Paper Citing NAMD - Abstract
Zhao, Xiongce; Rignall, Tauna R.; McCabe, Clare; Adney, William S.; Himmel, Michael E.
Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization
CHEMICAL PHYSICS LETTERS, 460:284-288, JUL 20 2008
We present free energy calculations for the Trichoderma reesei Cel7A (cellobiohydrolase I) linker peptide from molecular dynamics simulations directed towards understanding the linker role in cellulose hydrolysis. The calculations predict an energy storage mechanism of the linker under stretching/compression that is consistent with processive depolymerization. The linker exhibits two stable states at lengths of 2.5 nm and 5.5 nm during extension/compression, with a free energy difference of 10.5 kcal/mol between the two states separated by an energy barrier. The switching between stable states supports the hypothesis that the linker peptide has the capacity to store energy in a manner similar to a spring. (C) 2008 Elsevier B.V. All rights reserved.
