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Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free-Energy Simulation Methods

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CCS Chemistry 2021年第2期3卷 1026-1039页

作者： zhaoxi Sun john z.h.zhang State Key Laboratory of Precision Spectroscopy School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai 200062 NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 Department of Chemistry New York UniversityNYNY 10003

Threofuranosyl nucleic acid(TNA)is an analogue of DNA with a shift in the internucleotide linkages from the wild-type 5’-to-3’direction to 3’-to-2.’This alteration leads to higher chemical stability,less reactive groups,and lower conformational *** observations indicate that these characteristic changes are attributable to a minimal perturbation of the interaction network,but the thermodynamic stability of the duplex remains unaltered in the TNA *** applied the equilibrium and nonequilibrium free-energy simulations employing three popular assisted model building with energy refinement(AMBER)force fields for nucleotides to investigate this mutation-dependent behavior in the base flipping from T(DNA)residue to the T-to-TFT mutation(TNA)*** force fields were performed similarly,as described in the base-paired ***,after exploring the high-energy regions with free-energy simulations,we observed that these three force fields behaved *** reports conclude that the net-neutral and excess-salt simulations provided similar ***,our free-energy simulation indicated that the presence of excess salt affected the thermodynamic *** free-energy barrier along the base-flipping pathway was generally elevated upon the addition of excess salts,but the relative height of the free-energy barriers in DNA and TNA duplexes did not change *** phenomenon emphasizes the importance of adding sufficient salts in the simulation scheme to reproduce the experimental condition.

关键词： free-energy simulation base flipping,TNA AMBER force fields salt concentration

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Three-dimensional quantum dynamics study of vibrational predissociation of heI_2 van der Waals molecule for low vibrational excitation using the time-dependent wave packet method

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Science China Chemistry 1997年第4期40卷 442-448页

作者：关大任赵显邓从豪 john z.h.zhang Institute of Theoretical Chemistry Shandong UniversityJinan 250100China Department of Chemistry New York UniversityNew YorkNY 10003USA

Three-dimensional quantum mechanical calculations for vibrational predissociation of heI2(B) van der Waals molecules are presented using the time-dependent wave packet technique within the golden rule approxima *** total and partial decay widths,lifetimes,rates and their dependence on initial vibrational states were obtained for heI2 at low initial vibrational excited *** calculations show that the calculated tota decay widths,lifetimes and rates agree well with those extrapolated from experimental data available The predicted total decay widths as a function of initial vibrational states exhibit highly nonlinear *** very short propagation time (*** 1 ps) required in the golden rule wave packet calculation is determined by the duration time of the final state inter-action between the fragments on the vibrationally deexcited adiabatic potential *** final state interaction between the fragments is shown to play an important role in determining the final rotational distribution This interpreta tion clearly explains the dynamical effect that the final rotational distribution shifts to the lower rotational energy levels as the initial vibrational quantum number v increases.

关键词： time-dependent golden rule wave packet approach vibrational predissociation heI2 van der Waats molecule decay widths final rotational distribution

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Interaction Entropy and Quantitative Analysis of Protein-Protein Interaction

Interaction Entropy and Quantitative Analysis of Protein-Pro...

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第十三届全国量子化学会议

作者： john z.h.zhang School of Chemistry and Molecular Engineering East China Normal University NYU-ECNU Center for Computational Chemistry at New York University Shanghai Department of Chemistry New York University

＜正＞The theoretical calculation of protein-protein binding free energy is a grand challenge in computational biology. Accurate prediction of critical residues along with their specific and quantitative contributions to protein-protein binding free energy is extremely helpful to reveal binding mechanisms and identify druglike molecules that alter protein-protein interactions. In this talk we develop an efficient Interaction

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Force Field Development and Fragment based Ab Initio Molecular Dynamic Simulation for MetalloProteins

Force Field Development and Fragment based Ab Initio Molecul...

