Investigating the disorder-order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation

Journal of Molecular Recognition

Volumn 23, Issue 4, 2010, Pages 360-368

  Zhang, Yong ^a,b   Tan, Hongwei ^b   Chen, Guangju ^b   Jia, Zongchao ^c  

^a TECHNICAL INSTITUTE OF PHYSICS AND CHEMISTRY   (China)

^b BEIJING NORMAL UNIVERSITY   (China)

^c QUEEN S UNIVERSITY   (Canada)

Author keywords

Conformational transition; Interaction free energy; MM_PBSA; Targeted molecular dynamics; VDW interaction

Indexed keywords

CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE; CALMODULIN;

ARTICLE; BINDING SITE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE;

BINDING SITES; CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES; CALMODULIN; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY;

EID: 77954694216     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.1002     Document Type: Article

References (63)

1. 2+, and Calmodulin. Cell Signal. 14: 649-654.
2. Albrecht M, Wolfram B, Mirek C. 2004. Handbook of Metalloproteins. John Wiley & Sons: England.
3. Aqvist J. 1990. Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 94: 8021-8024.
4. Bahler M, Rhoads A. 2002. Calmodulin signaling via the IQ motif. FEBS Lett. 513: 107-113.
5. Best RB, Chen Y-G. 2005. Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure 13: 1755-1763.
6. Brokx RD, Lopez MM, Vogel HJ, Makhatadze GI. 2001. Energetics of target peptide binding by calmodulin reveals different modes of binding. J. Biol. Chem. 276: 14083-14091.
7. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross, WS, Kollman PA. 2006. AMBER 9. University of California: San Francisco.
8. Catalano A, O'Day DH. 2008. Calmodulin-binding proteins in the model origanism Dictyostelium: A complete & critical review. Cell Signal. 20: 277-291.
9. Cates MS, Berry MB, Ho EL, Li Q, Potter JD, George N, Phillips J. 1999. Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin. Structure 7: 1269-1278.
10. Cheng X, Wang H, Grant B, Sine SM, McCammon JA. 2006. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput. Biol. 2: 1173-1184.
11. Clapperton JA, Martin SR, Smerdon SJ, Gamblin SJ, Bayley PM. 2002. Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism. Biochemistry 41: 14669-14679.
12. Cohen P, Klee CB. 1980. Calmodulin. Elsevier: Amsterdam, Netherlands.
13. Connolly ML. 1983. Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709-713.
14. Crivici A, Ikura M. 1995. Molecular and structural basic of target recognition by calmodulin. Annu. Rev. Biophys. Biomol. Struct. 24: 85-116.
15. Dunitz JD. 1995. Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions. Chem. Biol. 2: 709-712.
16. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang CH, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic Z. 2001. Intrinsically disordered protein. J. Mol. Graphics Modell. 19: 26-59.
17. Dyson HJ, Wright PE. 2005. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6: 197-208.
18. Espinoza-Fonseca LM, Kast D, Thomas DD. 2007. Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin. Biophys. J. 93: 2083-2090.
19. Fallon JL, Halling DB, Hamilton SL, Quiocho FA. 2005. Structure of calmodulin bound to the hydrophobic IQ domain of the cardiac Ca(v)1.2 calcium channel. Structure 13: 1881-1886.
20. Gallagher PJ, Herring BP, Stull JT., 1997. Myosin light chain kinases. J. Muscle Res. Cell Motil. 18: 1-16.
21. Genest D, Garnier N, Arrault A, Marot C, Morin-Allory L, Genest M. 2008. Ligand-escape pathways from the ligand-binding domain of PPARx receptor as probed by molecular dynamics simulations. Eur. Biophys. J. 37: 369-379.
22. Goldberg J, Nairn AC, Kuriyan J. 1996. Structural basis for the autoinhibition of calcium/calmodulin-dependent protein kinase I. Cell 84: 875-887.
23. Gutteridge A, Thornton J. 2004. Conformational change in substrate binding, catalysis and product release: an open and shut case? FEBS Lett. 567: 67-73.
24. 2+/CaM-dependent kinases: from activation to function. Annu. Rev. Pharmacol. Toxicol. 41: 471-505.
25. Humphrey W, Dalke A, Schulten K. 1996. VMD-visual molecular dynamics. J. Mol. Graphics. 14: 33-38.
26. 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: 632-638.
27. James P, Vorherr T, Carafoli E. 1995. Calmodulin-binding domains: just two faced or multi-faced? Trends Biochem. Sci. 20: 38-42.
28. Jelesarov I, Bosshard HR. 1999. Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition. J. Mol. Recognit. 12: 3-18.
29. Kamerlin SCL, Ruckera R, Borescha S. 2006. A targeted molecular dynamics study of WPD loop movement in PTP1B. Biochem. Biophys. Res. Commun. 345: 1161-1166.
30. Kauzmann W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14: 1-63.
31. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Case DA, Cheatham TE. 2000. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accts. Chem. Res. 33: 889-897.
