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Molecular Recognition Mechanisms of Calmodulin Examined by Perturbation-Response Scanning

Published online by Cambridge University Press:  21 March 2011

A. Ozlem Aykut ,
Ali Rana Atilgan  and
Canan Atilgan
A. Ozlem Aykut
Affiliation:
Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
Ali Rana Atilgan
Affiliation:
Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
Canan Atilgan
Affiliation:
Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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Abstract

We analyze the apo and holo calmodulin (CaM) structures by sequentially inserting a perturbation on every residue of the protein, and monitoring the linear response. Residue crosscorrelation matrices obtained from 20 ns long molecular dynamics simulation of the apo-form are used as the kernel in the linear response. We determine two residues whose perturbation equivalently yields the experimentally determined displacement profiles of CaM, relevant to the binding of the trifluoperazine (TFP) ligand. They reside on structurally equivalent positions on the N- and C-terminus lobes of CaM, and are not in direct contact with the binding region. The direction of the perturbation that must be inserted on these residues is an important factor in recovering the conformational change, implying that highly selective binding must occur near these sites to invoke the necessary conformational change.

Keywords

biologicalself-assemblystructural
Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 1301: Symposium V/NN/OO/PP – Soft Matter, Biological Materials and Biomedical Materials—Synthesis, Characterization and Applications , 2011 , mrsf10-1301-oo09-09
Copyright
Copyright © Materials Research Society 2011

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