, Kulp DW, Wu Y, Cheng H, Roder H & DeGrado WF. (2011). Design of a switchable eliminase. Proc Natl Acad Sci U S A 26, 6823-7. [PubMed]

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. (2011). Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. J Med Chem 28, 2646-57. [PubMed]

Ghosh A, Qiu J, DeGrado WF & Hochstrasser RM. (2011). Tidal surge in the M2 proton channel, sensed by 2D IR spectroscopy. Proc Natl Acad Sci U S A 12, 6115-20. [PubMed]

Rogers JM, Polishchuk AL, Guo L, Wang J, DeGrado WF & Gai F. (2011). 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 5, 3815-21. [PubMed]

Cady SD, Wang J, Wu Y, DeGrado WF &Hong M. (2011). 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 30, 4274-84. [PubMed]

Carnevale V, Fiorin G, Levine BG, Degrado WF & Klein ML. (2011). Multiple Proton Confinement in the M2 Channel from the Influenza A Virus. J Phys Chem C Nanomater Interfaces 21, 20856-20863. [PubMed]

Donald JE, Zhang Y, Fiorin G, Carnevale V, Slochower DR, Gai F, Klein ML, DeGrado WF. (2011). Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion. Proc Natl Acad Sci U S A 8, 3958-63. [PubMed]

Donald JE, Kulp DW, DeGrado WF. (2011). Salt bridges: geometrically specific, designable interactions. Proteins 79, 898-915. [PubMed]

Wang J, Qiu JX, Soto C & DeGrado WF. (2011). Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus. Curr Opin Struct Biol 21, 68-80. [PubMed]

Balannik V, Obrdlik P, Inayat S, Steensen C, Wang J, Rausch JM, DeGrado WF, Kelety B & Pinto L. (2010). Solid-supported membrane technology for the investigation of the influenza A virus M2 channel activity. Pflugers Arch 459, 593-605. [PubMed]

Cady SD, Schmidt-Rohr K, Wang J, Soto CS, Degrado WF & Hong M. (2010). Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature 463, 689-692. [PubMed]

Balannik V, Carnevale V, Fiorin G, Levine BG, Lamb RA, Klein ML, Degrado WF & Pinto LH. (2010). Functional studies and modeling of pore-lining residue mutants of the influenza a virus M2 ion channel. Biochemistry 49, 696-708. [PubMed]

Fry HC, Lehmann A, Saven JG, Degrado WF & Therien MJ. (2010). 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 132, 3997-4005. [PubMed]

Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, Degrado WF & Samish I. . (2010). Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions.. Structure 9205, 924-35. [PubMed]

Fadeev AY & DeGrado WF. (2010). Lipid membranes supported on optically transparent nanosilicas: synthesis and application in characterization of protein-membrane interactions. J Colloid Interface Sci 1, 265-8. [PubMed]

Metcalf DG, Moore DT, Wu Y, Kielec JM, Molnar K, Valentine KG, Wand AJ, Bennett JS & DeGrado WF. (2010). NMR analysis of the alphaIIb beta3 cytoplasmic interaction suggests a mechanism for integrin regulation. Proc Natl Acad Sci U S 28, 22481-6. [PubMed]

Jo H, Culik RM, Korendovych IV, Degrado WF & Gai F. (2010). Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation. Biochemistry 14, 10354-6. [PubMed]

Polishchuk AL, Lear JD, Ma C, Lamb RA, Pinto LH & Degrado WF. (2010). A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein. Biochemistry 30, 10061-71. [PubMed]

Fiorin G, Carnevale V, DeGrado WF. (2010). Structural biology. The flu's proton escort. Science 22, 456-8. [PubMed]

Korendovych IV, Senes A, Kim YH, Lear JD, Fry HC, Therien MJ, Blasie JK, Walker FA & Degrado WF. (2010). De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex. J Am Chem Soc 10, 15516-8. [PubMed]

Korendovych IV, Kim YH, Ryan AH, Lear JD, Degrado WF & Shandler SJ. (2010). Computational design of a self-assembling -peptide oligomer. Org Lett 19, 5142-5. [PubMed]

Grigoryan G, Degrado WF. (2010). Probing designability via a generalized model of helical bundle geometry. JMB 28, 1079-100. [PubMed]

Donald JE, Zhu H, Litvinov RI, DeGrado WF & Bennett JS. (2010). Identification of interacting hot spots in the beta3 integrin stalk using comprehensive interface design. JBC 3, 38658-65. [PubMed]

Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS & DeGrado WF. (2010). Consensus motif for integrin transmembrane helix association. PNAS 12, 703-8. [PubMed]

Montalvo G, Waegele MM, Shandler S, Gai F, DeGrado WF. (2010). Infrared signature and folding dynamics of a helical beta-peptide. JACS 28, 5616-8. [PubMed]

Goldberg SD, Clinthorne GD, Goulian M & DeGrado WF. (2010). Transmembrane polar interactions are required for signaling in the Escherichia coli sensor kinase PhoQ. Proc Natl Acad Sci U S A 4, 8141-6. [PubMed]

Shandler SJ, Shapovalov MV, Dunbrack RL Jr & DeGrado WF. (2010). Development of a rotamer library for use in beta-peptide foldamer computational design. JAC 2, 7312-20. [PubMed]

Zhu H, Metcalf DG, Streu CN, Billings PC, Degrado WF & Bennett JS. (2010). Specificity for homooligomer versus heterooligomer formation in integrin transmembrane helices. J Mol Biol 3, 882-91. [PubMed]

Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF & Klein ML. (2010). Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. PNAS 24, 15075-80. [PubMed]

Goldberg SD, Derr P, DeGrado WF & Goulian M. (2009). Engineered single- and multi-cell chemotaxis pathways in E. coli. Mol Syst Biol 5, 283. [PubMed]

Kuroda K, Caputo GA & DeGrado WF. (2009). The role of hydrophobicity in the antimicrobial and hemolytic activities of polymethacrylate derivatives. Chemistry 15, 1123-1133. [PubMed]

Bell CB, Calhoun JR, Bobyr E, Wei PP, Hedman B, Hodgson KO, Degrado WF & Solomon, EI. (2009). 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 48, 59-73. [PubMed]

Miller MW, Basra S, Kulp DW, Billings PC, Choi S, Beavers MP, McCarty OJ, Zou Z, Kahn ML, Bennett JS & DeGrado WF. (2009). Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism. Proc Natl Acad Sci U S A 106, 719-724. [PubMed]

Basani RB, Zhu H, Thornton MA, Soto CS, Degrado WF, Kowalska MA, Bennett JS & Poncz M. (2009). 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 113, 902-910. [PubMed]

Khurana E, Dal Peraro M, DeVane R, Vemparala S, DeGrado WF & Klein ML. (2009). Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus. Proc Natl Acad Sci U S A 106, 1069-1074. [PubMed]

Signarvic RS, Degrado WF. (2009). Metal-Binding Dependent Disruption of Membranes by Designed Helices. J Am Chem Soc 0, Epub ahead of print. [PubMed]

Bissonnette ML, Donald JE, DeGrado WF, Jardetzky TS & Lamb RA. (2009). Functional analysis of the transmembrane domain in paramyxovirus F protein-mediated membrane fusion. J Mol Biol 386, 14-36. [PubMed]

Liu F, Dumont C, Zhu Y, DeGrado WF, Gai F & Gruebele M. (2009). A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha(3)D. J Chem Phys 130, 061101. [PubMed]

Tang J, Yin H, Qiu J, Tucker MJ, DeGrado WF & Gai F. (2009). Using two fuorescent probes to dissect the binding, insertion, and dimerization kinetics of a model membrane peptide. J Am Chem Soc 131, 3816-3817. [PubMed]

Choi S, Isaacs A, Clements D, Liu D, Kim H, Scott RW, Winkler JD & DeGrado WF. (2009). De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers. Proc Natl Acad Sci U S A 106, 6968-6973. [PubMed]

Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF & Hong M. (2009). Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus. J Am Chem Soc 131, 8066-8076. [PubMed]

Ma C, Polishchuk AL, Ohigashi Y, Stouffer AL, Schön A, Magavern E, Jing X, Lear JD, Freire E, Lamb RA, DeGrado WF & Pinto LH. (2009). Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel. Proc Natl Acad Sci U S A 106, 12283-12288. [PubMed]

Zhang Y, Kulp DW, Lear JD & DeGrado WF. (2009). Experimental and computational evaluation of forces directing the association of transmembrane helices. J Am Chem Soc 131, 11341-11343. [PubMed]

He F, Nair GR, Soto CS, Chang Y, Hsu L, Ronzone E, DeGrado WF & Binns AN. (2009). Molecular basis of ChvE function in sugar binding, sugar utilization, and virulence in Agrobacterium tumefaciens. J Bacteriol 191, 5802-5813. [PubMed]

