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Titolo:
THE APPLICATION OF DIFFERENT SOLVATION AND ELECTROSTATIC MODELS IN MOLECULAR-DYNAMICS SIMULATIONS OF UBIQUITIN - HOW WELL IS THE X-RAY STRUCTURE MAINTAINED
Autore:
FOX T; KOLLMAN PA;
Indirizzi:
UNIV CALIF SAN FRANCISCO,DEPT PHARMACEUT CHEM SAN FRANCISCO CA 94143 UNIV CALIF SAN FRANCISCO,DEPT PHARMACEUT CHEM SAN FRANCISCO CA 94143
Titolo Testata:
Proteins
fascicolo: 3, volume: 25, anno: 1996,
pagine: 315 - 334
SICI:
0887-3585(1996)25:3<315:TAODSA>2.0.ZU;2-5
Fonte:
ISI
Lingua:
ENG
Soggetto:
PARTICLE MESH EWALD; LONG-RANGE FORCES; NUCLEIC-ACIDS; FREE-ENERGY; COMPUTER-SIMULATION; IONIC-SOLUTIONS; LARGE PROTEIN; FIELD; DNA; CRYSTALS;
Keywords:
PARTICLE MESH EWALD; CUTOFF; PERIODIC BOX; SHELL; ROOT MEAN SQUARE DEVIATION; ATOMIC FLUCTUATION; ORDER PARAMETERS; FORCE FIELD; AQUEOUS SOLUTION;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Science Citation Index Expanded
Citazioni:
61
Recensione:
Indirizzi per estratti:
Citazione:
T. Fox e P.A. Kollman, "THE APPLICATION OF DIFFERENT SOLVATION AND ELECTROSTATIC MODELS IN MOLECULAR-DYNAMICS SIMULATIONS OF UBIQUITIN - HOW WELL IS THE X-RAY STRUCTURE MAINTAINED", Proteins, 25(3), 1996, pp. 315-334

Abstract

We present molecular dynamics simulations on ubiquitin with explicit solvent molecules and investigate the influence of different force fields [Weiner et al. (J. Am. Chem. Sec. 106:765-784, 1984; J. Comput. Chem. 7:230-252, 1986) vs. Cornell et al. (J. Am. Chem. Sec. 117:5179-5197, 1995)], different treatments of the long-range electrostatic interaction (8 Angstrom cutoff vs. particle mesh Ewald), and different solvation models (periodic box vs. small shell of water molecules) on the structure and the dynamics of the protein. Structural data are monitored by atomic root mean square deviations (RMSDs) from the crystal structure, the radius of gyration, the solvent-accessible surface area, and the pattern of the backbone hydrogen bonds. The dynamic behavior is assessed by the atomic fluctuations and the order parameters of the N-H backbone vectors.With the Cornell et al. force field and a periodic box model, the simulated structures stay much closer to the experimental X-ray structure than with the older Weiner et al. force field. A further improvement of the simulation is found when the electrostatic interaction is evaluated with the particle mesh Ewald method; after 1.2 ns of simulation the backbone RMSD amounts to only 1.13 Angstrom. The analysis of the dynamic parameters shows that this good structural agreement is not due to a damping of internal motion in the protein. For a given length of simulation time, the shell models achieve an agreement between simulated and experimental structures that is comparable tothe best models that employ a periodic box of solvent models. However, compared with the box models, the fluctuations of the protein atoms in the shell models are smaller, and only with simulation times as long as 2 ns do they become of comparable size to the experimental ones. (C) 1996 Wiley-Liss, Inc.

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Documento generato il 06/07/20 alle ore 05:24:29