Paper Citing NAMD - Abstract
Guardiani, Carlo; Di Marino, Daniele; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio
Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3589-3597, SEP 2014
Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.
