Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins.

ABSTRACT: There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble lik

SUBMITTER: Karp JM 

PROVIDER: S-EPMC4715900 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature