On the model granularity to simulate protein dynamics: A biological physics view on biomolecular computing

Natural Computing

Volumn 3, Issue 4, 2004, Pages 377-393

  Takano, Mitsunori ^a   Higo, Junichi ^b   Nakamura, Hironori K ^a   Sasai, Masaki ^c  

^a WASEDA UNIVERSITY   (Japan)

^b TOKYO UNIVERSITY OF PHARMACY AND LIFE SCIENCES   (Japan)

^c NAGOYA UNIVERSITY   (Japan)

Author keywords

Coarse grained model; Collective motion; Essential dynamics; Function; Robustness; Simulation; Structure

Indexed keywords

ACTIN; APROTININ; MOLECULAR MOTOR; MYOSIN; RIBONUCLEASE T1;

ANISOTROPY; ARTICLE; ATOM; COMPUTER MODEL; COMPUTER SIMULATION; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION;

EID: 13844317779     PISSN: 15677818     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11047-004-2639-6     Document Type: Article

References (32)

1. AR Atilgan SR Durell RL Jernigan MC Demirel O Keskin I Bahar 2001 Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophysical Journal 80 505-515
2. I Bahar AR Atilgan MC Demirel B Erman 1998 Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability Physical Review Letters 80 2733-2736
3. CL Brooks III DA Case 1993 Simulation of peptide conformational dynamics and thermodynamics Chemical Reviews 93 2487-2502
4. C Clementi H Nymeyer JN Onuchic 2000 Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins Journal of Molecular Biology 298 937-953
5. P Doruker AR Atilgan I Bahar 2000 Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α-amylase inhibitor PROTEINS: Structure, Function, and Genetics 40 51-524
6. DJ Evans GP Morriss 1983 The isothermal/isobaric molecular dynamics ensemble Physics Letter A 98 433-436
7. 2 in noncrystalline environments show a subunit transition from the open to the closed conformation Protein Science 5 62-71
8. MH Garzon 2003 Special issue on biomolecular machines and artificial evolution Genetic Programming and Evolvable Machines 4 107-109
9. GO N, Noguti T and Nishikawa T (1983) Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proceedings of the National Academy of Sciences of USA 80: 3696-3700
10. Hagiya M and Ohuchi A eds (2002) Preliminary Proceedings of the Eighth International Meeting on DNA Based Computers, and papers therein
11. 10-helix, β-turn, β-hairpin, and other disordered conformations Protein Science 10 1160-1171
12. J. Higo Y. Sugimoto K Wakabayashi H Nakamura 2001 Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data Journal of Computational Chemistry 22 1983-1994
13. J Higo H Umeyama 1997 Protein dynamics determined by backbone conformation and atom packing Protein Engineering 10 373-380
14. Himmel DM, Gourinath S, Reshetnikova L, Shen Y, Szent-Györgyi AG and Cohen C (2002) Crystallographic findings on the internally uncoupled and near-rigor states of myosin: Further insights into the mechanics of the motor. Proceedings of the National Academy of Sciences of USA 99: 12645-12650
15. RW Hockney 1970 The potential calculation and some application Methods in Computational Physics 9 135-211
16. WL Jorgensen J Chandrasekhar JD Madura RW Impey ML Klein 1983 Comparison of simple potential functions for simulating liquid water Journal of Chemical Physics 79 926-935
17. K Kaneko 1998 Life as complex systems: Viewpoint from intra-inter dynamics Complexity 3 6 53-60
18. SA Kauffman 1969 Metabolic stability and epigenesis in randomly connected nets Journal of Theoretical Biology 22 437-467
19. A Kitao F Hirata N Go 1991 The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum Chemical Physics 158 447-472
20. Kitao A and Wagner G (2000) A space-time structure determination of human CD2 reveals the CD58-binding mode. Proceedings of the National Academy of Sciences of USA 97: 2064-2068
21. N Koga S Takada 2001 Roles of native topology and chain-length scaling in protein folding: A simulation study with a GO-like model Journal of Molecular Biology 313 171-180
22. Kollman PA, Dixon, RW, Cornell WD, Chipot C and Pohorille A (1997) The development/application of a "minimalist" organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: Computer Simulations of Biological Systems
23. C Micheletti G Lattanzi A Maritan 2002 Elastic properties of proteins: Insight on the folding process and evolutionary selection of native structures Journal of Molecular Biology 321 909-921
24. HK Nakamura M Sasai M Takano 2004 Squeezed exponential kinetics to describe a nonglassy downhill folding as observed in a lattice protein model Proteins: Structure, Function, and Bioinformatics 55 99-106
25. F Oosawa 2000 The loose coupling mechanism in molecular machines of living cells Genes to Cells 5 9-16
26. LR Otterbein P Graceffa R Dominguez 2001 The crystal structure of uncomplexed actin in the ADP state Science 293 708-711
27. JW Ponder DA Case 2003 Force fields for protein simulation Advances in Protein Chemistry 66 27-85
28. JA Rose M Takano M Hagiya A Suyama 2003 A DNA computing-based genetic program for in vitro protein evolution via constrained pseudo-module shuffling Genetic Programming and Evolvable Machines 4 139-152
29. Sasai M and Wolynes PG (2002) Stochastic gene expression as a many-body problem. Proceedings of the National Academy of Sciences of USA 100: 2374-2379
30. Shea J-E, Onuchic JN and Brooks CL III (1999) Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A. Proceedings of the National Academy of Sciences of USA 96: 12512-12517
31. Takada S (1999) Going for the prediction of protein folding mechanisms. Proceedings of the National Academy of Sciences of USA 96: 11698-11700
32. M Takano T Yamato J Higo A Suyama K Nagayama 1999 Molecular dynamics of a 15-residue poly(L-alanine) in water: Helix formation and energetics Journal of the American Chemical Society 121 605-612