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第十五届全国化学动力学会议

作者：朱通 john z.h.zhang College of Chemistry and Molecular Engineering East China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai Department of Chemistry New York University

＜正＞A polarizable-charge transfer force field（QPCT）has been proposed to accurately describe the interaction dynamics of zinc–protein *** parameters of the QPCT force field were calibrated by quantum chemistry calculation and can capture the polarization and charge transfer *** are validated by molecular dynamic simulation of the hydration shell of the zinc ion,five proteins containing the most common zinc-binding sites,as

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Force Field Development and Quantum Fragment based Ab Initio Molecular Dynamics for MetalloProtein

Force Field Development and Quantum Fragment based Ab Initio...

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中国化学会第30届学术年会-第十九分会：化学中的量子与经典动力学

作者： Tong zhu john z.h.zhang Department of Physics East China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai Department of Chemistry New York University

A polarizable-charge transfer force field(QPCT) has been proposed to accurately describe the interaction dynamics of zinc–protein *** parameters of the QPCT force field were calibrated by quantum chemistry calculatio...

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The QM/MM Simulations of Specific Vibrations of GTP in Ras Protein

The QM/MM Simulations of Specific Vibrations of GTP in Ras P...

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中国化学会第十二届全国量子化学会议

作者： Fei Xia john z.h.zhang Department of Chemistry East China Normal University (ECNU) State Key Laboratory of Precision Spectroscopy and Department of Physics ECNU

The guanine nucleotide-binding proteins are responsible for various cellular processes in eukaryotic cells,including heterotrimeric G-proteins and members of Ras-related *** Ras protein has the catalytic activity of hydrolyzing the guanosine triphosphate（GTP）to guanosine diphosphate（GDP）,which is called the *** cycling of hydrolysis of GTP and GDP in Ras plays an important role in the signal processes involved in cell.A malfunction of Ras protein can lead to uncontrolled cell proliferation,which eventually causes *** take insight in the function of Ras family in controlling signal processes,an elaborate investigation of the hydrolysis mechanism of GTP in Ras protein needs to be performed at the atomic level with a combination of experimental and theoretical ***,a big amount of experimental data associated with the specific vibrations of P-O bonds in GTP measured from Fourier-transformed infrared spectroscopy（FTIR）is available,which provide the experimental implications of hydrolysis mechanism of *** therefore used QM/MM simulations to calculate the spectra and the normal vibrational modes GTP in various environments such as the aqueous solution,Ras and Ras GAP *** simulation results show the GTPs adopt distinctive structural conformations and coordination patterns with Mg2+cations in different *** calculated specific vibrational frequencies of bonds in GTP are in good agreement with the experimentally measured difference spectra,providing a very good validation of conformations obtained by the *** the first time,we suggest band assignments of the vibrational modes of GTP in Ras below800cm-1 by comparison of calculated and experimental spectra.

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Functional Loop dynamics of S-component in ECF transporter

Functional Loop dynamics of S-component in ECF transporter

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第十三届全国量子化学会议

作者： Linqiong Qiu Jianing Song john z.h.zhang School of Chemistry and Molecular Engineering East China Normal University State Key Laboratory of Precision Spectroscopy East China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai Department of Chemistry New York University Collaborative Innovation Center of Extreme Optics Shanxi University

ECF transporters are responsible for many micronutrients uptake in organisms. S component FolT of ECF transporter is recently crystallized and provides solid basis to study the micronutrients binding mechanism. In this work, Molecular Dynamics(MD) simulations are applied to study the dynamic difference of loops in floate-bound and floate-free state of FolT. Further, MD-RAMD(Random accelerate molecular dynamics) simulations and SMD simulations are used to enhance the sampling of conformational transitions of loops. The results show that loops play important role and are cooperated with each other in ligand binding process(Loop1, Loop3 and Loop5). Although the three loops are quite important in folate binding, Loop1 is supposed to be the gate controlling the folate binding, based on our dynamics analysis and static state analysis of open/closed XRD structures of FloT, which agrees well with the experimental data.

关键词： ECF transporter MD folate transporter functional loop gate loop

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Molecular dynamics simulation of protein crystal with polarized protein-specific force field

Molecular dynamics simulation of protein crystal with polari...

