Impact of Cl- and Na+ ions on simulated structure and dynamics of βARK1 PH domain

Proteins: Structure, Function and Genetics

Volumn 35, Issue 2, 1999, Pages 206-217

  Pfeiffer, Stefania ^a   Fushman, David ^a   Cowburn, David ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

Counter ions; Electrostatic interaction; Equilibration; GRK2 PH domain; Hydrogen bonds; Ionic solvent; Ionic strength; Molecular dynamics simulation; Proteins

Indexed keywords

CHLORIDE ION; PROTEIN; SODIUM ION; SOLVENT;

ARTICLE; COMPUTER SIMULATION; HYDROGEN BOND; IONIC STRENGTH; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE;

BETA-ADRENERGIC RECEPTOR KINASE; BLOOD PROTEINS; CHLORIDES; COMPUTER SIMULATION; CYCLIC AMP-DEPENDENT PROTEIN KINASES; IONS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHOSPHOPROTEINS; PROTEIN CONFORMATION; SODIUM;

EID: 0033135037     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990501)35:2<206::AID-PROT7>3.0.CO;2-A     Document Type: Article

References (54)

1. Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD. Molecular biology of the cell. New York: Garland Publishing Inc; 1994. 508 p.
2. McCammon JA, Harvey SC. Dynamcis of proteins and nucleic acids. Cambridge: Cambridge University Press; 1987.
3. van Gunsteren WF, Weiner PK, editors. Computer simulations of biomolecular systems. Leiden: Escom; 1989.
4. van Gunsteren WF, Berendsen HJC. Computer simulations of molecular dynamics: methodology, applications and perspectives in chemistry. Angew Chem Int Ed 1990;29:992-1023.
5. Cheatham III TE, Kollman PA. Molecular dynamics simulations of nucleic acids in solution: how sensitive are the results to small pertubations in the force field and environment? In: Sarma RH, Sarma MH, editors. Proceedings of the tenth conversation, State University of New York. Albany, NY: Adenine Press; 1998.
6. Mohan V, Smith PE, Pettitt BM. Molecular dynamics simulation of ions and water around triplex DNA. J Phys Chem 1993;97: 12984-12990.
7. Weerasinghe S, Smith PE, Mohan V, Cheng Y-K, Pettitt BM. Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution. J Am Chem Soc 1995;117:2147-2158.
8. MacKerell Jr AD. Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties. J Phys Chem 1997;101:646-650.
9. Tapia O, Velazquez I. Molecular dynamics simulations of DNA with protein's consistent GROMOS force field and the role of counterions' symmetry. J Am Chem Soc 1997;119:9534-9538.
10. Young MA, Jayaram B, Beveridge DL. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. J Am Chem Soc 1997;119:59-69.
11. Loncharich RJ, Brook BR. The effect of truncating long-range forces on protein dynamics. Proteins 1989;6:32-45.
12. Schreiber H, Steinhauser O. Cut-off size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 1992;31:5856-5860.
13. Guenot J, Kollman PA. Conformational and energetic effects of truncating nonbound interactions in aqueous protein dynamics simulation. J Comp Chem 1993;14:295-311.
14. Saito M. Molecular dynamics simulations of proteins in solution: artefacts caused by cutoff approximations. J Chem Phys 1994;101: 4055-4061.
15. Smith PE, Pettitt BM. Peptides in ionic solutions: a comparison of Ewald and switching function techniques. J Chem Phys 1991;95: 8430-8441.
16. Darden T, York D, Petersen L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 1993;98: 10089-10092.
17. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995;103: 8577-8593.
18. Bader JS, Chandler D. Computer simulation study of the mean forces between ferrous and ferric ions in water. J Phys Chem 1992;96:6423-6427.
19. 2 dodecamer. J Am Chem Soc 1993;115:1526-1537.
20. York DM, Wlodawer A, Pedersen LG, Darden TA. Atomic-level accuracy in simulation of large protein crystals. Proc Natl Acad Sci USA 1994;91:8715-8718.
21. Roberts ER, Schnitker J. Boundary conditions in simulations of aqueous ionic solutions: a systematic study. J Phys Chem 1995;99: 1322-1331.
22. York DM, Yang W, Lee H, Darden T, Pedersen LG. Towards the accurate modeling of DNA: the importance of long-range interactions. J Am Chem Soc 1995;117:5001-5002.
23. Cheatham III TE, Miller JL, Fox T, Darden A, Kollman PA. Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 1995;117:4193-4194.
