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Structure of cis-[Pt(NH_(3))(2-picoline)]^(2+)and DNA adduct and its bonding characteristics

Science china chemistry 2004年第1期47卷 67-74页

作者： jia muxin, liu kai, yang zuoyin & chen guangjudepartment of chemistry, beijing normal university, beijing 100875, china beijing General Research Institute of Mining and Metullargy, beijing 100044, china 1. Department of chemistry Beijing Normal University 100875 Beijing China 2. beijing General Research Institute of Mining and Metullargy 100044 Beijing China

Several methods including molecular mechanics, molecular dynamics, ONIOM that combines quantum chemistry with molecular mechanics and standard quantum chemistry are used to study the configuration and electron structures of an adduct of the DNA segment d(ATACATG*G*TACATA)·d(TATGTACCATGTAT) with cis-[Pt(NH3)(2-Picoline)]2+. The investigation shows that the configuration optimized by ONIOM is similar to that determined by NMR. Strong chemical bonds between Pt of the complex and two N7s of neighboring guanines in the DNA duplex and hydrogen bond between the NH3 of the complex and O6 of a nearby guanine have a large impact on the configuration of the adduct. Chemical bonds, the aforementioned hydrogen bond, and the interaction between a methyl of the complex and a methyl of the base in close proximity are critical for the complex to specifically recognize DNA.

关键词： cis-[PtCl2(NH3)(2-Pic)], DNA segment, ONIOM, molecular mechanics, molecular dynamics.

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Molecular and quantum mechanical studies on the monomer recognition of a highly-regular β-helical antifreeze protein

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Science china chemistry 2004年第1期47卷 34-40页

作者： yang zuoyin, jia Zongchao, liu Ruozhuang & chen guangjudepartment of chemistry, beijing normal university, beijing 100875, china Faculty of Science, beijing university of Chemical Technology, beijing 100029, china Department of Biochemistry, Queen’s university, Kingston, Ontario K7L 3N6, Canada 1. Department of chemistry Beijing Normal University 100875 Beijing China 2. Faculty of Science Beijing University of Chemical Technology 100029 Beijing China 3. Department of Biochemistry Queen? University K7L 3N6 Kingston Ontario Canada

The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomer? β-sheets would be involved in interaction area and the side chains on two p-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the twoβ-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two TCTs mainly depends on inter-molecular hydroxyls. Therefore, our results demonstrate that during the course of interaction the most favorable association of TmAFPs is via their β-sheets.

关键词： antifreeze protein, recognition, dynamics simulation, molecular mechanics, quantum chemistry.

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Molecular basis for antifreeze activity difference of two insect antifreeze protein isoforms

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Science china chemistry 2007年第2期50卷 266-271页

作者： ZHOU YanXia TAN HongWei yang zuoyin jia ZongChao liu RuoZhuang chen GuangJu Department of chemistry Beijing Normal UniversityBeijing 100875China Faculty of Science Beijing University of Chemical TechnologyBeijing 100029China Department of Biochemistry Queen’s UniversityKingstonOntarioK7L3N6Canada

The insect spruce budworm(Choristoneura fumiferana) produces antifreeze protein(AFP) to assist in the protection of the over-wintering larval stage and contains multiple isoforms. Structures for two isoforms,known as CfAFP-501 and CfAFP-337,show that both possess similar left-handed β-helical structure,although thermal hysteresis activity of the longer isoform CfAFP-501 is three times that of CfAFP-337. The markedly enhanced activity of CfAFP-501 is not proportional to,and cannot be simply accounted for,by the increased ice-binding site resulting from the two extra coils in CfAFP-501. In or-der to investigate the molecular basis for the activity difference and gain better understanding of AFPs in general,we have employed several different computational methods to systematically study the structural properties and ice interactions of the AFPs and their deletion models. In the context of intact AFPs,a majority of the coils in CfAFP-501 has better ice interaction and causes stronger ice lattice disruption than CfAFP-337,strongly suggesting a cooperative or synergistic effect among β-helical coils. The synergistic effect would play a critical role and make significant contributions to the anti-freeze activity β-helical antifreeze proteins. This is the first time that synergistic effect and its implica-tion for antifreeze activity are reported for β-helical antifreeze proteins.

关键词： insect antifreeze protein synergistic effect antifreeze activity β-helix quantum chemistry molecular mechanics molecular dynamics

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