San Antonio JD, Zoeller JJ, Habursky K, Turner K, Pimtong W, Burrows M, Choi S, Basra S, Bennett JS, DeGrado WF & Iozzo RV. (2009). A key role for the integrin alpha2beta1 in experimental and developmental angiogenesis. Am J Pathol 175, 1338-1347. [PubMed]

Metcalf DG, Kulp DW, Bennett JS & DeGrado WF. (2009). Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer. J Mol Biol 392, 1087-1101. [PubMed]

Faiella M, Andreozzi C, de Rosales RT, Pavone V, Maglio O, Nastri F, DeGrado WF & Lombardi A. (2009). An artificial di-iron oxo-protein with phenol oxidase activity. Nat Chem Biol 5, 882-884. [PubMed]

Balannik V, Wang J, Ohigashi Y, Jing X, Magavern E, Lamb RA, Degrado WF & Pinto LH. (2009). Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Biochemistry 48, 11872-11882. [PubMed]

Nguyen PA, Soto CS, Polishchuk A, Caputo GA, Tatko CD, Ma C, Ohigashi Y, Pinto LH, DeGrado WF & Howard KP. (2008). pH-Induced Conformational Change of the Influenza M2 Protein C-Terminal Domain. Biochemistry 47, 9934-6. [PubMed]

Grigoryan G & DeGrado WF. (2008). Modest membrane hydrogen bonds deliver rich results. Nat Chem Biol 4, 393-4. [PubMed]

Calhoun JR, Bell 3rd CB, Smith TJ, Thamann TJ, DeGrado WF & Solomon EI. (2008). 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 130, 9188-9. [PubMed]

Stouffer AL, Ma C, Cristian L, Ohigashi Y, Lamb RA, Lear JD, Pinto LH & DeGrado WF. (2008). The interplay of functional tuning, drug resistance, and thermodynamic stability in the evolution of the M2 proton channel from the influenza A virus. Nature 7, 1067-1076. [PubMed]

Ma C, Soto CS, Ohigashi Y, Taylor A, Bournas V, Glawe B, Udo MK, DeGrado WF, Lamb RA & Pinto LH. (2008). Identification of the Pore-lining Residues of the BM2 Ion Channel Protein of Influenza B Virus. J Biol Chem 283, 15921-31. [PubMed]

Calhoun JR, Liu W, Spiegel K, Dal Peraro M, Klein ML, Valentine KG, Wand AJ & DeGrado WF. (2008). Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement. Structure 16, 210-5. [PubMed]

Goldberg SD, Soto CS, Waldburger CD & DeGrado WF. (2008). Determination of the physiological dimer interface of the PhoQ sensor domain. J Mol Biol 379, 656-65. [PubMed]

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. (2008). Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. J Am Chem Soc 130, 11921-7. [PubMed]

Caputo GA, Litvinov RI, Li W, Bennett JS, DeGrado WF & Yin H. (2008). Computationally designed peptide inhibitors of protein-protein interactions in membranes. Biochemistry 47, 8600-6. [PubMed]

ShuJ Y, Tan C, DeGrado WF & Xu T. (2008). New design of helix bundle peptide-polymer conjugates. Biomacromolecules 9, 2111-7. [PubMed]

Moore DT, Berger BW & DeGrado WF. (2008). Protein-protein interactions in the membrane: sequence, structural, and biological motifs. Structure 16, 991-1001. [PubMed]

Stouffer AL, Ma C, Cristian L, Ohigashi Y, Lamb RA, Lear JD, Pinto LH & DeGrado WF. (2008). The interplay of functional tuning, drug resistance, and thermodynamic stability in the evolution of the M2 proton channel from the influenza A virus. Structure 16, 1067-1076. [PubMed]

Scott RW, DeGrado WF & Tew GN. (2008). De novo designed synthetic mimics of antimicrobial peptides. Curr Opin Biotechnol 19, 620-7. [PubMed]

Senes A, Chadi DC, Law PB, Walters RF, Nanda V & DeGrado WF. (2007). 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 366, 436-48. [PubMed]

Metcalf DG, Law PB & DeGrado WF. (2007). Mutagenesis data in the automated prediction of transmembrane helix dimers. Proteins 67, 375-84. [PubMed]

Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS & DeGrado WF. (2007). Computational design of peptides that target transmembrane helices. Science 0, 315. [PubMed]

Cady SD, Goodman C, Tatko CD, DeGrado WF & Hong M. (2007). Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a (2)h, (13)c, and (15)n solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle. J Am Chem Soc 129, 5719-29. [PubMed]

Goodman CM, Choi S, Shandler S & DeGrado WF. (2007). Foldamers as versatile frameworks for the design and evolution of function. Nat Chem Biol 3, 252-262. [PubMed]

Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM & Vinogradov SA. (2007). Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores. J Phys Chem A 111, 6977-90. [PubMed]

Dal Peraro M, Spiegel K, Lamoureux G, Vivo MD, DeGrado WF & Klein ML. (2007). Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J Struct Biol 157, 444-53. [PubMed]

Mukherjee S, Chowdhury P, DeGrado WF & Gai F. (2007). Site-specific hydration status of an amphipathic peptide in AOT reverse micelles. Langmuir 23, 11174-9. [PubMed]

Choi S, Vilaire G, Marcinkiewicz C, Winkler JD, Bennett JS & DeGrado WF. (2007). Small molecule inhibitors of integrin alpha2beta1. J Med Chem 50, 5457-62. [PubMed]

White TC, Berny MA, Robinson DK, Yin H, DeGrado WF, Hanson SR & McCarty OJ. (2007). The leech product saratin is a potent inhibitor of platelet integrin alpha2beta1 and von Willebrand factor binding to collagen. Febs J 274, 1481-91. [PubMed]

Wang PC, Vilaire G, DeGrado WF & Bennett JS. (2007). Interactions of ADP-stimulated human platelets with PEGylated polystyrene substrates prepared by surface amidation. Colloids Surf B Biointerfaces 58, 225-30. [PubMed]

Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG & DeGrado WF. (2007). De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc 129, 10732-40. [PubMed]

Tang J, Signarvic RS, DeGrado WF & Gai F. (2007). Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers. Biochemistry 46, 13856-63. [PubMed]

Balakrishnan G, Hu Y, Bender GM, Getahun Z, DeGrado WF & Spiro TG. (2007). Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy. J Am Chem Soc 129, 12801-8. [PubMed]

Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S & DeGrado WF. (2007). Structural basis for the function and inhibition of an influenza virus proton channel. Nature 451, 596-9. [PubMed]

Litvinov RI, Vilaire G, Li W, DeGrado WF, Weisel JW & Bennett JS. (2006). Activation of individual alphallbbeta3 integrin molecules by disruption of transmembrane domain interactions in the absence of clustering. Biochemistry 45, 4957-64. [PubMed]

Nanda V & DeGrado WF. (2006). Computational design of heterochiral peptides against a helical target. J Am Chem Soc 128, 809-16. [PubMed]

North B, Cristian L, Fu Stowell X, Lear JD, Saven JG & Degrado WF. (2006). Characterization of a membrane protein motif, the ser zipper, using designed peptides. J Mol Biol 359, 930-9. [PubMed]

Pophristic V, Vemparala S, Ivanov I, Liu Z, Klein ML & DeGrado WF. (2006). Controlling the Shape and Flexibility of Arylamides: A Combined ab Initio, ab Initio Molecular Dynamics, and Classical Molecular Dynamics Study. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 110, 3517-3526. [PubMed]

Tatko CD, Nanda V, Lear JD & DeGrado WF. (2006). Polar networks control oligomeric assembly in membranes. J Am Chem Soc 128, 4170-1. [PubMed]

Yin H, Frederick KK, Liu D, Wand AJ & DeGrado WF. (2006). Arylamide derivatives as peptidomimetic inhibitors of calmodulin. Org Lett 8, 223-5. [PubMed]

Yin H, Gerlach LO, Miller MW, Moore DT, Liu D, Vilaire G, Bennett JS & DeGrado WF. (2006). Arylamide derivatives as allosteric inhibitors of the integrin alpha(2)beta(1)/type 1 collagen interaction. Bioorg Med Chem Lett 16, 3380-82. [PubMed]

Stouffer AL, DeGrado WF & Lear JD. (2006). Analytical Ultracentrifugation Studies of the Influenza M2 Homotetramerization Equilibrium in Detergent Solutions. Progr Colloid Polym Sci 131, 108-115.

Walters RF & DeGrado WF. (2006). Helix-packing motifs in membrane proteins. Proc Natl Acad Sci U S A 103, 13658-63. [PubMed]

Bunagan MR, Cristian L, DeGrado WF & Gai F. (2006). Truncation of a cross-linked GCN4-p1 coiled coil leads to ultrafast folding. Biochemistry 45, 10981-6. [PubMed]

DeGrado WF & Woolfson DN. (2006). Engineering and design. Curr Opin Struct Biol 16, 505-7.

