The molecular origin of the action of helicases is explored, starting with a model built based on the different X-ray structures of the large tumor antigen (LTag) hexameric helicase and a simplified model containing the ionized phosphate backbones of a single-strand DNA. The coupling between the protein structural changes and the translocation process is quantified using an effective electrosta...

The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity se...

We have coupled hybrid quantum mechanics (density functional theory; Car-Parrinello)/molecular mechanics molecular dynamics simulations to a grand-canonical scheme, to calculate the in situ redox potential of the Cu(2+) + e(-) --> Cu(+) half reaction in azurin from Pseudomonas aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and finite...

The experimentally observed high surface conductivity of hydrogenated diamond films is explained through ab initio results as well as model calculations based on the tight-binding molecular dynamics method. Our results support the previously reported experimental results indicating that the surface conductivity of the hydrogenated diamond surfaces is due to the surface adsorption of a H(3)O(+) ...

The anti-oxidant activities for a diverse set of flavonoids as TEAC (Trolox equivalent anti-oxidant capacity), assay were subjected to 3D-QSAR (3 dimensional quantitative structural-activity relationship) studies using CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis). The obtained results indicated superiority of CoMSIA model over CoMFA...

Seamless integration of artificial components with biological systems to form an elegant biotic-abiotic interface or smart surface has promising application potential in biomedical engineering. The specific aim of this study is to implement the actuation and modulation of binding behavior between biomolecules under electrostatic stimuli, and investigate the corresponding force interaction betwe...

We present a methodology to develop coarse-grained lipid models such that electrostatic interactions between the coarse-grained sites can be derived accurately from an all-atom molecular dynamics trajectory and expressed as an effective pairwise electrostatic potential with appropriate screening functions. The reference nonbonded forces from the all-atom trajectory are decomposed into separate ...

Pronounced improvements in the understanding of semiconductor device performance are expected if electrostatic potential distributions can be measured quantitatively and reliably under working conditions with sufficient sensitivity and spatial resolution. Here, we employ off-axis electron holography to characterize an electrically-biased Si p-n junction by measuring its electrostatic potential,...

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessib...