Surface Topography Effects of Globular Biomolecules on Hydration Water.

Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.

The different modes of binding of the dust mite allergens, Der f 7 and Der p 7, on a monoclonal antibody WH9 contribute to the differential reactivity.

Background: Der f 7 and Der p 7 are important house dust mite allergens. An IgE-binding inhibition monoclonal antibody WH9 reacts ten folds stronger against Der p 7 than to Der f 7. The purpose of this study is to identify the antigenic determinant(s) and the structural basis of Der f 7 recognize by WH9.

The molecular mechanism of ligand unbinding from the human telomeric G-quadruplex by steered molecular dynamics and umbrella sampling simulations.

G-quadruplexes are attractive drug targets in cancer therapy. Understanding the mechanisms of the binding-unbinding processes involving biomolecules and molecular recognition is essential for designing new drugs of G-quadruplexes. We performed steered molecular dynamics and umbrella sampling simulations to investigate the molecular mechanism and kinetics of ligand unbinding processes of the basket, propeller and hybrid G-quadruplex structures.

Relative stability of G-quadruplex structures: Interactions between the human Bcl2 promoter region and derivatives of carbazole and diphenylamine.

The bcl2 promoter region forms a G-quadruplex structure, which is a crucial target for anticancer drug development. In this study, we provide theoretical predictions of the stability of different G-quadruplex folds of the 23-mer bcl2 promoter region and G-quadruplex ligand. We take into account the whole G-quadruplex structure, including bound-cations and solvent effects, in order to compute the ligand binding free energy using molecular dynamics simulation.

Epitope mapping and in silico characterization of interactions between Der p 7 allergen and MoAb WH9.

Der p 7 is an important house dust mite allergen. However, antigenic determinants of Der p 7 are largely unknown. The purpose of this study is to analyze the determinants of Der p 7 and determine the structural basis of interactions between Der p 7 and WH9, an IgE-binding inhibition mouse monoclonal antibody (MoAb).