Collective dynamics of ecori-dna complex by elastic network model and molecular dynamics simulations

Pemra Doruker*, Lennart Nilsson, Ozge Kurkcuoglu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

Abstract

Anisotropic network model (ANM) is used to analyze the collective motions of restriction enzyme EcoRI in free form and in complex with DNA. For comparison, three independent molecular dynamics (MD) simulations, each of 1.5 ns duration, are also performed for the EcoRI-DNA complex in explicit water. Although high mobility (equilibrium fluctuations) of inner and outer loops that surround the DNA is consistent in both methods and experiments, MD runs sample different conformational subspaces from which reliable collective dynamics cannot be extracted. However, ANM employed on different conformations from MD simulations indicates very similar collective motions. The stems of the inner loops are quite immobile even in the free enzyme and form a large, almost fixed, pocket for DNA binding. As a result, the residues that make specific and non-specific interactions with the DNA exhibit very low fluctuations in the free enzyme. The vibrational entropy difference between the EcoRI complex and free protein + unkinked DNA is positive (favorable), which may partially counteract the unfavorable enthalpy difference of DNA kink formation. Dynamic domains in EcoRI complex and cross-correlations between residue fluctuations indicate possible means of communication between the distal active sites.

Original languageEnglish
Pages (from-to)1-15
Number of pages15
JournalJournal of Biomolecular Structure and Dynamics
Volume24
Issue number1
DOIs
Publication statusPublished - Aug 2006
Externally publishedYes

Funding

P. D. acknowledges funding by an EMBO short-term fellowship. Partial support by other sources (TUBITAK Project 104M247, DPT Project 03K120250, B.A.P. Project 06A509D, PD-TUBA-GEBIP/2002-1-9, COSBIOM FP6-2004-ACC-SSA-2, project no. 517991, and the Swedish Research Council) is also acknowledged.

FundersFunder number
EMBO short-term
TUBITAKCOSBIOM FP6-2004-ACC-SSA-2, PD-TUBA-GEBIP/2002-1-9, 104M247, 517991, 06A509D, 03K120250
Vetenskapsrådet

    Keywords

    • Anisotropic network model
    • Dynamic domains
    • Essential subspace
    • Kink formation
    • Restriction endonucleases

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