A comparison of structural and dynamic properties of different simulation methods applied to SH3

The dynamic and static properties of molecular dynamics simulations using various methods for treating solvent were compared. The SH3 protein domain was chosen as a test case because of its small size and high surface-to-volume ratio. The simulations were analyzed in structural terms by examining cr...

Full description

Saved in:
Bibliographic Details
Published in:Biophysical journal 1996-02, Vol.70 (2), p.684-692
Main Authors: van Aalten, D.M., Amadei, A., Bywater, R., Findlay, J.B., Berendsen, H.J., Sander, C., Stouten, P.F.
Format: Article
Language:English
Subjects:
Algorithms
Binding Sites
Biophysical Phenomena
Biophysics
Computer Simulation
Crystallization
Ligands
Models, Chemical
Models, Molecular
Molecular Structure
Protein Structure, Secondary
Solvents
src Homology Domains - physiology
Stochastic Processes
Thermodynamics
Citations: Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:The dynamic and static properties of molecular dynamics simulations using various methods for treating solvent were compared. The SH3 protein domain was chosen as a test case because of its small size and high surface-to-volume ratio. The simulations were analyzed in structural terms by examining crystal packing, distribution of polar residues, and conservation of secondary structure. In addition, the "essential dynamics" method was applied to compare each of the molecular dynamics trajectories with a full solvent simulation. This method proved to be a powerful tool for the comparison of large concerted atomic motions in SH3. It identified methods of simulation that yielded significantly different dynamic properties compared to the full solvent simulation. Simulating SH3 using the stochastic dynamics algorithm with a vacuum (reduced charge) force field produced properties close to those of the full solvent simulation. The application of a recently described solvation term did not improve the dynamic properties. The large concerted atomic motions in the full solvent simulation as revealed by the essential dynamics method were analyzed for possible biological implications. Two loops, which have been shown to be involved in ligand binding, were seen to move in concert to open and close the ligand-binding site.
ISSN:0006-3495
1542-0086
DOI:10.1016/S0006-3495(96)79608-X