A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide

European Biophysics Journal

Volumn 36, Issue 3, 2007, Pages 213-224

  Mark, Pekka ^a,b   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b ALBANOVA UNIVERSITY CENTER   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; CYCLOPHILIN A; DIPEPTIDE; PROLINE;

ARTICLE; CHEMICAL STRUCTURE; CIS ISOMER; HYDRATION; ISOMERIZATION; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SIMULATION; TRANS ISOMER;

BINDING SITES; COMPUTER SIMULATION; CYCLOPHILIN A; DIPEPTIDES; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; WATER;

EID: 33847672224     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-006-0121-3     Document Type: Article

References (61)

1. Ackerson B, Rey O, Canon J, Krogstad P (1998) Cells with high Cyclophilin A content support replication of human immunodeficiency virus type 1 gag mutants with decreased ability to incorporate Cyclophilin A. J Virol 72(1):303-308
2. Allen MP, Tildesley DJ (1987) Computer simulations of liquids. Oxford Science Publications, Oxford
3. Berendsen HJC, Grigera JR, Straatsma TP (1987) The missing term in effective pair potentials. J Phys Chem 91:6269-6271
4. Braun W, Kallen J, Mikol V, Walkinshaw MD, Wüthrich K (1995) Three-dimensional structure and actions of immunosuppressants and their immunophilins. FASEB J 9(1):63-72
5. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217
6. Cardenas ME, Lim E, Heitman J (1995) Mutations that perturb Cyclophilin A ligand binding pocket confer cyclosporin a resistance in Saccharomyces cerevisiae. J Biol Chem 270(36):20997-21002
7. Clubb RT, Ferguson SB, Walsh CT, Wagner G (1994) Three-dimensional solution structure of Escherichia coli periplasmic cyclophilin. Biochemistry 33(10):2761-2772
8. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092
9. Eisenmesser EZ, Bosco DA, Akke M, Kern D (2002) Enzyme dynamics during catalysis. Science 295(5559):1520-1523
10. Fischer G, Wittmann-Liebold B, Lang K, Kiefhaber T, Schmid FX (1989) Cyclophilin and peptidyl-prolyl cis-trans isomerase are probably identical proteins. Nature 337(6206):476-478
11. Fischer S, Michnick S, Karplus M (1993) A mechanism for rotamase catalysis by the FK506 binding protein (fkbr). Biochemistry 32(50):13830-13837
12. Franke EK, Yuan HE, Luban J (1994) Specific incorporation of Cyclophilin A into hiv-1 virions. Nature 372(6504):359-362
13. Gamble TR, Vajdos FF, Yoo S, Worthylake DK, Houseweart M, Sundquist WI, Hill CP (1996) Crystal structure of human Cyclophilin A bound to the amino-terminal domain of hiv-1 capsid. Cell 87(7):1285-1294
14. Grathwohl C, Wüthrich K (1981) NMR studies of the rates of proline cis-trans isomerization in oligopeptides. Biopolymers 20(12):2623-2633
15. Göthel SF, Marahiel MA (1999) Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci 55(3):423-436
16. Hennig L, Christner C, Kipping M, Schelbert B, Rücknagel KP, Grabley S, Küllertz G, Fischer G (1998) Selective inactivation of parvulin-like peptidyl-prolyl cis/trans isomerases by juglone. Biochemistry 37(17):5953-5960
17. Hoover WG (1985) Canonical dynamics: equilibrium phase-scape distribution. Phys Rev A 31(3):1695-1697
18. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33-38
19. Hur S, Bruice TC (2002) The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin. J Am Chem Soc 124(25):7303-7313
20. Ivery MT (2000) Immunophilins: switched on protein binding domains? Med Res Rev 20(6):452-484
