Exploring the Mechanism of Flexible Biomolecular Recognition with Single Molecule Dynamics

Qiang Lu, H. Peter Lu, and Jin Wang
Phys. Rev. Lett. 98, 128105 – Published 21 March 2007

Abstract

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

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  • Received 30 January 2006

DOI:https://doi.org/10.1103/PhysRevLett.98.128105

©2007 American Physical Society

Authors & Affiliations

Qiang Lu1,2, H. Peter Lu3,*, and Jin Wang1,2,†

  • 1State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People’s Republic of China
  • 2Department of Chemistry and Department of Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
  • 3Department of Chemistry, 141 Overman Hall, Bowling Green State University, Bowling Green, Ohio 43403, USA

  • *Electronic address: hplu@bgsu.edu
  • Electronic address: jin.wang.1@stonybrook.edu

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Issue

Vol. 98, Iss. 12 — 23 March 2007

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