32. 2+/calmodulin dependent kinase kinase peptide. J. Mol. Biol. 312: 59-68.
33. Lewit-Bentley A, Réty S. 2000. EF-hand calcium-binding proteins. Curr. Opin. Struct. Biol. 10: 637-643.
34. {thorn} permeation across the gramicidin A channel. J. Phys. Chem. B 110: 12789-12795.
35. Lumry R, Rajender S. 2004. Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: a ubiquitous properly of water. Biopolymers 10: 1125-1227.
36. Mashl RJ, Jakobsson E. 2008. End-point targeted molecular dynamics: large-scale conformational changes in potassium channels. Biophys. J. 94: 4307-4319.
37. Meador WE, Means AR, Quiocho FA. 1993. Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structures. Science 262: 1718-1721.
38. Meador WE, Means AR, Quiocho FA. 1992. Target enzyme recognition by calmodulin: 2.4A ° structure of calmodulin peptide complex. Science 257: 1251-1255.
39. Mendieta Js, Gago F, Ramirez G. 2005. Binding of 5'-GMP to the GluR2 AMPA receptor: insight from targeted molecular dynamics simulations. Biochemistry 44: 14470-14476.
40. Mirny L, Shakhnovich E. 2001. Protein folding theory: from lattice to all-atom models. Annu. Rev. Biophys. Biomol. Struct. 30: 361-396.
41. O'Neil KT, DeGrado WF. 1990. How calmodulin binds its targets: sequence independent recognition of amphiphilic alphahelices. Trends Biochem. Sci. 15: 59-64.
42. Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, Dunker AK. 2005. Coupled folding and binding with a-helix-forming molecular recognition elements. Biochemistry 44: 12454-12470.
43. Onuchic JN, Nymeyer H, Garcia AE, Chahine J, Socci ND. 2000. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Adv. Prot. Chem. 53: 87-152.
44. 2+-calmodulin-dependent kinase kinase. Nat. Struct. Biol. 6: 819-824.
45. Ryckaert J, Ciccotti G, Berendsen H. 1977. Numerical integration the cartesian equations of motion with constraints: molecular dynamics of n-alkanes. J. Comp. Physiol. 23: 327-341.
46. Sagui C, Darden T. 1999. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu. Rev. Biophys. Biomol. Struct. 28: 155-179.
47. Sandhu KS, Dash D. 2006. Conformational flexibility may explain multiple cellular roles of PEST motifs. Proteins 63: 727-732.
48. Sandhu KS, Dash D. 2007. Dynamics a-helix: conformations that do not conform. Proteins 68: 109-122.
49. Schlitter J, Engels M, Kruger P. 1994. Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J. Mol. Graph. 12: 84-89.
50. Shamsir MS, Dalby AR. 2005. One gene, two diseases and three conformations: molecular dynamics simulations of mutants of human prion protein at room temperature and elevated temperatures. Proteins 59: 275-290.
51. Sitkoff D, Sharp KA, Honig B. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98: 1978-1988.
52. Swift RV, McCammon JA. 2008. Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics. Biochemistry 47: 4102-4111.
53. Tompa P, Szasz C, Buday L. 2005. Structural disorder throws new light on moonlighting. Trends Biochem. Sci. 30: 484-489.
54. Tse JKY, Giannetti AM, Bradshaw JM. 2007. Thermodynamics of calmodulin trapping by Ca2{thorn}/calmodulin-dependent protein kinase ii: subpicomolar Kd determined using competition titration calorimetry. Biochemistry 46: 4017-4027.
55. Tsvetkov PO, Ezraty B, Mitchell JK, Devred F, Peyrot V, Derrick PJ, Barras F, Makarov AA, Lafitte D. 2005. Calorimetry and mass spectrometry study of oxidized calmodulin interaction with target and differential repair by methionine sulfoxide reductases. Biochimie 87: 473-480.
56. Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PW. 2003. Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding. Proc. Natl Acad. Sci. USA 100: 5148-5153.
57. Vetter SW, Leclerc E. 2003. Novel aspects of calmodulin target recognition and activation. Eur. J. Biochem. 270: 404-414.
58. Wall ME, Clarage JB, Phillips GN. 1997. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 5: 1599-1612.
59. Warner DJ, Paterson IC, Sessions RB. 2009. Investigating the conformational preferences of transforming growth factor-b isoforms using targeted molecular dynamics simulations. J. Chem. Theory Comput. 5: 482-490.
60. Wintrode PL, Privalov PL. 1997. Energetics of target peptide recognition by calmodulin: a calorimetric study. J. Mol. Biol. 266: 1050-1062.
61. Yamauchi E, Nakatsu T, Matsubara M, Kato H, Taniguchi H. 2003. Crystal structure of a MARCKS peptide containing the calmodulin-binding domain in complex with Ca(2{thorn})-calmodulin. Nat. Struct. Biol. 10: 226-231.
62. Yap KL, Kim J, Truong K, Sherman M, Yuan T, Ikura M. 2000. Calmodulin target database. J. Struct. Funct. Genomics 1: 8-14.
63. Zhang J, Li C, Chen K, Zhu W, Shen X, Jiang H. 2006. Conformational transition pathway in the allosteric process of human glucokinase. Proc. Natl Acad. Sci. USA 103: 13368-13373.