DNA polymerase conformational dynamics and the role of fidelity-conferring residues: Insights from computational simulations

DNA polymerase conformational dynamics and the role of fidelity-conferring residues: Insights from computational simulations

Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a compreh...

Podrobná bibliografie
Hlavní autoři:	Meli, M, Sustarsic, M, Craggs, T, Kapanidis, A, Colombo, G
Médium:	Journal article
Jazyk:	English
Vydáno:	Frontiers Media 2016

Podobné jednotky

The rate-limiting step of DNA synthesis by DNA polymerase occurs in the fingers-closed conformation
Autor: Evans, GW, a další
Vydáno: (2021)

Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion.
Autor: Hohlbein, J, a další
Vydáno: (2013)

Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase
Autor: Craggs, T, a další
Vydáno: (2019)

In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA Polymerase I
Autor: Sustarsic, M
Vydáno: (2015)

Optimized Internalization of Fluorescently Labeled Biomolecules into Live Bacteria
Autor: Sustarsic, M, a další
Vydáno: (2014)

Conformational transitions in DNA polymerase I revealed by single-molecule FRET.
Autor: Santoso, Y, a další
Vydáno: (2010)

Fidelity of DNA polymerases in the detection of intraindividual variation of mitochondrial DNA
Autor: Paulo Cseri Ricardo, a další
Vydáno: (2020-01-01)

RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding
Autor: Mazumder, A, a další
Vydáno: (2021)

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: Implications for transcription start-site selection
Autor: Robb, N, a další
Vydáno: (2013)

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.
Autor: Robb, N, a další
Vydáno: (2013)

Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing
Autor: Zamft, Bradley Michael, a další
Vydáno: (2013)

Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing.
Autor: Bradley Michael Zamft, a další
Vydáno: (2012-01-01)

The architecture of RNA polymerase fidelity
Autor: Kaplan Craig D
Vydáno: (2010-06-01)

Biochemical analysis of DNA polymerase η fidelity in the presence of replication protein A.
Autor: Samuel C Suarez, a další
Vydáno: (2014-01-01)

Phosphorylation Induced Conformational Transitions in DNA Polymerase β
Autor: Amit Srivastava, a další
Vydáno: (2022-06-01)

A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control
Autor: Chunhong Long, a další
Vydáno: (2019-01-01)

High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
Autor: de Paz, Alexandra M, a další
Vydáno: (2021)

High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
Autor: de Paz, Alexandra M, a další
Vydáno: (2022)

DNA polymerase theta purified from human cells is a high-fidelity enzyme.
Autor: Maga, G, a další
Vydáno: (2002)

Fidelity of a Bacterial DNA Polymerase in Microgravity, a Model for Human Health in Space
Autor: Aaron H Rosenstein, a další
Vydáno: (2021-11-01)

DNA Polymerase: Structural Homology, Conformational Dynamics, and the Effects of Carcinogenic DNA Adducts
Autor: Richard G. Federley, a další
Vydáno: (2010-01-01)

Six steps closer to FRET-driven structural biology.
Autor: Craggs, T, a další
Vydáno: (2012)

Kinetic Approaches to Understanding the Mechanisms of Fidelity of the Herpes Simplex Virus Type 1 DNA Polymerase
Autor: Yali Zhu, a další
Vydáno: (2010-01-01)

The effect of different divalent cations on the kinetics and fidelity of <em>Bacillus stearothermophilus</em> DNA polymerase
Autor: Ashwani Kumar Vashishtha, a další
Vydáno: (2018-04-01)

A simple method for in-house Pfu DNA polymerase purification for high-fidelity PCR amplification
Autor: Prabu Siva Sankar, a další
Vydáno: (2019-05-01)

Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity
Autor: Vasileios Paschalis, a další
Vydáno: (2017-01-01)

A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.
Autor: Agata Jacewicz, a další
Vydáno: (2013-01-01)

Real-time single-molecule observations of conformational changes in DNA polymerase
Autor: Evans, GW
Vydáno: (2013)

Observational Study of Conformity in Yet Another Medical Learning Environment: Conformity to Preceptors During High-Fidelity Simulation
Autor: Beran TN, a další
Vydáno: (2023-12-01)

Effect of a Monofunctional Phenanthriplatin-DNA Adduct on RNA Polymerase II Transcriptional Fidelity and Translesion Synthesis
Autor: Kellinger, Matthew W., a další
Vydáno: (2014)

Correction to ‘Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity’
Autor: Vasileios Paschalis, a další
Vydáno: (2017-01-01)

New in vitro dna polymerase activity and fidelity assay reveals age-dependent changes in Arabidopsis Thaliana
Autor: Andrey Golubov, a další
Vydáno: (2011-06-01)

Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path
Autor: Thomas Dodd, a další
Vydáno: (2020-10-01)

Comparative analysis of T4 DNA ligases and DNA polymerases used in chromosome conformation capture assays
Autor: Michal Schwartz, a další
Vydáno: (2015-04-01)

Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism.
Autor: Kapanidis, A, a další
Vydáno: (2006)

Global conformational dynamics of a Y-family DNA polymerase during catalysis.
Autor: Cuiling Xu, a další
Vydáno: (2009-10-01)

Efficient fidelity control by stepwise nucleotide selection in polymerase elongation Abstract: Polymerases select nucleotides
Autor: Yu Jin
Vydáno: (2014-01-01)

High-Fidelity In Vitro Recombination Using a Proofreading Polymerase
Autor: Milena Ninkovic, a další
Vydáno: (2001-03-01)

Biochemical characterization of the fidelity of poliovirus RNA-dependent RNA polymerase
Autor: Vaccaro Joseph A, a další
Vydáno: (2007-05-01)

PFU DNA polymerase--a study of amplification error rate and subsequent impliations for high fidelity mutational spectrometry
Autor: Buzzee, Sheila Gay
Vydáno: (2007)