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For: Liu LP, Deber CM. Guidelines for membrane protein engineering derived from de novo designed model peptides. Biopolymers 2000;47:41-62. [PMID: 9692326 DOI: 10.1002/(sici)1097-0282(1998)47:1<41::aid-bip6>3.0.co;2-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Number Cited by Other Article(s)
51
Cano-Sanchez P, Severino B, Sureshbabu VV, Russo J, Inui T, Ding FX, Arshava B, Becker J, Naider F. Effects of N- and C-terminal addition of oligolysines or native loop residues on the biophysical properties of transmembrane domain peptides from a G-protein coupled receptor. J Pept Sci 2007;12:808-22. [PMID: 17131294 DOI: 10.1002/psc.816] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
52
Rath A, Johnson RM, Deber CM. Peptides as transmembrane segments: Decrypting the determinants for helix–helix interactions in membrane proteins. Biopolymers 2007;88:217-32. [PMID: 17206630 DOI: 10.1002/bip.20668] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
53
Johnson RM, Rath A, Deber CM. The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinityThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease. Biochem Cell Biol 2006;84:1006-12. [PMID: 17215886 DOI: 10.1139/o06-192] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
54
Esteban-Martín S, Salgado J. Self-assembling of peptide/membrane complexes by atomistic molecular dynamics simulations. Biophys J 2006;92:903-12. [PMID: 17085495 PMCID: PMC1779969 DOI: 10.1529/biophysj.106.093013] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
55
Kell DB. Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in Budapest. FEBS J 2006;273:873-94. [PMID: 16478464 DOI: 10.1111/j.1742-4658.2006.05136.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
56
Burrows LL, Stark M, Chan C, Glukhov E, Sinnadurai S, Deber CM. Activity of novel non-amphipathic cationic antimicrobial peptides against Candida species. J Antimicrob Chemother 2006;57:899-907. [PMID: 16524895 DOI: 10.1093/jac/dkl056] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
57
Kovacs JM, Mant CT, Hodges RS. Determination of intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides in the absence of nearest-neighbor or conformational effects. Biopolymers 2006;84:283-97. [PMID: 16315143 PMCID: PMC2744689 DOI: 10.1002/bip.20417] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
58
Chan C, Burrows LL, Deber CM. Alginate as an auxiliary bacterial membrane: binding of membrane-active peptides by polysaccharides*. ACTA ACUST UNITED AC 2005;65:343-51. [PMID: 15787964 DOI: 10.1111/j.1399-3011.2005.00217.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
59
Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 2005;433:377-81. [PMID: 15674282 DOI: 10.1038/nature03216] [Citation(s) in RCA: 745] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Accepted: 11/16/2004] [Indexed: 11/08/2022]
60
Sato T, Saito Y, Aimoto S. Synthesis of theC-terminal region of opioid receptor like 1 in an SDS micelle by the native chemical ligation: effect of thiol additive and SDS concentration on ligation efficiency. J Pept Sci 2005;11:410-6. [PMID: 15635671 DOI: 10.1002/psc.634] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
61
Choi MY, Partridge AW, Daniels C, Du K, Lukacs GL, Deber CM. Destabilization of the transmembrane domain induces misfolding in a phenotypic mutant of cystic fibrosis transmembrane conductance regulator. J Biol Chem 2004;280:4968-74. [PMID: 15537638 DOI: 10.1074/jbc.m410069200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
62
Lee D, Powers JP, Pflegerl K, Vasil M, Hancock R, Hodges R. Effects of single D-amino acid substitutions on disruption of beta-sheet structure and hydrophobicity in cyclic 14-residue antimicrobial peptide analogs related to gramicidin S. ACTA ACUST UNITED AC 2004;63:69-84. [PMID: 15009528 PMCID: PMC1464084 DOI: 10.1046/j.1399-3011.2003.00106.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
63
Orgel JPRO. Sequence context and modified hydrophobic moment plots help identify `horizontal' surface helices in transmembrane protein structure prediction. J Struct Biol 2004;148:51-65. [PMID: 15363787 DOI: 10.1016/j.jsb.2004.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Revised: 06/02/2004] [Indexed: 11/28/2022]
64
Chan C, Burrows LL, Deber CM. Helix Induction in Antimicrobial Peptides by Alginate in Biofilms. J Biol Chem 2004;279:38749-54. [PMID: 15247257 DOI: 10.1074/jbc.m406044200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
65
Tang YC, Deber CM. Aqueous solubility and membrane interactions of hydrophobic peptides with peptoid tags. Biopolymers 2004;76:110-8. [PMID: 15054891 DOI: 10.1002/bip.10566] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
66
Laczkó I, Bottka S, Tóth GK, Malvy C, Bertrand JR, Hollósi M. Interaction of fusogenic peptides with an antisense oligonucleotide in solution and in the presence of micelles: conformational studies. Biochem Biophys Res Commun 2004;313:356-61. [PMID: 14684168 DOI: 10.1016/j.bbrc.2003.11.129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
67
Melnyk RA, Partridge AW, Yip J, Wu Y, Goto NK, Deber CM. Polar residue tagging of transmembrane peptides. Biopolymers 2004;71:675-85. [PMID: 14991677 DOI: 10.1002/bip.10595] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
68
George SR, Ng GYK, Lee SP, Fan T, Varghese G, Wang C, Deber CM, Seeman P, O'Dowd BF. Blockade of G protein-coupled receptors and the dopamine transporter by a transmembrane domain peptide: novel strategy for functional inhibition of membrane proteins in vivo. J Pharmacol Exp Ther 2003;307:481-9. [PMID: 12970389 DOI: 10.1124/jpet.103.053843] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
69
Maeda M, Melnyk RA, Partridge AW, Liu LP, Deber CM. Transmembrane segment peptides with double D-amino acid replacements: helicity, hydrophobicity, and antimicrobial activity. Biopolymers 2003;71:77-84. [PMID: 12712502 DOI: 10.1002/bip.10383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
70
Urban S, Freeman M. Substrate specificity of rhomboid intramembrane proteases is governed by helix-breaking residues in the substrate transmembrane domain. Mol Cell 2003;11:1425-34. [PMID: 12820957 DOI: 10.1016/s1097-2765(03)00181-3] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
71
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;12:647-65. [PMID: 12649422 PMCID: PMC2323850 DOI: 10.1110/ps.0236503] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
72
Tang YC, Deber CM. Hydrophobicity and helicity of membrane-interactive peptides containing peptoid residues. Biopolymers 2002;65:254-62. [PMID: 12382286 DOI: 10.1002/bip.10236] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
73
Stark M, Liu LP, Deber CM. Cationic hydrophobic peptides with antimicrobial activity. Antimicrob Agents Chemother 2002;46:3585-90. [PMID: 12384369 PMCID: PMC128737 DOI: 10.1128/aac.46.11.3585-3590.2002] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
74
Yamaguchi H, Kodama H, Osada S, Jelokhani-Niaraki M, Kato F, Kondo M. The Position of Aib Residues Defines the Antimicrobial Activity of Aib-Containing Peptides. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.1563] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
75
Meijberg W, Booth PJ. The activation energy for insertion of transmembrane alpha-helices is dependent on membrane composition. J Mol Biol 2002;319:839-53. [PMID: 12054874 DOI: 10.1016/s0022-2836(02)00342-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
76
Ding FX, Schreiber D, VerBerkmoes NC, Becker JM, Naider F. The chain length dependence of helix formation of the second transmembrane domain of a G protein-coupled receptor of Saccharomyces cerevisiae. J Biol Chem 2002;277:14483-92. [PMID: 11854278 DOI: 10.1074/jbc.m111382200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
77
Ridder A, Thissen L, Killian A, de Kruijff B. Insertion and glycosylation of Pf3-derived membrane proteins in microsomes. FEBS Lett 2002;512:341-4. [PMID: 11852107 DOI: 10.1016/s0014-5793(02)02312-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
78
Larsen SD, Barf T, Liljebris C, May PD, Ogg D, O'Sullivan TJ, Palazuk BJ, Schostarez HJ, Stevens FC, Bleasdale JE. Synthesis and biological activity of a novel class of small molecular weight peptidomimetic competitive inhibitors of protein tyrosine phosphatase 1B. J Med Chem 2002;45:598-622. [PMID: 11806712 DOI: 10.1021/jm010393s] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
79
Deber CM, Liu LP, Wang C, Goto NK, Reithmeier RA. The hydrophobicity threshold for peptide insertion into membranes. CURRENT TOPICS IN MEMBRANES 2002. [DOI: 10.1016/s1063-5823(02)52018-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
80
Buku A, Price JA. Further studies on the structural requirements for mast cell degranulating (MCD) peptide-mediated histamine release. Peptides 2001;22:1987-91. [PMID: 11786181 DOI: 10.1016/s0196-9781(01)00538-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
81
Palliser CC, Parry DA. Quantitative comparison of the ability of hydropathy scales to recognize surface beta-strands in proteins. Proteins 2001;42:243-55. [PMID: 11119649 DOI: 10.1002/1097-0134(20010201)42:2<243::aid-prot120>3.0.co;2-b] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
82
Deber CM, Wang C, Liu LP, Prior AS, Agrawal S, Muskat BL, Cuticchia AJ. TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales. Protein Sci 2001;10:212-9. [PMID: 11266608 PMCID: PMC2249854 DOI: 10.1110/ps.30301] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
83
Tieleman DP, Berendsen HJ, Sansom MS. Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces. Biophys J 2001;80:331-46. [PMID: 11159406 PMCID: PMC1301237 DOI: 10.1016/s0006-3495(01)76018-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
84
Baleja JD. Structure determination of membrane-associated proteins from nuclear magnetic resonance data. Anal Biochem 2001;288:1-15. [PMID: 11141300 DOI: 10.1006/abio.2000.4815] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
85
Takahashi Y, Yamashita T, Ueno A, Mihara H. Construction of Peptides That Undergo Structural Transition from α-Helix to β-Sheet and Amyloid Fibril Formation by the Introduction of N-Terminal Hydrophobic Amino Acids. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00524-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
86
Wang C, Deber CM. Peptide mimics of the M13 coat protein transmembrane segment. Retention of helix-helix interaction motifs. J Biol Chem 2000;275:16155-9. [PMID: 10747951 DOI: 10.1074/jbc.m000723200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
87
Deber CM, Liu LP, Wang C. Perspective: peptides as mimics of transmembrane segments in proteins. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999;54:200-5. [PMID: 10517157 DOI: 10.1034/j.1399-3011.1999.00118.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
88
Burkhart BM, Gassman RM, Langs DA, Pangborn WA, Duax WL, Pletnev V. Gramicidin D conformation, dynamics and membrane ion transport. Biopolymers 1999;51:129-44. [PMID: 10397797 DOI: 10.1002/(sici)1097-0282(1999)51:2<129::aid-bip3>3.0.co;2-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
89
Liu LP, Deber CM. Combining hydrophobicity and helicity: a novel approach to membrane protein structure prediction. Bioorg Med Chem 1999;7:1-7. [PMID: 10199651 DOI: 10.1016/s0968-0896(98)00233-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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