Current Physical Chemistry - Volume 2, Issue 4, 2012

Advances in theoretical methods, coupled with ever increasing computing power, mean that the techniques of quantum chemistry can now be routinely applied to biological molecules. This review will describe the current state of such calculations, ranging from high accuracy benchmark studies on model systems to efficient but more approximate description of entire macromolecules. Particular focus will be placed on rec Read More

Computational tools have been used extensively to examine protein-protein and protein-ligand interactions. Continuum electrostatics calculations and molecular dynamics simulations can provide insight into the structural stability, binding, and function of proteins, and in turn can serve as predictive tools for guiding the design of experiments to probe specific molecular phenomena. In this review, we describe methods and Read More

Post-translational phosphorylation is a ubiquitous mechanism for cellular regulation, playing a crucial role in a diverse array of processes. At the molecular level, the phosphorylation seems to cause electrostatic perturbations which modulate the energy landscape governing protein folding, activity, protein-protein interactions and, conformational dynamics. However, details on structural effects induced by phosphorylation of Read More

Located at the interface between the cell and organelle interior and exterior, membrane proteins are key players in a number of fundamental biological processes. In recent years, molecular dynamics simulations have become an increasingly important tool in the study of membrane proteins. Increases in computer power and the ongoing development in atomistic and coarse-grained MD techniques now permit simula Read More

Traditionally it has been assumed that drugs interact with membranes via specific binding with membrane proteins. This view has recently been questioned as more and more data support the perspective that membrane-mediated drug-protein interactions are also important, and some drugs interact directly with lipids too. Meanwhile unraveling the mechanisms of drug-induced effects on membranes is exceptionally diffi Read More

Replica-exchange molecular dynamics (REMD) method is one of the enhanced conformational sampling techniques in MD simulations of proteins or other systems with rugged-energy landscapes. In REMD method, copies of original simulation system at different temperatures are simulated separately and simultaneously. Every few steps, temperatures between neighboring replicas are exchanged if the Metropolis criteria for Read More

A new class of compounds, the large-ring cyclodextrins (LR-CDs), attracted attention in recent years, and advances were marked in the study of their physicochemical properties in spite of existing difficulties in their synthesis, isolation and purification. Practical applications were also reported of this new class of compounds. Understanding the mechanism of their action requires knowledge of the macroring conformational dyn Read More

Conformational dynamics and flexibility form the link between protein structure and function. Molecular dynamics (MD) simulations have been valuable for our understanding of conformational energy landscape and protein dynamics at the atomic scale, which is difficult to probe experimentally. In this respect, the essential dynamics of proteins revealed by principal component analysis of MD simulation data provi Read More