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For: Russell SJ, Blandl T, Skelton NJ, Cochran AG. Stability of cyclic beta-hairpins: asymmetric contributions from side chains of a hydrogen-bonded cross-strand residue pair. J Am Chem Soc 2003;125:388-95. [PMID: 12517150 DOI: 10.1021/ja028075l] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Number Cited by Other Article(s)
51
Smith MH, Miles TF, Sheehan M, Alfieri KN, Kokona B, Fairman R. Polyglutamine fibrils are formed using a simple designed beta-hairpin model. Proteins 2010;78:1971-9. [PMID: 20408173 DOI: 10.1002/prot.22713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
52
Stabilizing capping motif for beta-hairpins and sheets. Proc Natl Acad Sci U S A 2010;107:10466-71. [PMID: 20484672 DOI: 10.1073/pnas.0913534107] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
53
He Y, Chen C, Xiao Y. United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding. J Comput Biol 2009;16:1719-30. [DOI: 10.1089/cmb.2008.0070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
54
Wu L, McElheny D, Huang R, Keiderling TA. Role of Tryptophan−Tryptophan Interactions in Trpzip β-Hairpin Formation, Structure, and Stability. Biochemistry 2009;48:10362-71. [PMID: 19788311 DOI: 10.1021/bi901249d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
55
Chiu HP, Kokona B, Fairman R, Cheng RP. Effect of Highly Fluorinated Amino Acids on Protein Stability at a Solvent-Exposed Position on an Internal Strand of Protein G B1 Domain. J Am Chem Soc 2009;131:13192-3. [DOI: 10.1021/ja903631h] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
56
Eidenschink L, Crabbe E, Andersen NH. Terminal sidechain packing of a designed beta-hairpin influences conformation and stability. Biopolymers 2009;91:557-64. [PMID: 19263490 DOI: 10.1002/bip.21177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
57
George Priya Doss C, Sethumadhavan R. Computational and structural analysis of deleterious functional SNPs in ARNT oncogene. Interdiscip Sci 2009;1:220-8. [DOI: 10.1007/s12539-009-0042-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/08/2009] [Accepted: 05/08/2009] [Indexed: 11/30/2022]
58
Xiao Y, Chen C, He Y. Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways. Int J Mol Sci 2009;10:2838-2848. [PMID: 19582232 PMCID: PMC2705519 DOI: 10.3390/ijms10062838] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/18/2009] [Accepted: 06/19/2009] [Indexed: 01/30/2023]  Open
59
Eidenschink L, Kier BL, Huggins KNL, Andersen NH. Very short peptides with stable folds: building on the interrelationship of Trp/Trp, Trp/cation, and Trp/backbone-amide interaction geometries. Proteins 2009;75:308-22. [PMID: 18831035 PMCID: PMC2656586 DOI: 10.1002/prot.22240] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
60
Doss CGP, Sethumadhavan R. Investigation on the role of nsSNPs in HNPCC genes--a bioinformatics approach. J Biomed Sci 2009;16:42. [PMID: 19389263 PMCID: PMC2682794 DOI: 10.1186/1423-0127-16-42] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 04/24/2009] [Indexed: 01/01/2023]  Open
61
Laufer B, Chatterjee J, Frank AO, Kessler H. Can N-methylated amino acids serve as substitutes for prolines in conformational design of cyclic pentapeptides? J Pept Sci 2009;15:141-6. [PMID: 18985637 DOI: 10.1002/psc.1076] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
62
Takekiyo T, Wu L, Yoshimura Y, Shimizu A, Keiderling TA. Relationship between Hydrophobic Interactions and Secondary Structure Stability for Trpzip β-Hairpin Peptides. Biochemistry 2009;48:1543-52. [DOI: 10.1021/bi8019838] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
63
Bour P, Kim J, Kapitan J, Hammer RP, Huang R, Wu L, Keiderling TA. Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide. Chirality 2008;20:1104-19. [DOI: 10.1002/chir.20560] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
64
Tam EM, Runyon ST, Santell L, Quan C, Yao X, Kirchhofer D, Skelton NJ, Lazarus RA. Noncompetitive inhibition of hepatocyte growth factor-dependent Met signaling by a phage-derived peptide. J Mol Biol 2008;385:79-90. [PMID: 18973760 DOI: 10.1016/j.jmb.2008.09.091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 09/12/2008] [Accepted: 09/16/2008] [Indexed: 01/25/2023]
65
Nowick JS. Exploring beta-sheet structure and interactions with chemical model systems. Acc Chem Res 2008;41:1319-30. [PMID: 18798654 PMCID: PMC2728010 DOI: 10.1021/ar800064f] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
66
Noy K, Kalisman N, Keasar C. Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials. BMC STRUCTURAL BIOLOGY 2008;8:27. [PMID: 18510728 PMCID: PMC2427033 DOI: 10.1186/1472-6807-8-27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Accepted: 05/29/2008] [Indexed: 11/10/2022]
67
Webb TR, Venegas RE, Wang J, Deschenes A. Generation of New Synthetic Scaffolds Using Framework Libraries Selected and Refined via Medicinal Chemist Synthetic Expertise. J Chem Inf Model 2008;48:882-8. [DOI: 10.1021/ci7001928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
68
O'Nuallain B, Allen A, Ataman D, Weiss DT, Solomon A, Wall JS. Phage display and peptide mapping of an immunoglobulin light chain fibril-related conformational epitope. Biochemistry 2007;46:13049-58. [PMID: 17944486 DOI: 10.1021/bi701255m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
69
Levin S, Nowick JS. An artificial beta-sheet that dimerizes through parallel beta-sheet interactions. J Am Chem Soc 2007;129:13043-8. [PMID: 17918935 DOI: 10.1021/ja073391r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
70
Hughes RM, Benshoff ML, Waters ML. Effects of chain length and N-methylation on a cation-pi interaction in a beta-hairpin peptide. Chemistry 2007;13:5753-64. [PMID: 17431866 DOI: 10.1002/chem.200601753] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
71
Jäger M, Dendle M, Fuller AA, Kelly JW. A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function. Protein Sci 2007;16:2306-13. [PMID: 17766376 PMCID: PMC2204138 DOI: 10.1110/ps.072904107] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
72
Andersen NH, Olsen KA, Fesinmeyer RM, Tan X, Hudson FM, Eidenschink LA, Farazi SR. Minimization and optimization of designed beta-hairpin folds. J Am Chem Soc 2007;128:6101-10. [PMID: 16669679 PMCID: PMC3164952 DOI: 10.1021/ja054971w] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
73
Fisk JD, Schmitt MA, Gellman SH. Thermodynamic analysis of autonomous parallel beta-sheet formation in water. J Am Chem Soc 2007;128:7148-9. [PMID: 16734453 PMCID: PMC2723805 DOI: 10.1021/ja060942p] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
74
Cheng Z, Miskolzie M, Campbell RE. In vivo screening identifies a highly folded beta-hairpin peptide with a structured extension. Chembiochem 2007;8:880-3. [PMID: 17457813 DOI: 10.1002/cbic.200600565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
75
Ou DM, Chen CC, Chen CM. Contact-induced structure transformation in transmembrane prion propagation. Biophys J 2007;92:2704-10. [PMID: 17259269 PMCID: PMC1831692 DOI: 10.1529/biophysj.106.098335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
76
Nowick JS. What I have learned by using chemical model systems to study biomolecular structure and interactions. Org Biomol Chem 2006;4:3869-85. [PMID: 17047863 DOI: 10.1039/b608953b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
77
Shi T, Spain SM, Rabenstein DL. A Striking Periodicity of thecis/trans Isomerization of Proline Imide Bonds in Cyclic Disulfide-Bridged Peptides. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
78
