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

TY - JOUR

T1 - Paths of long-range communication in the E2 enzymes of family 3

T2 - a molecular dynamics investigation

AU - Papaleo, Elena

AU - Lindorff-Larsen, Kresten

AU - Gioia, Luca De

PY - 2012/9/28

Y1 - 2012/9/28

N2 - 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. This journal is

AB - 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. This journal is

U2 - 10.1039/c2cp41224a

DO - 10.1039/c2cp41224a

M3 - Journal article

C2 - 22706570

SN - 1463-9076

VL - 14

SP - 12515

EP - 12525

JO - Physical Chemistry Chemical Physics

JF - Physical Chemistry Chemical Physics

ER -