NPSA: An Implicit Solvent Model for Protein Docking and Unfolding Simulations

Ting Wang & Rebecca Wade

EML Research gGmbH, 69118 Heidelberg, Germany

http://projects.villa-bosch.de/mcm

We have developed an implicit solvent model called NPSA particularly for protein simulations because including explicit water molecules in calculations can dramatically increase the computing time and the storage space. The NPSA model is a modification of a distance-dependent dielectric model plus a solvent accessible surface term. Charged residues are neutralized but with high polarity. Ting Wang and Rebecca Wade, Proteins. 50: 158-169, 2003.

Barnase-Bartar docking movies with the NPSA model and other two implicit solvent models-DDD and GB.

At the start of the simulations, both barnase and barstar are in unbound conformations and are separated by 5 angstroms from the bound orientations. With the NPSA and the DDD models the two proteins got docked but run away from each other with the GB model. Moreover, the conformational change of the loop around Arg59 in barnase was reproduced only with the NPSA model.

Unfolding simulations (coming soon)

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