J. H. Zhang

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We performed 45 ns atomistic force field based molecular dynamics (MD) simulations to explore the structure and dynamics of the Kvl.2 voltage-dependent potassium ion channel in both open and closed state conformations. The Kv1.2 crystal structure (PDB 2A79) based open state model and homologically derived closed state model are embedded in a hydrated lipid(More)
Energy-coupling factor (ECF) transporters are responsible for uptake of micronutrients in prokaryotes. The recently reported crystal structure of an ECF transporter RibU provided a foundation for understanding the structure and transport mechanism of ECF transporters. In the present study, molecular dynamics (MD) was carried out to study the conformational(More)
We report full ab initio Hartree-Fock calculation to compute quantum mechanical interaction energies for beta-trypsin/benzamidine binding complex. In this study, the full quantum mechanical ab initio energy calculation for the entire protein complex with 3238 atoms is made possible by using a recently developed MFCC (molecular fractionation with conjugate(More)
Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully(More)
Conspectus The desire to study molecular systems that are much larger than what the current state-of-the-art ab initio or density functional theory methods could handle has naturally led to the development of novel approximate methods, including semiempirical approaches, reduced-scaling methods, and fragmentation methods. The major computational limitation(More)
An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y.(More)
We present a computational study of a recently developed molecular fractionation with conjugated caps (MFCC) method for application to peptide/protein that has disulfide bonds. Specifically, we employ the MFCC approach to generate peptide fragments in which a disulfide bond is cut and a pair of conjugated caps are inserted. The method is tested on two(More)
We studied the effect of herbicide and nitrogen supply on photosynthesis in Perilla frutescens L. Britt. Plants were exposed to combined treatment of urea and herbicide, fenoxaprop-P-ethyl (FPE), in various concentrations. FPE reduced significantly chlorophyll (Chl) content, photosynthetic rate, and stomatal conductance, but increased significantly(More)
An effective polarizable bond (EPB) model has been developed for computer simulation of proteins. In this partial polarizable approach, all polar groups of amino acids are treated as polarizable, and the relevant polarizable parameters were determined by fitting to quantum calculated electrostatic properties of these polar groups. Extensive numerical tests(More)