Wade H, Stayrook SE & DeGrado WF. (2006). The structure of a designed diiron(III) protein: implications for cofactor stabilization and catalysis. Angew Chem Int Ed Engl 45, 4951-4. [PubMed]

Lopez CF, Nielsen SO, Srinivas G, Degrado WF & Klein ML. (2006). Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics. J Chem Theory Comp 2, 649-655. [PubMed]

Yin H, Litvinov RI, Vilaire G, Zhu H, Li W, Caputo GA, Moore DT, Lear JD, Weisel JW, DeGrado WF & Bennett JS. (2006). Activation of platelet alphaIIbbeta3 by an exogenous peptide corresponding to the transmembrane domain of alphaIIb. J Biol Chem 281, 36732-41. [PubMed]

Fang C, Senes A, Cristian L, DeGrado WF & Hochstrasser RM. (2006). Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer. Proc Natl Acad Sci U S A 103, 16740-5. [PubMed]

Li W, Metcalf DG, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, DeGrado WF & Bennett JS. (2005). A push-pull mechanism for regulating integrin function. Proc Natl Acad Sci U S A 102, 1424-9. [PubMed]

Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ & DeGrado WF. (2005). Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor. J Am Chem Soc 127, 1346-7. [PubMed]

Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A & DeGrado WF. (2005). Artificial diiron proteins: From structure to function. Biopolymers 80, 264-278. [PubMed]

Stouffer AL, Nanda V, Lear JD & DeGrado WF. (2005). Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function. J Mol Biol 347, 169-79. [PubMed]

Lahr SJ, Engel DE, Stayrook SE, Maglio O, North B, Geremia S, Lombardi A & DeGrado WF. (2005). Analysis and design of turns in alpha-helical hairpins. J Mol Biol 346, 1441-54. [PubMed]

Duong-Ly KC, Nanda V, DeGrado WF & Howard KP. (2005). The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Sci 14, 856-61. [PubMed]

Nanda V & DeGrado WF. (2005). Automated use of mutagenesis data in structure prediction. Proteins 59, 454-66. [PubMed]

Kuroda K & DeGrado WF. (2005). Amphiphilic polymethacrylate derivatives as antimicrobial agents. J Am Chem Soc 127, 4128-9. [PubMed]

Slovic AM, Lear JD & DeGrado WF. (2005). De novo design of a pentameric coiled-coil: decoding the motif for tetramer versus pentamer formation in water-soluble phospholamban. J Pept Res 65, 312-21. [PubMed]

Adamian L, Nanda V, DeGrado WF & Liang J. (2005). Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins 59, 496-509. [PubMed]

Maglio O, Nastri F, Calhoun J, Lahr S, Wade H, Pavone V, DeGrado WF & Lombardi A. (2005). Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops. J Biol Inorg Chem 10, 539-549. [PubMed]

Summa CM, Levitt M & DeGrado WF. (2005). An Atomic Environment Potential for use in Protein Structure Prediction. J Mol Biol 352, 986-1001. [PubMed]

Slovic AM, Stayrook SE, North B & DeGrado WF. (2005). 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 348, 777-87. [PubMed]

Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG & DeGrado WF. (2005). De novo design of a redox-active minimal rubredoxin mimic. J Am Chem Soc 127, 5804-5. [PubMed]

Wang T, Lau WL, DeGrado WF & Gai F. (2005). T-jump Infrared Study of the Folding Mechanism of Coiled- coil GCN4-p1. Biophys J 89, 4180-7. [PubMed]

Willcox PJ, Reinhart-King CA, Lahr SJ, DeGrado WF & Hammer DA. (2005). Dynamic heterodimer-functionalized surfaces for endothelial cell adhesion. Biomaterials 26, 4757-66. [PubMed]

Cristian L, Nanda V, Lear JD & DeGrado WF. (2005). Synergistic Interactions between Aqueous and Membrane Domains of a Designed Protein Determine its Fold and Stability. J Mol Biol 348, 1225-1233. [PubMed]

Wei PP, Skulan AJ, Wade H, DeGrado WF & Solomon EI. (2005). 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 127, 16098-106. [PubMed]

Ivanov I, Vemparala S, Pophristic V, Kuroda K, DeGrado WF, McCammon JA & Klein ML. (2005). Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics. J Am Chem Soc 128, 1778-9. [PubMed]

Tucker MJ, Getahun Z, Nanda V, DeGrado WF, & Gai F. (2004). A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides. J Am Chem Soc 126, 5078-9. [PubMed]

Li R, Gorelik R, Nanda V, Law PB, Lear JD, DeGrado WF & Bennett JS. (2004). Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes. J Biol Chem 279, 26666-73. [PubMed]

