The interaction between complement fragment C3d and complement receptor 2 (CR2) is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement s...

Molecules adsorbed on a substrate surface can self-assemble into a monolayer. This article models the process of self-assembly guided by an external object. The molecules are electric dipoles, diffusing on the surface at an elevated temperature. Pre-pattern a flat mask with a submonolayer of immobile atoms, which gives rise to a patterned contact potential field. Bring the mask to a small dista...

Calculation of the electrostatic potential of protein-protein complexes has led to the general assertion that protein-protein interfaces display "charge complementarity" and "electrostatic complementarity". In this study, quantitative measures for these two terms are developed and used to investigate protein-protein interfaces in a rigorous manner. Charge complementarity (CC) was defined using ...

The wetting of water on corrugated and flat hexagonal boron nitride (h-BN) monolayers on Rh(111) is studied within a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. Water is treated by QM methods, whereas the interactions between liquid and substrate are described at the MM level. The electrostatic properties of the substrate are reproduced by assigning specifically generated par...

PURPOSE OF REVIEW The immunogenic capacity of donor human leukocyte antigen (HLA) to induce humoral immune responses is not an intrinsic property of the mismatched alloantigen but depends on the HLA phenotype of the recipient. In recent years, advances in molecular sequence technology and information from X-ray crystallography have enabled structural comparison of donor and recipient HLA type p...

The data previously reported on the enthalpy of hydration, partial molar volumes and heat capacities of alkylated pyrimidine nucleic acid bases, e.g. uracil, thymine and cytosine, were correlated with the following structural parameters: molecular volume, volume of solvation shell, accessible molecular surface area and its atomic partition as well as and electrostatic potential charge. The simp...

New advances in molecular dynamics and Monte Carlo simulations have led to impressive increases in the speed of sampling phase space for complex biological systems. These methods have been combined with new fast algorithms for computing long range electrostatic interactions for new polarizable force fields. In addition, new methods for sampling low energy molecular conformations allow the rapid...

This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computationa...

Fluorescein-PE is a fluorescence probe that is used as a membrane label or a sensor of surface associated processes. Fluorescein-PE fluorescence intensity depends not only on bulk pH, but also on the local electrostatic potential, which affects the local membrane interface proton concentration. The pH sensitivity and hydrophilic character of the fluorescein moiety was used to detect conformatio...

The thermodynamic potential for fixed charges in dielectric continua is given for arbitrary values of the polarization density. Minimization of the functional gives the equilibrium polarization density ~equivalently image charges! and the electrostatic potential throughout the media. The functional, which in general involves volume integrals, for the case of piecewise uniform dielectrica is red...