21. Kallen J, Walkinshaw MD (1992) The x-ray structure of a tetrapeptide bound to the active site of human Cyclophilin A. FEBS Lett 300(3):286-290
22. Kallen J, Spitzfaden C, Zurini MG, Wider G, Widmer H, Wüthrich K, Walkinshaw MD (1991) Structure of human Cyclophilin and its binding site for Cyclosporin A determined by x-ray crystallography and NMR spectroscopy. Nature 353(6341):276-279
23. Kallen J, Mikol V, Taylor P, Walkinshaw MD (1998) X-ray structures and analysis of 11 cyclosporin derivatives complexed with Cyclophilin A. J Mol Biol 283(2):435-449
24. Ke H (1992) Similarities and differences between human Cyclophilin A and other beta-barrel structures. Structural refinement at 1.63 A resolution. J Mol Biol 228(2):539-550
25. Ke H, Zydowsky LD, Liu J, Walsh CT (1991) Crystal structure of recombinant human t-cell cyclophilin a at 2.5 A resolution. Proc Natl Acad Sci USA 88(21):9483-9487
26. Ke H, Mayrose D, Cao W (1993a) Crystal structure of cyclophilin a complexed with substrate ala-pro suggests a solvent-assisted mechanism of cis-trans isomerization. Proc Natl Acad Sci USA 90(8):3324-3328
27. Ke H, Zhao Y, Luo F, Weissman I, Friedman J (1993b) Crystal structure of murine cyclophilin c complexed with immunosuppressive drug cyclosporin a. Proc Natl Acad Sci USA 90(20):11850-11854
28. Ke H, Mayrose D, Belshaw PJ, Alberg DG, Schreiber SL, Chang ZY, Etzkorn FA, Ho S, Walsh CT (1994) Crystal structures of cyclophilin a complexed with cyclosporin a and n-methyl-4-[(E)-2-butenyl]-4,4-dimethylthreonine cyclosporin a. Structure 2(1):33-44
29. Konno M, Ito M, Hayano T, Takahashi N (1996) The substrate-binding site in escherichia coli cyclophilin a preferably recognizes a cis-proline isomer or a highly distorted form of the trans isomer. J Mol Biol 256(5):897-908
30. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher III WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
31. Mark P, Nilsson L (2001a) Structure and dynamics of the TIP3P, SPC, and SPC/È water models at 298 K. J Phys Chem A 105(43):9954-9960
32. Mark P, Nilsson L (2001b) Molecular dynamics simulations of the ala-pro dipeptide in water: conformational dynamics of trans and cis isomers using different water models. J Phys Chem B 105(33):8028-8035
33. Mark P, Nilsson L (2002a) Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations. J Comput Chem 23(13):1211-1219
34. Mark P, Nilsson L (2002b) A molecular dynamics study of tryptophan in water. J Phys Chem B 106(36):9440-9445
35. Mikol V, Kallen J, Pflügl G, Walkinshaw MD (1993) X-ray structure of a monomeric Cyclophilin A-Cyclosporin A crystal complex at 2.1 A resolution. J Mol Biol 234(4):1119-1130
36. Mikol V, Kallen J, Walkinshaw MD (1994) X-ray structure of a Cyclophilin B/cyclosporin complex: comparison with Cyclophilin A and delineation of its calcineurin-binding domain. Proc Natl Acad Sci USA 91(11):5183-5186
37. Mikol V, Ma D, Carlow CK (1998) Crystal structure of the cyclophilin-like domain from the parasitic nematode brugia malayi. Protein Sci 7(6):1310-1316
38. Nosé S (1984) A molecular dynamics method for simulations in the canonical ensemble. Mol Phys 52:255-268
39. Nosé S (1990) Constant-temperature molecular dynamics. J Phys Condens Matter 2:115-119
40. Orozco M, Tirado-Rives J, Jorgensen WL (1993) Mechanism for the rotamase activity of FK506 binding protein from molecular dynamics simulations. Biochemistry 32(47):12864-12874
41. Ottiger M, Zerbe O, Güntert P, Wüthrich K (1997) The nmr solution conformation of unligated human Cyclophilin A. J Mol Biol 272(1):64-81
