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J Biomol NMR. 2015 Jan;61(1):35-45. doi: 10.1007/s10858-014-9879-2. Epub 2014 Nov 22.

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

Author information

1
Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.

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 like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

PMID:
25416617
PMCID:
PMC4715900
DOI:
10.1007/s10858-014-9879-2
[Indexed for MEDLINE]
Free PMC Article

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