Conformational interconversion in compstatin probed with molecular dynamics simulations

Proteins: Structure, Function and Genetics

Volumn 53, Issue 1, 2003, Pages 130-141

  Mallik, Buddhadeb ^a   Lambris, John D ^b   Morikis, Dimitrios ^a  

^a University of California Riverside   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Beta turn; Complement; Compstatin; Inhibitor; Molecular dynamics; NMR; Peptide; Secondary structure; Structure

Indexed keywords

COMPSTATIN; CYCLOPEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STRUCTURE ACTIVITY RELATION;

COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PEPTIDES, CYCLIC; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

EID: 0041819705     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10491     Document Type: Article

References (46)

1. Sahu A, Kay BK, Lambris JD. Inhibition of human complement by a C3-binding peptide isolated from a phage-displayed random peptide library. J Immunol 1996;157:884-891.
2. Sahu A, Soulika AM, Morikis D, Spruce L, Moore WT, Lambris JD. Binding kinetics, structure-activity relationship, and biotransformation of the complement inhibitor compstatin. J Immunol 2000;165:2491-2499.
3. Furlong ST, Dutta AS, Coath MM, Gormley JJ, Hubbs SJ, Lloyd D, Mauger RC, Strimpler AM, Sylvester MA, Scott CW, Edwards PD. C3 activation is inhibited by analogs of compstatin but not by serine protease inhibitors or peptidyl alpha-ketoheterocycles. Immunopharmacology 2000;48:199-212.
4. Sahu A, Morikis D, Lambris JD. Complement inhibitors targeting C3, C4, and C5. In: Lambris JD, Holers VM, editors. Therapeutic interventions in the complement system. Totowa, NJ: Humana Press, 2000;9:75-112.
5. Sahu A, Lambris JD. Complement inhibitors: a resurgent concept in anti-inflammatory therapeutics. Immunopharmacology 2000;49:133-148.
6. Soulika AM, Khan MM, Hattori T, Bowen FW, Richardson BA, Hack CE, Sahu A, Edmunds LH Jr, Lambris JD. Inhibition of heparin/protamine complex-induced complement activation by Compstatin in baboons. Clin Immunol 2000;96:212-221.
7. Fiane AE, Mollnes TE, Videm V, Hovig T, Hogasen K, Mellbye OJ, Spruce L, Moore WT, Sahu A, Lambris JD. Compstatin, a peptide inhibitor of C3, prolongs survival of ex vivo perfused pig xenografts. Xenotransplantation 1999;6:52-65.
8. Fiane AE, Mollnes TE, Videm V, Hovig T, Hogasen K, Mellbye OJ, Spruce L, Moore WT, Sahu A, Lambris JD. Prolongation of ex vivo-perfused pig xenograft survival by the complement inhibitor Compstatin. Transplant Proc 1999;31:934-935.
9. Nilsson B, Larsson R, Hong J, Elgue G, Ekdahl KN, Sahu A, Lambris JD. Compstatin inhibits complement and cellular activation in whole blood in two models of extracorporeal circulation. Blood 1998;92:1661-1667.
10. Morikis D, Assa-Munt N, Sahu A, Lambris JD. Solution structure of Compstatin, a potent complement inhibitor. Protein Sci 1998;7:619-627.
11. Klepeis JL, Floudas CA, Morikis D, Lambris JD. Predicting peptide structures using NMR data and deterministic global optimization. J Comp Chem. 1999;20:1354-1370.
12. Morikis D, Roy M, Sahu A, Troganis A, Jennings PA, Tsokos GC, Lambris JD. The structural basis of compstatin activity examined by structure- function-based design of peptide analogs and NMR. J Biol Chem 2002;277:14942-14953.
13. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J Comp Chem 1983;4:187-217.
14. Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;112:6127-6129.
15. Dominy B, Brooks CLI. Development of a generalized Born model parameterization for proteins and nucleic acids. J Phys Chem 1999;103:3765-3773.
16. Ryckaert J-P, Cicotti G, Berendsen HC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
17. Wilmot CM, Thornton JM. Beta-turns and their distortions: a proposed new nomenclature. Protein Eng 1990;3:479-493.
18. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
19. Koradi R, Billeter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55, 29-32.
20. Wilmot CM, Thornton JM. Analysis and prediction of the different types of β-turns in proteins. J Mol Biol 1988;203:221-232.
21. Thornton JM, Sibanda BL, Edwards MS, Barlow DJ. Analysis, design and modification of loop regions in proteins. Bioessays 1988;8:63-69.
22. Hutchinson EG, Thornton JM. A revised set of potentials for beta-turn formation in proteins. Protein Sci 1994;3:2207-2216.
23. Venkatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968;6:1425-1436.
24. Lewis PN, Momany FA, Scheraga HA. Chain reversals in proteins. Biochim Biophys Acta 1973;303:211-229.
25. Chou PY, Fasman GD. Beta-turns in proteins. J Mol Biol 1977;115:135-175.
26. Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981;34:167-339.
27. Rose GD, Gierasch LM, Smith JA. Turns in peptides and proteins. Adv Protein Chem 1985;37:1-109.
28. Chou KC. Prediction of tight turns and their types in proteins. Anal Biochem 2000;286:1-16,
29. Dyson HJ, Wright PE. Defining solution conformations of small linear peptides. Annu Rev Biophys Biophys Chem 1991;20:519-538.
30. Dyson HJ, Wright PE. Antigenic peptides. FASEB J 1995;9:37-42.
31. Dyson HJ, Cross KJ, Houghten RA, Wilson LA, Wright PE, Lerner RA. The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn. Nature 1985;318:480-483.
32. Dyson HJ, Rance M, Houghten RA, Lerner RA, Wright PE. Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J Mol Biol 1988;201:161-200.
33. Dyson HJ, Rance M, Houghten RA, Wright PE, Lerner RA. Folding of immunogenic peptide fragments of proteins in water solution. II. The nascent helix. J Mol Biol 1988;201:201-217.
34. Osterhout JJ Jr, Baldwin RL, York EJ, Stewart JM, Dyson HJ, Wright PE. 1H NMR studies of the solution conformations of an analogue of the C-peptide of ribonuclease A. Biochemistry 1989;28:7059-7064.
35. Merutka G, Morikis D, Bruschweiler R, Wright PE. NMR evidence for multiple conformations in a highly helical model peptide. Biochemistry 1993;32:13089-13097.
36. Bruschweiler R, Morikis D, Wright PE. Hydration of the partially folded peptide RN-24 studied by multidimensional NMR. J Biomol NMR 1995;5:353-356.
37. 10-helix and alpha-helix in Ala-rich peptides: a hydrogen exchange and high field NMR study. J Mol Biol 1997;267:963-974.
38. Blanco FJ, Jimenez MA, Herranz J, Rico M, Santoro J, Nieto JL. NMR evidence of a short linear peptide that folds into a β-hairpin in aqueous solution. J Am Chem Soc 1993;115:5887-5888.
39. Ramirez-Alvarado M, Blanco FJ, Serrano L. De novo design and structural analysis of a model beta-hairpin peptide system. Nat Struct Biol 1996;3:604-612.
40. 1H NMR chemical shifts. J Am Chem Soc 2002;124:14903-14909.
41. Sharman GJ, Searle MS. Cooperative interaction between the three strands of a designed antiparallel beta-sheet. J Am Chem Soc 1998;120:5291-5300.
42. Das C, Raghotharna S, Balaram P. A designed three stranded beta-sheet peptide as a multiple beta-hairpin model. J Am Chem Soc 1998;120:5812-5813.
43. Gibbs AC, Bjorndahl TC, Hodges RS, Wishart DS. Probing the structural determinants of type II′ beta-turn formation in peptides and proteins. J Am Chem Soc 2002;124:1203-1213.
44. Brooks CLI. Protein and peptide folding explored with molecular simulations. Acc Chem Res 2002;35:447-454.
45. Klepeis JL, Floudas CA. Free energy calculations for peptides via deterministic global optimization. J Chem Phys 1999;110:7491-7512.
46. Klepeis JL, Floudas CA. Ab initio tertiary structure prediction of proteins. J Glob Optimiz 2003;25:113-140.