42. Pflügl G, Kallen J, Schirmer T, Jansonius JN, Zurini MG, Walkinshaw MD (1993) X-ray structure of a decameric cyclophilin-cyclosporin crystal complex. Nature 361(6407):91-94
43. Pflügl GM, Kallen J, Jansonius JN, Walkinshaw MD (1994) The molecular replacement solution and x-ray refinement to 2.8 A of a decameric complex of human cyclophilin a with the immunosuppressive drug cyclosporin a. J Mol Biol 244(4):385-409
44. Pliyev BK, Gurvits BY (1999) Peptidyl-prolyl cis-trans isomerases: structure and functions. Biochemistry (Mosc) 64(7): 738-751
45. Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327-341
46. Sayle R, Milner-White EJ (1995) RasMol: biomolecular graphics for all. Trends Biochem Sci 20:374-376
47. Scholz C, Schindler T. Dolinski K, Heitman J, Schmid FX (1997) Cyclophilin active site mutants have native prolyl isomerase activity with a protein substrate. FEBS Lett 414(1):69-73
48. Scholz C, Maier P, Dolinski K, Heitman J, Schmid FX (1999) R73A and H144Q mutants of the yeast mitochondrial cyclophilin cpr3 exhibit a low prolyl isomerase activity in both peptide and protein-folding assays. FEBS Lett 443(3):367-369
49. Sherry B, Zybarth G, Alfano M, Dubrovsky L, Mitchell R, Rich D, Ulrich P, Bucala R, Cerami A, Bukrinsky M (1998) Role of Cyclophilin A in the uptake of hiv-1 by macrophages and T lymphocytes. Proc Natl Acad Sci USA 95(4):1758-1763
50. Spitzfaden C, Weber HP, Braun W, Kallen J, Wider G, Widmer H, Walkinshaw MD, Wüthrich K (1992) Cyclosporin A-cyclophilin complex formation. A model based on x-ray and NMR data. FEBS Lett 300(3):291-300
51. Spitzfaden C, Braun W, Wider G, Widmer H, Wüthrich K (1994) Determination of the NMR solution structure of the Cyclophilin A-Cyclosporin A complex. J Biomol NMR 4(4):463-482
52. Takahashi N, Hayano T, Suzuki M (1989) Peptidyl-prolyl cis-trans isomerase is the Cyclosporin A-binding protein Cyclophilin. Nature 337(6206):473-475
53. Taylor P, Husi H, Kontopidis G, Walkinshaw MD (1997) Structures of cyclophilin-ligand complexes. Prog Biophys Mol Biol 67(2-3):155-181
54. Thali M, Bukovsky A, Kondo E, Rosenwirth B, Walsh CT, Sodroski J, Göttlinger HG (1994) Functional association of cyclophilin a with hiv-1 virions. Nature 372(6504):363-365
55. Theriault Y, Logan TM, Meadows R, Yu L, Olejniczak ET, Holzman TF, Simmer RL, Fesik SW (1993) Solution structure of the Cyclosporin A/Cyclophilin complex by NMR. Nature 361(6407):88-91
56. Yoo S, Myszka DG, Yeh C, McMurray M, Hill CP, Sundquist WI (1997) Molecular recognition in the hiv-1 capsid/cyclophilin a complex. J Mol Biol 269(5):780-795
57. van Gunsteren WF, Berendsen HJC (1990) Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew Chem Int Ed Engl 29:992-1023
58. Zhao Y, Ke H (1996a) Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization. Biochemistry 35(23):7356-7361
59. Zhao Y, Ke H (1996b) Mechanistic implication of crystal structures of the cyclophilin-dipeptide complexes. Biochemistry 35(23):7362-7368
60. Zhao Y, Chen Y, Schutkowski M, Fisher G, Ke H (1997) Cyclophilin A complexed with a fragment of hiv-1 gag protein: insight into hiv-1 infectious activity. Structure 5(1):139-146
61. Zydowsky LD, Etzkorn FA, Chang HY, Ferguson SB, Stolz LA, Ho SI, Walsh CT (1992) Active site mutants of human cyclophilin a separate peptidyl-prolyl isomerase activity from cyclosporin a binding and calcineurin inhibition. Protein Sci 1(9):1092-1099