Force field-dependant structural divergence revealed during long time simulations of calbindin d9k

Elad Project, Esther Nachliel, M. Gutman

Research output: Contribution to journalArticlepeer-review

Abstract

The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S2 order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison widi experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data.

Original languageEnglish
Pages (from-to)1864-1872
Number of pages9
JournalJournal of Computational Chemistry
Volume31
Issue number9
DOIs
StatePublished - 15 Jul 2010

Keywords

  • Experimental structure
  • Force field
  • Molecular dynamics
  • Protein folding
  • Secondary structure
  • Structural divergence

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