| Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain. | |
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MedLine Citation:
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PMID: 22208276 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
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The dynamics of a protein plays an important role in protein functionality. Here, we examine the differences in the dynamics of a minimally restructuring protein, EcoRI, when it is bound to its cognate DNA and to a noncognate sequence which differs by just a single basepair. Molecular dynamics simulations of the complexes and essential dynamics analyses reveal that the overall dynamics of the protein subunits change from a coordinated motion in the cognate complex to a scrambled motion in the noncognate complex. This dynamical difference extends to the protein-DNA interface where EcoRI tries to constrict the DNA in the cognate complex. In the noncognate complex, absence of the constricting motion of interfacial residues, overall change in backbone dynamics and structural relaxation of the arms enfolding the DNA leave the DNA less-kinked relative to the situation in the cognate complex, thus indicating that the protein is poised for linear diffusion along the DNA rather than for catalytic action. In a larger context, the results imply that the DNA sequences dictate protein dynamics and that when a protein chances upon the recognition sequence some of the key domains of the protein undergo dynamical changes that prepare the protein for eventual catalytic action. |
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Authors:
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V Ramakrishnan; S Jagannathan; A R Shaikh; R Rajagopalan |
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Publication Detail:
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Type: Journal Article |
Journal Detail:
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Title: Journal of biomolecular structure & dynamics Volume: 29 ISSN: 1538-0254 ISO Abbreviation: J. Biomol. Struct. Dyn. Publication Date: 2012 Feb |
Date Detail:
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Created Date: 2012-01-02 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 8404176 Medline TA: J Biomol Struct Dyn Country: United States |
Other Details:
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Languages: eng Pagination: 743-56 Citation Subset: IM |
Affiliation:
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The Singapore-MIT Alliance, National University of Singapore, Singapore 117576 V. R. and S. J. contributed equally to the work reported. vigneshwar.r@nus.edu.sg. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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