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Issue 36, 2012
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Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

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Abstract

Molecular dynamics (MD) simulations have the ability to help reveal the relationship between protein structure, dynamics and function. Here, we describe MD simulations of the representative members of family 3 of E2 enzymes that we performed and analyzed with the aim of providing a quantitative description of the functional dynamics in this biologically important set of proteins. In particular, we combined a description of the protein as a network of interacting residues with the dynamical cross-correlation method to characterize the correlated motions observed in the simulations. This approach enabled us to detect communication between distal residues in these enzymes, and thus to reliably define all the likely intramolecular pathways of communication. We observed functionally relevant differences between the closed and open conformations of the enzyme, and identified the critical residues involved in the long-range communication paths. Our results highlight how molecular simulations can be used to aid in providing atomic-level details to communication paths within proteins.

Graphical abstract: Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

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Publication details

The article was received on 17 Apr 2012, accepted on 21 May 2012 and first published on 22 May 2012


Article type: Paper
DOI: 10.1039/C2CP41224A
Phys. Chem. Chem. Phys., 2012,14, 12515-12525

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    Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

    E. Papaleo, K. Lindorff-Larsen and L. De Gioia, Phys. Chem. Chem. Phys., 2012, 14, 12515
    DOI: 10.1039/C2CP41224A

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