Small-world view of the amino acids that play a key role in protein folding

M. Vendruscolo, N. V. Dokholyan, E. Paci, and M. Karplus
Phys. Rev. E 65, 061910 – Published 25 June 2002
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Abstract

We use geometrical considerations to provide a different perspective on the fact that a few selected amino acids, the so-called “key residues,” act as nucleation centers for protein folding. By constructing graphs corresponding to protein structures we show that they have the “small-world” feature of having a limited set of vertices with large connectivity. These vertices correspond to the key residues that play the role of “hubs” in the network of interactions that stabilize the structure of the transition state.

  • Received 25 May 2001

DOI:https://doi.org/10.1103/PhysRevE.65.061910

©2002 American Physical Society

Authors & Affiliations

M. Vendruscolo1, N. V. Dokholyan2, E. Paci1,3, and M. Karplus2,3

  • 1Oxford Centre for Molecular Sciences, Central Chemistry Laboratory, South Parks Road, OX1 3QH Oxford, United Kingdom
  • 2Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
  • 3Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 4 rue Blaise Pascal, 67000 Strasbourg, France

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Issue

Vol. 65, Iss. 6 — June 2002

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