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...

Бүрэн тодорхойлолт

Номзүйн дэлгэрэнгүй
Үндсэн зохиолчид:	Meli, M, Sustarsic, M, Craggs, T, Kapanidis, A, Colombo, G
Формат:	Journal article
Хэл сонгох:	English
Хэвлэсэн:	Frontiers Media 2016

Ижил төстэй зүйлс

The rate-limiting step of DNA synthesis by DNA polymerase occurs in the fingers-closed conformation
-н: Evans, GW, зэрэг
Хэвлэсэн: (2021)

Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion.
-н: Hohlbein, J, зэрэг
Хэвлэсэн: (2013)

Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase
-н: Craggs, T, зэрэг
Хэвлэсэн: (2019)

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

Optimized Internalization of Fluorescently Labeled Biomolecules into Live Bacteria
-н: Sustarsic, M, зэрэг
Хэвлэсэн: (2014)

Conformational transitions in DNA polymerase I revealed by single-molecule FRET.
-н: Santoso, Y, зэрэг
Хэвлэсэн: (2010)

Fidelity of DNA polymerases in the detection of intraindividual variation of mitochondrial DNA
-н: Paulo Cseri Ricardo, зэрэг
Хэвлэсэн: (2020-01-01)

RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding
-н: Mazumder, A, зэрэг
Хэвлэсэн: (2021)

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

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

Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing
-н: Zamft, Bradley Michael, зэрэг
Хэвлэсэн: (2013)

Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing.
-н: Bradley Michael Zamft, зэрэг
Хэвлэсэн: (2012-01-01)

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

Biochemical analysis of DNA polymerase η fidelity in the presence of replication protein A.
-н: Samuel C Suarez, зэрэг
Хэвлэсэн: (2014-01-01)

Phosphorylation Induced Conformational Transitions in DNA Polymerase β
-н: Amit Srivastava, зэрэг
Хэвлэсэн: (2022-06-01)

A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control
-н: Chunhong Long, зэрэг
Хэвлэсэн: (2019-01-01)

High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
-н: de Paz, Alexandra M, зэрэг
Хэвлэсэн: (2021)

High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
-н: de Paz, Alexandra M, зэрэг
Хэвлэсэн: (2022)

DNA polymerase theta purified from human cells is a high-fidelity enzyme.
-н: Maga, G, зэрэг
Хэвлэсэн: (2002)

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

DNA Polymerase: Structural Homology, Conformational Dynamics, and the Effects of Carcinogenic DNA Adducts
-н: Richard G. Federley, зэрэг
Хэвлэсэн: (2010-01-01)

Six steps closer to FRET-driven structural biology.
-н: Craggs, T, зэрэг
Хэвлэсэн: (2012)

Kinetic Approaches to Understanding the Mechanisms of Fidelity of the Herpes Simplex Virus Type 1 DNA Polymerase
-н: Yali Zhu, зэрэг
Хэвлэсэн: (2010-01-01)

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

A simple method for in-house Pfu DNA polymerase purification for high-fidelity PCR amplification
-н: Prabu Siva Sankar, зэрэг
Хэвлэсэн: (2019-05-01)

Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity
-н: Vasileios Paschalis, зэрэг
Хэвлэсэн: (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.
-н: Agata Jacewicz, зэрэг
Хэвлэсэн: (2013-01-01)

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

Observational Study of Conformity in Yet Another Medical Learning Environment: Conformity to Preceptors During High-Fidelity Simulation
-н: Beran TN, зэрэг
Хэвлэсэн: (2023-12-01)

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

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

New in vitro dna polymerase activity and fidelity assay reveals age-dependent changes in Arabidopsis Thaliana
-н: Andrey Golubov, зэрэг
Хэвлэсэн: (2011-06-01)

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

Comparative analysis of T4 DNA ligases and DNA polymerases used in chromosome conformation capture assays
-н: Michal Schwartz, зэрэг
Хэвлэсэн: (2015-04-01)

Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism.
-н: Kapanidis, A, зэрэг
Хэвлэсэн: (2006)

Global conformational dynamics of a Y-family DNA polymerase during catalysis.
-н: Cuiling Xu, зэрэг
Хэвлэсэн: (2009-10-01)

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

High-Fidelity In Vitro Recombination Using a Proofreading Polymerase
-н: Milena Ninkovic, зэрэг
Хэвлэсэн: (2001-03-01)

Biochemical characterization of the fidelity of poliovirus RNA-dependent RNA polymerase
-н: Vaccaro Joseph A, зэрэг
Хэвлэсэн: (2007-05-01)

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