Slovic AM, Kono H, Lear JD, Saven JG & DeGrado WF. (2004). Computational design of water-soluble analogues of the potassium channel KcsA. Proc Natl Acad Sci U S A 101, 1828-33. [PubMed]

Lau WL, Ege DS, Lear JD, Hammer DA & DeGrado WF. (2004). Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization. Biophys J 86, 272-84. [PubMed]

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Liu D, Choi S, Chen B, Doerksen RJ, Clements DJ, Winkler JD, Klein ML & DeGrado WF. (2004). Nontoxic membrane-active antimicrobial arylamide oligomers. Angew Chem Int Ed Engl 43, 1158-62. [PubMed]

Doerksen RJ, Chen B, Liu D, Tew GN, DeGrado WF & Klein ML. (2004). Controlling the Conformation of Arylamides: Computational Studies of Intramolecular Hydrogen Bonds between Amides and Ethers or Thioethers. Chemistry, A European Journal 10, 5008-5016. [PubMed]

Lear JD, Stouffer AL, Gratkowski H, Nanda V & DeGrado WF. (2004). Association of a model transmembrane Peptide containing gly in a heptad sequence motif. Biophys J 87, 3421-9. [PubMed]

Kaplan J & DeGrado WF. (2004). De novo design of catalytic proteins. Proc Natl Acad Sci U S A 101, 11566-70. [PubMed]

Senes A, Engel DE & DeGrado WF. (2004). Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol 14, 465-79. [PubMed]

Baltzer L & DeGrado WF. (2004). Engineering and design: Expanding the protein world. Curr Opin Struct Biol 14, 455-7.

Ghirlanda G, Osyczka A, Liu W, Antolovich M, Smith KM, Dutton PL, Wand AJ & DeGrado WF. (2004). De Novo Design of a D(2)-Symmetrical Protein that Reproduces the Diheme Four-Helix Bundle in Cytochrome bc(1). J Am Chem Soc 126, 8141-8147. [PubMed]

Li R, Bennett JS & DeGrado WF. (2004). Structural basis for integrin alphaIIbbeta3 clustering. Soc Trans 32, 412-5. [PubMed]

Wang T, Zhu Y, Getahun Z, Du D, Huang C, DeGrado W & Gai F. (2004). Length dependent helix-coil transition kinetics of nine alanine-based peptides. J. Phys. Chem. B 108, 15301-10.

Ghirlanda G, Hilcove SA, Pidikiti R, Johansson JS, Lear JD, DeGrado WF & Eckenhoff RG. (2004). Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide. FEBS letters 578, 140-4. [PubMed]

Nanda V & DeGrado WF. (2004). Simulated evolution of emergent chiral structures in polyalanine. J Am Chem Soc 126, 14459-67. [PubMed]

Howard KP, Liu W, Crocker E, Nanda V, Lear JD, DeGrado WF & Smith SO. (2004). Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle. Protein Science 14, 1019–-1024. [PubMed]

Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF & Gai F. (2003). Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein. Proc Natl Acad Sci U S A 100, 15486-91. [PubMed]

Cristian L, Lear JD & DeGrado WF. (2003). Use of thiol-disulfide equilibria to measure the energetics of assembly of transmembrane helices in phospholipid bilayers. Proc Natl Acad Sci U S A 100, 14772-7. [PubMed]

Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF & Saven JG. (2003). Computational design and characterization of a monomeric helical dinuclear metalloprotein. J Mol Biol 334, 1101-15. [PubMed]

Signarvic RS & DeGrado WF. (2003). De novo design of a molecular switch: phosphorylation-dependent association of designed peptides. J Mol Biol 334, 1-12. [PubMed]

Cristian L, Lear JD & DeGrado WF. (2003). Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange. Protein Sci 12, 1732-40. [PubMed]

Lear JD, Gratkowski H, Adamian L, Liang J & DeGrado WF. (2003). Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry 42, 6400-7. [PubMed]

DeGrado WF. (2003). Computational biology: Biosensor design. Nature 423, 132-3. [PubMed]

Li R, Mitra N, Gratkowski H, Vilaire G, Litvinov R, Nagasami C, Weisel JW, Lear JD, DeGrado WF & Bennett JS. (2003). Activation of integrin alphaIIbbeta3 by modulation of transmembrane helix associations. Science 300, 795-8. [PubMed]

Maglio O, Nastri F, Pavone V, Lombardi A & DeGrado WF. (2003). Preorganization of molecular binding sites in designed diiron proteins. Proc Natl Acad Sci U S A 100, 3772-7. [PubMed]

