Journal ArticleDOI
Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions Per Se
TLDR
These studies bridge static microscopic crystal structures with macroscopic kinetic data by delineating a specific sequence and suggest new lines of experimentation in the study of polymerase mechanisms, which should provide further insights into mechanisms of error discrimination and DNA synthesis fidelity.About:
This article is published in Journal of Molecular Biology.The article was published on 2002-04-12. It has received 92 citations till now. The article focuses on the topics: DNA polymerase & Polymerase.read more
Citations
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Journal ArticleDOI
DNA Replication Fidelity
TL;DR: Current understanding of replication fidelity is reviewed, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity.
Journal ArticleDOI
Structure and Mechanism of DNA Polymerase β
TL;DR: In this review, recent crystallographic studies of pol β in various liganded and conformational states during the insertion of right and wrong nucleotides as well as during the bypass of damaged DNA are described.
Journal ArticleDOI
DNA polymerase fidelity: kinetics, structure, and checkpoints.
TL;DR: Some polymerases apparently show more discrimination between correctly paired and mispaired dNTPs in the binding step, and polymerases may differ in terms of which step of the reaction is rate-limiting in correct and incorrect insertion reactions.
Book ChapterDOI
Structure and mechanism of DNA polymerases.
Paul J. Rothwell,Gabriel Waksman +1 more
TL;DR: This review presents and discusses the kinetic, structural, and single-molecule works that have contributed to the understanding of DNA polymerase function.
Journal ArticleDOI
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Vinod K. Batra,William A. Beard,David D. Shock,Joseph M. Krahn,Lars C. Pedersen,Samuel H. Wilson +5 more
TL;DR: A crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Book
Principles of Nucleic Acid Structure
TL;DR: The goal of this series is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields.
Journal ArticleDOI
Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation.
C. Altona,M. Sundaralingam +1 more
Journal ArticleDOI
Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.
TL;DR: A combinatorial disulfide cross-linking strategy was used to prepare a stalled complex of human immunodeficiency virus-type 1 (HIV-1) reverse transcriptase with a DNA template:primer and a deoxynucleoside triphosphate (dNTP), and the crystal structure of the complex was determined at a resolution of 3.2 angstroms.