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中国化学会第十二届全国量子化学会议

作者： Yongxiu Li john z.h.zhang Ye Mei State Key Laboratory of Precision Spectroscopy Department of Physics and Institute of Theoretical and Computational ScienceEast China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai

The explicitly polarized force field model is indispensable in the simulation of protein crystal due to its particular electrostatic environment which is different from that in water *** polarized protein-specific charge（PPC）has shown important priorities for the study of protein-ligand binding and protein ***,the applicability of PPC in the simulation of protein crystal is yet to be *** 250 ns molecular simulations were carried out to study the structure and dynamics of crystal toxin protein Ⅱ from the scorpion Androctonus australis hector employing PPC as well as the standard AMBER99SB force field to investigate the effect of electrostatic polarization on the crystal *** simulation results showed that under PPC,the monomer in the subunit cell and the lattice in the supercell were more stable with much smaller RMSDs and the lattice atomic fluctuations were also better in line with the crystallographic *** of the interactions at interfaces in the X-ray structure were well preserved,underscoring the important effect of polarization on maintaining the crystal ***,our results also showed that the hydrogen bond between Asp53 and Gln37 and the cation-лinteraction between Arg56 and his64 were not as stable,indicating that further optimization of force field with van der Waals interaction parameters is desired.

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Fragment Quantum Mechanical Calculation of large systems and Its Applications

Fragment Quantum Mechanical Calculation of large systems and...

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中国化学会第30届学术年会-第十八分会：电子结构理论方法的发展与应用

作者： Xiao he Jinfeng Liu Tong zhu john z.h.zhang Department of Physics and State Key Laboratory of Precision Spectroscopy East China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai

The major computational limitation of conventional ab initio methods is the scaling problem,because the cost of ab initio calculation scales as nth power or worse with the system *** desire to study such large molecular systems has naturally led to the development of novel approximate methods,including semiempirical approaches,the hybrid quantum mechanical/molecular mechanical(QM/MM)methods,linear-scaling methods,and fragmentation *** the past two decades,the fragmentation method has opened a new door for the development of QM methods and their applications to large *** this talk,I will describe molecular fractionation with conjugate caps(MFCC)based methods with applications to biomolecular *** MFCC approach was initially developed for calculating QM proteinligand interaction energies and can also be used to calculate the full electron density and total energy of protein based on density functional theory(DFT).Recently,we developed the electrostatically embedded generalized molecular fractionation with conjugate caps(EE-GMFCC)method on top of the MFCC *** introducing the electrostatic embedding field for each fragment calculation and reducing the computational cost for long-range two-body QM interactions,the EE-GMFCC method is capable of accurately reproducing the molecular properties(such as dipole moment,electron density,and electrostatic potential),the total energy,and electrostatic solvation energy from full system QM calculations for *** EE-GMFCC method has been applied for protein structure optimization,vibrational spectrum calculation,protein-ligand binding affinity prediction and ab initio molecular dynamics simulation of proteins.

关键词： Quantum chemistry Fragmentation method linear-scaling EE-GMFCC Protein energy

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Interaction Entropy for protein-ligand hot spot predicition

Interaction Entropy for protein-ligand hot spot predicition

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第十三届全国量子化学会议

作者： Xiao Liu Yu N.Yan john z.h.zhang State Key Laboratory for Precision Spectroscopy School of Chemistry and Molecular EngineeringEast China Normal University Department of Chemistry New York University

The theoretical calculation of protein-ligand binding free energy is a grand challenge in computational *** prediction of critical residues along with their specific and quantitative contributions to protein-ligand binding free energy is extremely helpful to reveal binding mechanisms and identify drug-like molecules that alter protein-ligand *** this paper,we propose an interaction entropy approach combined with the MM/GBSA method for solvation to compute residue-specific protein-ligand binding free *** the current approach,the entropic loss in binding free energy of individual residues is explicitly computed from MD simulation by using the interaction entropy *** this approach the entropic contribution to binding free energy is determined from fluctuation of the interaction in MD *** for an extensive set of ALK protein-ligand interaction systems showed that by including the entropic contribution,we can clearly find the hot spot residues,it is helpful for new drug design.

关键词： interaction entropy hot spot protein-ligand

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