24. Perera L, Essmann U, Berkowitz ML. Effect of treatment of long-range forces on the dynamics of ions in aqueous solutions. J Chem Phys 1995;102:450-458.
25. Asp anticodon hairpin: 3 ns of multiple molecular dynamics simulations. Biophys J 1996;71:940-954.
26. Fox T, Kollman PA. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the x-ray structure "maintained"? Proteins 1996;25:315-334.
27. Ewald PP. Die Berechnung optischer und elektrostatischer Gitter-potentiale. Ann Phys (Leipzig) 1921;64:253-287.
28. Marlow GE, Perkyns JS, Pettitt BM. Salt effects on peptide solutions: theory and simulation. Chem Rev 1993;93:2503-2521.
29. Avbelj F, Moult J, Kitson DH, James MNG, Hagler AT. Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A. Biochemistry 1990;29:8658-8676.
30. Wriggers W, Mehler E, Pitici F, Weinstein H, Schulten K. Structure and dynamics of calmodulin in solution. Biophys J 1998;74: 1622-1639.
31. Ibragimova GT, Wade RC. Importance of explicit salt ions for protein stability in molecular dynamics simulation. Biophys J 1998;74:2906-2911.
32. Smith PE, Dang LX, Pettitt BM. Simulation of the structure and dynamics of the bis(penicillamine) enkephalin zwitterion. J Am Chem Soc 1991;113:67-73.
33. Smith PE, Pettitt BM. Effects of salt on the structure and dynamics of the bis(penicillamine) enkephalin zwitterion: A simulation study. J Am Chem Soc 1991;113:6029-6037.
34. Fushman D, Najmabadi-Haske T, Cahill SM, Zheng J, LeVine III HA, Cowburn D. The solution structure and dynamics of the pleckstrin homology domain of the G-receptor kinase 2 (βARK-1): a binding partner of Gβγ subunits. J Biol Chem 1998;273:2835-2843.
35. Koch WJ, Inglese J, Stone WC, Lefkowitz RJ. The binding site for the βγ subunits of heterotrimeric G proteins on the β-adrenergic receptor kinase. J Biol Chem 1993;268:8256-8260.
36. Touhara K, Inglese J, Pitcher JA, Shaw G, Lefkowitz RJ. Binding of G protein βγ-subunits to pleckstrin homology domains. J Biol Chem 1994;269:10217-10220.
37. Mahadevan D, Thanki N, Singh J, et al. Structural studies on the PH domains of DBL, SOS1, IRS-1, and β-ARK1 and their differential binding to G(βγ) subunits. Biochemistry 1995;34:9111-9117.
38. Case DA, Pearlman DA, Caldwell JW, et al. AMBER 5. San Francisco: University of California; 1997.
39. Pearlman DA, Case DA, Caldwell JW, et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Commun 1995;91:1-41.
40. Cornell WD, Cieplak P, Bayly CI, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
41. Kollman PA, Dixon R, Cornell W, Fox T, Chipot C, Phorille A. The development/application of a "minimalist" organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: Wilkinson A, Weiner P, van Gunsteren WF, editors. Computer simulations of biomelecular systems, volume 3. Leiden: Escom; 1997. p 83-96.
42. Jorgensen WL, Chandreskhar JD, Madura JD, Imprey W, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
43. Aqvist J. Ion-water interaction potentials derived from free energy pertubation simulations. J Phys Chem 1990;94:8021-8024.
44. Smith DE, Dang LX. Computer simulations of NaCl association in polarized water. J Chem Phys 1994;100:3757-3766.
45. Ryckaert JP, Cicotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys 1977;23:327-341.
46. Mazur AK. Hierarchy of fast motions in protein dynamics. J Phys Chem B 1998;102:473-479.
47. Güntert P, Braun W, Wüthrich K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS, and GLOMSA. J Mol Biol 1991;217: 517-530.
48. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
49. Allen MP, Tildesley DJ. Computer simulations of liquids. Oxford: Clarendon Press; 1987.
50. Atkins PW. Physical chemistry. New York: Oxford University Press; 1986. 832 p.
51. Hubbard JB. Non-equilibrium theories of electrolyte solutions. In: Bellissent-Funel MC, Neilson GW, editors. The physics and chemistry of aqueous ionic solutions. Dordrecht, Netherlands: D. Reidel; 1987. p 95-128.
52. Hyberts SG, Goldberg MS, Havel TF, Wagner G. The solution structure of eglin c based on measurements on many NOEs and coupling constants and its comparison with x-ray structures. Protein Sci 1992;1:736-751.
53. Quennouille MH. Notes on bias in estimation. Biometrica 1956;43: 353-360.
54. Evans SV. SETOR: hardware lighted three-dimensional solid model representations of macromolecules. J Mol Graph 1993;11: 134-138.