1994
DOI: 10.1016/s0006-3495(94)80798-2
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Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins

Abstract: The role played by non-homogeneous interactions in stabilizing cooperative structural changes in proteins was investigated by exhaustive simulations of all compact conformations compatible with several well-defined globule-like shapes in three dimensions. Conformational free energies corresponding to the association of residues i and j were computed both for the unperturbed system, all subject to identical intramolecular interactions, and for the perturbed system in which a single pair of residues is probed by… Show more

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Cited by 12 publications
(3 citation statements)
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References 26 publications
(32 reference statements)
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“…As a first step, an exhaustive enumeration of all conformations compatible with a given 3-D shape is made. 24 We note that in an n ϫ n ϫ n cubic lattice all conformations have equal numbers of contacts, n ϩ n 1/3 Ϫ 2n 2/3 , and the factor distinguishing the conformations is their distribution of non-bonded contacts, i.e., the distribution of coordination numbers, and the size and geometry of clusters of sites in close contact.…”
Section: General Approachmentioning
confidence: 93%
“…As a first step, an exhaustive enumeration of all conformations compatible with a given 3-D shape is made. 24 We note that in an n ϫ n ϫ n cubic lattice all conformations have equal numbers of contacts, n ϩ n 1/3 Ϫ 2n 2/3 , and the factor distinguishing the conformations is their distribution of non-bonded contacts, i.e., the distribution of coordination numbers, and the size and geometry of clusters of sites in close contact.…”
Section: General Approachmentioning
confidence: 93%
“…Elastic Network Models of proteins, such as the Gaussian Network Model (GNM) and Anisotropic Network Models (ANM) of proteins as developed by Tirion ( 1996 ), Bahar, Erman, and Jernigan (Bahar and Jernigan, 1994 , 1998 ; Bahar et al, 1997a ; Demirel et al, 1998 ; Atilgan et al, 2001 ; Doruker et al, 2002a , b ; Doruker and Jernigan, 2003 ; Sen et al, 2006 ), computationally yield information about protein fluctuation dynamics, the directions of motions of the residues and atoms around their equilibrium positions. This information has already been used by Bahar, Jernigan, Kloczkowski, and many others with significant success (Bahar and Jernigan, 1994 ; Keskin et al, 2002a , b ; Isin et al, 2012 ) to explain functional motions and mechanisms in proteins, nucleic acids, and large biological assemblies, such as the ribosome. ANM could be used as an alternative to calculate the normal modes from a single structure when insufficient numbers of experimental structures or structures having sufficient variability are not available to perform PC analysis, then normal modes from the elastic network models could also be used to compute entropies (Zimmermann et al, 2012 ) (But, as we show below, contact entropies are simpler and provide significant gains).…”
Section: Anisotropic Network Models (Anm) Can Substitute Of Insufficmentioning
confidence: 99%
“…Globular proteins differ from random coils in having dense, compact cores partly as a result of the segregation between hydrophobic and polar residues. Because of their dense cores, compact self-avoiding walks (chains) on lattices provide an excellent model for globular proteins. A compact self-avoiding walk is defined here as a self-avoiding walk with a compact shape, such that all sites within the shape are occupied; there can be no voids. With the self-avoiding walk method it is theoretically possible to generate and enumerate all possible compact conformations within a given volume, but the time required for computations grows geometrically with the length of the chain …”
mentioning
confidence: 99%