An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme

1994 ◽  
Vol 18 (1) ◽  
pp. 19-33 ◽  
Author(s):  
Gregory E. Arnold ◽  
Rick L. Ornstein
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Bacteriophage T4 ◽  
Model Systems ◽  
Dynamics Simulation ◽  
T4 Lysozyme ◽  
Explicit Solvent ◽  
Solvent Model ◽  
Explicit Solvent Model ◽  
Implicit And Explicit

scholarly journals Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins

2016 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
A Priori ◽  
Model Systems ◽  
Dynamics Simulation ◽  
High Mass ◽  
Mean Square ◽  
Dynamics Simulations

ABSTRACTPredicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2for Cγ, when the sampling was done, for each of these proteins, over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations using AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive toa prioriprediction of crystallographic B-factors of a folded globular protein.

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