PMID: 12786180Jun 6, 2003Paper

Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Guido TianaRicardo A Broglia

Abstract

Some dimeric proteins first fold and then dimerize (three-state dimers) while others first dimerize and then fold (two-state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences following one or the other mechanism on the basis of the distribution of the ground state energy between bulk and interface contacts. The topology of contacts is very different for the bulk than for the interface: while the bulk displays a rich network of interactions, the dimer interface is built up of a set of essentially independent contacts. Consequently, the two sets of interactions play very different roles both, in the folding and in the evolutionary history of the protein. Three-state dimers, where a large fraction of energy is concentrated in few contacts buried in the bulk, and where the relative contact energy of interface contacts is considerably smaller than that associated with bulk contacts, fold according to a hierarchical pathway controlled by local elementary structures, as also happens in the folding of single-domain monomeric proteins. On the other hand, two-state dimers display a relative contact energy of interface contacts, which is larger than the corresponding quantity associated with th...Continue Reading

References

Dec 1, 1994·Protein Science : a Publication of the Protein Society·N V Grishin, M A Phillips
Dec 1, 1995·Protein Science : a Publication of the Protein Society·M J BennettD Eisenberg
Apr 16, 1998·Protein Science : a Publication of the Protein Society·D XuR Nussinov
Oct 28, 1998·Proceedings of the National Academy of Sciences of the United States of America·R A BrogliaE Vigezzi
Feb 27, 1999·Nature Structural Biology·E I Shakhnovich
Jun 13, 1994·Physical Review Letters·E I Shakhnovich
Sep 5, 2002·Proteins·Guido Tiana, Ricardo A Broglia
Nov 8, 2002·Nature·Christopher D SnowMartin Gruebele

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Citations

Nov 21, 2007·BMC Structural Biology·Josselin Noirel, Thomas Simonson

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