Bending of the calmodulin central helix: A theoretical study

Protein Science

Volumn 5, Issue 10, 1996, Pages 2044-2053

  Van Der Spoel, David ^a   De Groot, Bert L ^a   Hayward, Steven ^a   Berendsen, Herman J C ^a   Vogel, Hans J ^b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

calmodulin; essential dynamics; molecular dynamics simulations; normal modes; protein folding

Indexed keywords

CALMODULIN;

ARTICLE; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; SECOND MESSENGER;

EID: 0029959124     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560051011     Document Type: Article

References (59)

1. Amadei A, Linssen ABM, Berendsen HJC. 1993. Essential dynamics of proteins. Proteins Struct Funct Genet 17:412-425.
2. Babu YS, Bugg CE, Cook WJ. 1988. Structure of calmodulin refined at 2.2 Å. J Mol Biol 204:191-204.
3. Baisera MA, Wriggers W, Oono Y, Schulten K. 1996. Principle component analysis and long time protein dynamics. J Phys Chem 100:2567-2572.
4. 15N relaxation using inverse detected NMR spectroscopy: The central helix is flexible. Biochemistry 31:5269-5218.
5. 10/α-helix transition: Implications for a natural reaction coordinate. J Am Chem Soc 116:6307-6315.
6. Bayley PM, Martin SR. 1992. The α-helical content of calmodulin is increased by solution conditions favoring protein crystallization. Biochim Biophys Acta 1160:16-21.
7. Berendsen HJC, Postma JPM, DiNola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.
8. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. 1981. Interaction models for water in relation to protein hydration. In: Pullman B, ed. Intermolecular forces. Dordrecht: D. Reidel Publishing Company, pp 331-342.
9. Berendsen HJC, van der Spoel D, van Drunen R. 1995. GROMACS: A message-passing parallel molecular dynamics implementation. Comp Phys Commun 91:43-56.
10. Brooks B, Karplus M. 1983. Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 80:6571-6575.
11. Brooks CL III, Case DA. 1993. Simulations of peptide conformational dynamics and thermodynamics. Chem Rev 93:2487-2502.
12. Burley SK, Petsko GA. 1989. Electrostatic interactions in aromatic oligopeptides contribute to protein stability. Trends Biotech 7:354-359.
13. Caflisch A, Karplus M. 1994. Molecular dynamics studies of protein and peptide folding and unfolding. In: Merz KM Jr, Le Grand SM, eds. The protein folding problem and tertiary structure prediction. Boston: Birkhaeuser. pp 193-230.
14. Case DA. 1994. Normal mode analysis of protein dynamics. Curr Opin Struct Biol 4:285-290.
15. Chakrabartty A, Baldwin RL. 1995. Stability of α-helices. Adv Protein Chem 46:141-176.
16. Chattopadhyaya R, Meador WE, Means AR, Quiocho FA. 1992. Calmodulin structure refined at 1.7 Å resolution. J Mol Biol 228:1177.
17. Clore GM, Bax A, Ikura M, Gronenborn AM. 1993. Structure of calmodulin-target peptide complexes. Curr Opin Struct Biol 3:838-845.
18. Daggett V, Levitt M. 1992. Molecular dynamics simulations of helix denaturation. J Mol Biol 223:1121-1138.
19. Finn BE, Forsen S. 1995. The evolving model of calmodulin structure, function and activation. Structure 3:7-11.
20. Garcia AE. 1992. Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68:2696-2699.
21. Gō N, Noguti T, Nishikawa T. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Nail Acad Sci USA 80:3696-3700.
22. Hayward S, Gō N. 1995. Collective variable description of native protein dynamics. Annu Rev Phys Chem 46:223-250.
23. Hayward S, Kitao A, Hirata F, Gō N. 1993. Effect of solvent on collective motions in globular proteins. J Mol Biol 234:1207-1217.
24. Heidom DB, Trewhella J. 1988. Comparison of the crystal and solution structures of calmodulin and troponin C. Biochemistry 27:909-915.
25. Hirst JD, Brooks CL III. 1995. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry 34:7614-7621.
26. Ikura M. 1996. Calcium binding and conformational response in EF-hand proteins. Trends Biochem 21:14-17.
27. Ikura M, Clore GM, Gronenborn AM, Zhu G, Klee CB, Bax A. 1992. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science 256:632.
28. 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. Biochemistry 30:9216-9228.
29. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
30. Kataoka M, Persechini A, Tokunaga F, Kretsinger RH. 1996. The linker of calmodulin lacking Glu 84 is elongated in solution, although it is bent in the crystal. Proteins Struct Funct Genet 25:335-341.
