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Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides

  • Lei Zhang
  • Wei LiEmail author
  • Tao Fang
  • Shuhua Li
Regular Article

Abstract

Ab inito molecular dynamics (AIMD) based on the generalized energy-based fragmentation (GEBF) approach is employed for the ultrafast conformational dynamics of two unsolvated polypeptides, \(3_{10}\)-helical acetyl(ala)\(_{18}\hbox {NH}_2\) and a subunit of DNA polymerase \(\beta\). In the GEBF approach, the energies and energy gradients of subsystems are obtained with M06-2X functionals, which can describe intramolecular noncovalent interaction. The results are compared with those obtained from the simulations based on AMBER99 and CHARMM22 force fields, and semiempirical density-functional tight-binding (DFTB) and DFTB with empirical dispersion correction (DFTB-D) methods. Our results show that the GEBF-M06-2X simulations may provide reasonable results for the conformational changes of the two unsolvated polypeptides due to the description of intramolecular noncovalent interactions. The AMBER99, CHARMM22, DFTB, and DFTB-D simulations give quite different results. The GEBF-M06-2X-based AIMD simulations are expected to be applied to the fast or ultrafast conformational dynamics of large unsolvated polypeptides and to be employed for improving the empirical force fields.

Keywords

Ab initio molecular dynamics Fragment-based approach  Noncovalent interactions Conformational dynamics Unsolvated polypeptides 

Notes

Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant Nos. 21473087 and 21333004), the National Basic Research Program (Grant No. 2011CB808501) and the Natural Science Foundation in Jiangsu Province of China (BK20130748). This work was also supported by the Fundamental Research Funds for the Central Universities and a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions. We are grateful to the IBM Blade cluster system provided by the High Performance Computing Center at Nanjing University for our calculations.

Supplementary material

214_2015_1799_MOESM1_ESM.pdf (2.7 mb)
Supplementary material 1 (pdf 2730 KB)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople’s Republic of China

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