Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants.

ABSTRACT: Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein. The predict

SUBMITTER: Wang L 

PROVIDER: S-EPMC3966310 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature