Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases
about
A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription ElongationA new paradigm of DNA synthesis: three-metal-ion catalysis.Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Adenosine-5′ Tetraphosphate: Evidence for Distributed Use of Catalytic Binding Energy in Amino Acid Activation by Class I Aminoacyl-tRNA SynthetasesMismatched dNTP incorporation by DNA polymerase does not proceed via globally different conformational pathwaysThe structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism.Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA PolymeraseAt the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?Perspective: Defining and quantifying the role of dynamics in enzyme catalysisOn possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactionsA water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.DNA polymerase fidelity: comparing direct competition of right and wrong dNTP substrates with steady state and pre-steady state kineticsPreferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion.DNA duplex stability: the role of preorganized electrostatics.Conformational dependence of a protein kinase phosphate transfer reaction.Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus.Energy analysis of chemistry for correct insertion by DNA polymerase beta.Prechemistry versus preorganization in DNA replication fidelity.Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects.An abridged transition state model to derive structure, dynamics, and energy components of DNA polymerase β fidelity.Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta.Exploring the role of large conformational changes in the fidelity of DNA polymerase betaThe associative nature of adenylyl transfer catalyzed by T4 DNA ligase.Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies.The empirical valence bond as an effective strategy for computer-aided enzyme design.Steric and electrostatic effects at the C2 atom substituent influence replication and miscoding of the DNA deamination product deoxyxanthosine and analogs by DNA polymerases.Transition state in DNA polymerase β catalysis: rate-limiting chemistry altered by base-pair configuration.Basic mechanism of transcription by RNA polymerase II.Why nature really chose phosphate.Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization.The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase.Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading.Kinetics and thermodynamics of exonuclease-deficient DNA polymerases.A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases.Proton transfer in the mechanism of polyadenylate polymerase.Nucleic acid polymerases use a general acid for nucleotidyl transfer.C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation.Mismatched and matched dNTP incorporation by DNA polymerase beta proceed via analogous kinetic pathways.Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis.Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ.
P2860
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P2860
Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases
description
2005 nî lūn-bûn
@nan
2005 թուականի Ապրիլին հրատարակուած գիտական յօդուած
@hyw
2005 թվականի ապրիլին հրատարակված գիտական հոդված
@hy
2005年の論文
@ja
2005年論文
@yue
2005年論文
@zh-hant
2005年論文
@zh-hk
2005年論文
@zh-mo
2005年論文
@zh-tw
2005年论文
@wuu
name
Computer simulations of protei ...... on fidelity of DNA polymerases
@ast
Computer simulations of protei ...... on fidelity of DNA polymerases
@en
type
label
Computer simulations of protei ...... on fidelity of DNA polymerases
@ast
Computer simulations of protei ...... on fidelity of DNA polymerases
@en
prefLabel
Computer simulations of protei ...... on fidelity of DNA polymerases
@ast
Computer simulations of protei ...... on fidelity of DNA polymerases
@en
P2860
P356
P1476
Computer simulations of protei ...... on fidelity of DNA polymerases
@en
P2093
Jan Florián
Myron F Goodman
P2860
P304
P356
10.1073/PNAS.0408173102
P407
P577
2005-04-29T00:00:00Z