31. Kazmirski SL, Alonso DOV, Cohen FE, Prusiner SB, Daggett V. 1995. Theoretical studies of sequence effects on the conformational properties of a fragment of the prion protein: Implications for scrapie formation. Curr Biol 2:305-315.
32. Kitao A, Hirata F, Gō N. 1991. The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of mellitin in water and in vacuum. Chem Phys 158:447-472.
33. Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
34. Kuboniwa H, Tjandra N, Grzesiek S, Ren H, Klee CB, Bax A. 1995. Solution structure of calcium-free calmodulin. Nature Struct Biol 2:768-776.
35. Levitt M, Sander C, Stern PS. 1983. The normal modes of a protein: Native bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 10:181-199.
36. Meador WE, Means AR, Quiocho FA. 1992. Target enzyme recognition by calmodulin: 2.4 Ångström structure of a calmodulin-peptide complex. Science 257:1251.
37. Mehler EL, Pascual-Ahuir JL, Weinstein H. 1991. Structural dynamics of calmodulin and troponin C. Protein Eng 4:625-637.
38. Persechini A, Kretsinger RH. 1988. The central helix of calmodulin functions as a flexible tether. J Biol Chem 263:12175-12178.
39. Ryckaert JP, Ciccotti G, Berendsen HJC. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J Comp Phys 23:327-341.
40. Soman KV, Karimi A, Case DA. 1991. Unfolding of an α-helix in water. Biopolymers 31:1351-1361.
41. Spera S, Ikura M, Bax A. 1991. Measurements of the exchange rates of rapidly exchanging amide protons: Application to the study of calmodulin and its complex with a myosin light chain kinase fragment. J Biomol NMR 1:155-165.
42. Terwilliger TC, Eisenberg D. 1982. The structure of melittin. I. Structure determination and partial refinement. J Biol Chem 257:6010-6015.
43. Tirado-Rives J, Jorgensen WL. 1991. Molecular dynamics simulations of the unfolding of an α-helical analogue of ribonuclease A S-peptide in water. Biochemistry 30:3864-3871.
44. 15N-NMR relaxation measurements. Eur J Biochem 230:1014-1024.
45. Török K, Lane AN, Martin SR, Janot JM, Bayley PM. 1992. Effects of calcium binding on the internal dynamics properties of bovine brain calmodulin studied by NMR and optical spectroscopy. Biochemistry 31:3452-3462.
46. van Aalten DMF, Amadei A, Linssen ABM, Eijsink VGH, Berendsen HJC. 1995. The essential dynamics of thermolysin: Confirmation of the hingebending motion and comparison of simulations in vacuum and water. Proteins Struct Funct Genet 22:45-54.
47. van Buuren AR, Berendsen HJC. 1993. Molecular dynamics simulation of the stability of a 22-residue alpha-helix in water and 30% trifluoroethanol. Biopolymers 33:1159-1166.
48. van Buuren AR, Marrink SJ, Berendsen HJC. 1993. A molecular dynamics study of the decane/water interface. J Phys Chem 97:9206-9212.
49. van der Spoel D, van Buuren AR, Apol E, Meulenhoff PJ, Tieleman DP, Sijbers ALTM, van Drunen R, Berendsen HJC. 1996a. Gromacs user manual, version 1.3. Nijenborgh 4, 9747 AG Groningen, The Netherlands. Internet: http://rugmd0.chem.rug.nl/∼gmx.
50. van der Spoel D, van Buuren AR, Tieleman DP, Berendsen HJC. 1996b. Molecular dynamics simulations of peptides from BPTI: A closer look at amidearomatic interactions. J Biomol NMR. Forthcoming.
51. van der Spoel D, Vogel HJ, Berendsen HJC. 1996c. Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein. Proteins Struct Funct Genet 24:450-466.
52. van Gunsteren WF, Berendsen HJC. 1987. Gromos-87 manual. Biomos BV, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
53. Vogel HJ. 1994. Calmodulin: A versatile calcium mediator protein. Biochem Cell Biol 72:357-376.
54. Vogel HJ, Zhang M. 1995. Protein engineering and NMR studies of calmodulin. Mol Cell Biochem 149/150:3-15.
55. Vorherr T, Kessler O, Mark A, Carafoli E. 1992. Construction and molecular dynamics simulation of calmodulin in the extended and in a bent conformation. Eur J Biochem 204:931-937.
56. Vriend G. 1990. WHAT IF: A molecular modeling and drug design program. J Mol Graphics 8:52-56.
57. 2+-binding and structural dynamics in the functions of calmodulin. Annu Rev Physiol 56:213-236.
58. Zhang M, Tanaka T, Ikura M. 1995. Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nature Struct Biol 2:758-767.
59. Zhang M, Vogel HJ. 1994. Two dimensional NMR studies of selenomethionine calmodulin. J Mol Biol 234:545-554.