DeGrado WF, Gratkowski H & Lear JD. (2003). How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci 12, 647-65. [PubMed]

Li R, Hoess RH, Bennett JS & DeGrado WF. (2003). Use of phage display to probe the evolution of binding specificity and affinity in integrins. Protein Eng 16, 65-72. [PubMed]

Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM & DeGrado WF. (2003). The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR. Protein Sci 12, 520-31. [PubMed]

DeGrado WF, Di Costanzo, L Geremia S, Lombardi A, Pavone V, & Randaccio L. (2003). Sliding helix and change of coordination geometry in a model di-MnII protein. Angew Chem Int Ed Engl 42, 417-20. [PubMed]

Slovic AM, Summa CM, Lear JD, & DeGrado WF. (2003). Computational design of a water-soluble analog of phospholamban. Protein Sci 12, 337-48. [PubMed]

Papoian GA, DeGrado WF, & Klein ML. (2003). 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 125, 560-9. [PubMed]

Getahun Z, Huang CY, Wang T, De Leon B, DeGrado WF & Gai F. (2003). Using nitrile-derivatized amino acids as infrared probes of local environment. J Am Chem Soc 125, 405-11. [PubMed]

Li R, Babu CR, Valentine K, Lear JD, Wand AJ, Bennett JS & DeGrado WF. (2002). Characterization of the monomeric form of the transmembrane and cytoplasmic domains of the integrin beta 3 subunit by NMR spectroscopy. Biochemistry 41, 15618-24. [PubMed]

Huang CY, He S, DeGrado WF, McCafferty DG & Gai F. (2002). Light-induced helix formation. J Am Chem Soc 124, 12674-5. [PubMed]

Cheng RP & DeGrado WF. (2002). Long-range interactions stabilize the fold of a non-natural oligomer. J Am Chem Soc 124, 11564-5. [PubMed]

Summa CM, Rosenblatt MM, Hong JK, Lear JD & DeGrado WF. (2002). Computational de novo design, and characterization of an A(2)B(2) diiron protein. J Mol Biol 321, 923-38. [PubMed]

Gratkowski H, Dai QH, Wand AJ, DeGrado WF & Lear JD. (2002). Cooperativity and specificity of association of a designed transmembrane peptide. Biophys J 83, 1613-9. [PubMed]

Howard KP, Lear JD & DeGrado WF. (2002). Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein. Proc Natl Acad Sci U S A 99, 8568-72. [PubMed]

Ghirlanda G, Lear JD, Ogihara NL, Eisenberg D & DeGrado WF. (2002). A hierarchic approach to the design of hexameric helical barrels. J Mol Biol 319, 243-53. [PubMed]

Marsh EN & DeGrado WF. (2002). Noncovalent self-assembly of a heterotetrameric diiron protein. Proc Natl Acad Sci U S A 99, 5150-4. [PubMed]

Tew GN, Liu D, Chen B, Doerksen RJ, Kaplan J, Carroll PJ, Klein ML & DeGrado WF. (2002). De novo design of biomimetic antimicrobial polymers. Proc Natl Acad Sci U S A 99, 5110-4. [PubMed]

Huang CY, Getahun Z, Zhu Y, Klemke JW, DeGrado WF & Gai F. (2002). Helix formation via conformation diffusion search. Proc Natl Acad Sci U S A 99, 2788-93. [PubMed]

Di Costanzo L, Wade H, Geremia S, Randaccio L, Pavone V, DeGrado WF & Lombardi A. (2001). Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center. J Am Chem Soc 123, 12749-57. [PubMed]

DeGrado WF. (2001). Introduction: protein design. Chem Rev 101, 3025-6. [PubMed]

Cheng RP, Suich DJ, Cheng H, Roder H & DeGrado WF. (2001). Template-constrained somatostatin analogues: a biphenyl linker induces a type-V' turn. J Am Chem Soc 123, 12710-1. [PubMed]

Huang CY, Getahun Z, Wang T, DeGrado WF & Gai F. (2001). Time-resolved infrared study of the helix-coil transition using (13)C-labeled helical peptides. J Am Chem Soc 123, 12111-2. [PubMed]

Cheng RP, Gellman SH & DeGrado WF. (2001). beta-Peptides: from structure to function. Chem Rev 101, 3219-32. [PubMed]

Li R, Babu CR, Lear JD, Wand AJ, Bennett JS & DeGrado WF. (2001). Oligomerization of the integrin alphaIIbbeta3: roles of the transmembrane and cytoplasmic domains. Proc Natl Acad Sci U S A 98, 12462-7. [PubMed]