Shi T, Spain SM, Rabenstein DL. A Striking Periodicity of thecis/trans Isomerization of Proline Imide Bonds in Cyclic Disulfide-Bridged Peptides. Angew Chem Int Ed Engl 2006;45:1780-3. [PMID: 16470897 DOI: 10.1002/anie.200503470] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
79
Streicher WW, Makhatadze GI. Calorimetric evidence for a two-state unfolding of the beta-hairpin peptide trpzip4. J Am Chem Soc 2006;128:30-1. [PMID: 16390106 DOI: 10.1021/ja056392x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
80
Bour P, Keiderling TA. Vibrational Spectral Simulation for Peptides of Mixed Secondary Structure:  Method Comparisons with the Trpzip Model Hairpin. J Phys Chem B 2005;109:23687-97. [PMID: 16375349 DOI: 10.1021/jp054107q] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
81
Phillips ST, Piersanti G, Bartlett PA. Quantifying amino acid conformational preferences and side-chain-side-chain interactions in beta-hairpins. Proc Natl Acad Sci U S A 2005;102:13737-42. [PMID: 16162669 PMCID: PMC1202387 DOI: 10.1073/pnas.0506646102] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Indexed: 11/18/2022]  Open
82
Pastor MT, Giménez-Giner A, Pérez-Payá E. The Role of an Aliphatic-Aromatic Interaction in the Stabilization of a Model β-Hairpin Peptide. Chembiochem 2005;6:1753-6. [PMID: 16149104 DOI: 10.1002/cbic.200500178] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
83
Larson RS, Brown DC, Ye C, Hjelle B. Peptide antagonists that inhibit Sin Nombre virus and hantaan virus entry through the beta3-integrin receptor. J Virol 2005;79:7319-26. [PMID: 15919886 PMCID: PMC1143646 DOI: 10.1128/jvi.79.12.7319-7326.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]  Open
84
Sim J, Kim SY, Lee J. Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method. Bioinformatics 2005;21:2844-9. [PMID: 15814555 DOI: 10.1093/bioinformatics/bti423] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
85
Stotz CE, Topp EM. Applications of model β‐hairpin peptides. J Pharm Sci 2004;93:2881-94. [PMID: 15452845 DOI: 10.1002/jps.20188] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
86
Searle MS, Ciani B. Design of β-sheet systems for understanding the thermodynamics and kinetics of protein folding. Curr Opin Struct Biol 2004;14:458-64. [PMID: 15313241 DOI: 10.1016/j.sbi.2004.06.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
87
Santiveri CM, Santoro J, Rico M, Jiménez MA. Factors involved in the stability of isolated beta-sheets: Turn sequence, beta-sheet twisting, and hydrophobic surface burial. Protein Sci 2004;13:1134-47. [PMID: 15044739 PMCID: PMC2280049 DOI: 10.1110/ps.03520704] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 01/15/2004] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
88
Williams NH. 15  Bioinspired organic chemistry. ACTA ACUST UNITED AC 2004. [DOI: 10.1039/b402174f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
89
Searle MS. Insights into stabilizing weak interactions in designed peptide ?-hairpins. Biopolymers 2004;76:185-95. [PMID: 15054898 DOI: 10.1002/bip.10577] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
90
Dhanasekaran M, Prakash O, Gong YX, Baures PW. Expected and unexpected results from combined β-hairpin design elements. Org Biomol Chem 2004;2:2071-82. [PMID: 15254635 DOI: 10.1039/b315228f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
91
Cristian L, Lear JD, DeGrado WF. Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange. Protein Sci 2003;12:1732-40. [PMID: 12876322 PMCID: PMC2323959 DOI: 10.1110/ps.0378603] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
92
Blandl T, Cochran AG, Skelton NJ. Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns. Protein Sci 2003;12:237-47. [PMID: 12538887 PMCID: PMC2312432 DOI: 10.1110/ps.0228603] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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