Walsh ST, Lee AL, DeGrado WF & Wand AJ. (2001). Dynamics of a de novo designed three-helix bundle protein studied by 15N, 13C, and 2H NMR relaxation methods. Biochemistry 40, 9560-9. [PubMed]

Huang CY, Klemke JW, Getahun Z, DeGrado WF & Gai F. (2001). Temperature-dependent helix-coil transition of an alanine based peptide. J Am Chem Soc 123, 9235-8. [PubMed]

North B, Summa CM, Ghirlanda G & DeGrado WF. (2001). D(n)-symmetrical tertiary templates for the design of tubular proteins. J Mol Biol 311, 1081-90. [PubMed]

Lear JD, Gratkowski H & DeGrado WF. (2001). De novo design, synthesis and characterization of membrane-active peptides. Biochem Soc Trans 29, 559-64. [PubMed]

Liu D & DeGrado WF. (2001). De novo design, synthesis, and characterization of antimicrobial beta-peptides. J Am Chem Soc 123, 7553-9. [PubMed]

Cheng RP & DeGrado WF. (2001). De novo design of a monomeric helical beta-peptide stabilized by electrostatic interactions. J Am Chem Soc 123, 5162-3. [PubMed]

Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF & Tirrell DA. (2001). Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability. Angew Chem Int Ed Engl 40, 1494-1496. [PubMed]

Pasternak A, Kaplan J, Lear JD & Degrado WF. (2001). Proton and metal ion-dependent assembly of a model diiron protein. Protein Sci 10, 958-69. [PubMed]

Tang Y, Ghirlanda G, Vaidehi N, Kua J, Mainz DT, Goddard IW, DeGrado WF & Tirrell DA. (2001). Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine. Biochemistry 40, 2790-6. [PubMed]

Ogihara NL, Ghirlanda G, Bryson JW, Gingery M, DeGrado WF & Eisenberg D. (2001). Design of three-dimensional domain-swapped dimers and fibrous oligomers. Proc Natl Acad Sci U S A 98, 1404-9. [PubMed]

Gratkowski H, Lear JD & DeGrado WF. (2001). Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci U S A 98, 880-5. [PubMed]

Walsh ST, Sukharev VI, Betz SF, Vekshin NL & DeGrado WF. (2001). Hydrophobic core malleability of a de novo designed three-helix bundle protein. J Mol Biol 305, 361-73. [PubMed]

Dalby PA, Hoess RH & DeGrado WF. (2000). Evolution of binding affinity in a WW domain probed by phage display. Protein Sci 9, 2366-76. [PubMed]

Talaga DS, Lau WL, Roder H, Tang J, Jia Y, DeGrado WF & Hochstrasser RM. (2000). Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy. Proc Natl Acad Sci U S A 97, 13021-6. [PubMed]

Salom D, Hill BR, Lear JD & DeGrado WF. (2000). pH-dependent tetramerization and amantadine binding of the transmembrane helix of M2 from the influenza A virus. Biochemistry 39, 14160-70. [PubMed]

Hill RB, Raleigh DP, Lombardi A & DeGrado WF. (2000). De novo design of helical bundles as models for understanding protein folding and function. Acc Chem Res 33, 745-54. [PubMed]

Suich DJ, Mousa SA, Singh G, Liapakis G, Reisine T & DeGrado WF. (2000). Template-constrained cyclic peptide analogues of somatostatin: subtype-selective binding to somatostatin receptors and antiangiogenic activity. Bioorg Med Chem 8, 2229-41. [PubMed]

O'Neil KT, Bach 2nd AC & DeGrado WF. (2000). Structural consequences of an amino acid deletion in the B1 domain of protein G. Proteins 41, 323-33. [PubMed]

Lombardi A, Summa CM, Geremia S, Randaccio L, Pavone V & DeGrado WF. (2000). Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins. Proc Natl Acad Sci U S A 97, 6298-305. [PubMed]

Hill RB & DeGrado WF. (2000). A polar, solvent-exposed residue can be essential for native protein structure. Structure Fold Des 8, 471-9. [PubMed]

Helluin O, Chan C, Vilaire G, Mousa S, DeGrado WF & Bennett JS. (2000). The activation state of alphavbeta 3 regulates platelet and lymphocyte adhesion to intact and thrombin-cleaved osteopontin. J Biol Chem 275, 18337-43. [PubMed]

Choma C, Gratkowski H, Lear JD & DeGrado WF. (2000). Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol 7, 161-6. [PubMed]