4.7 Article

Human Polβ Natural Polymorphic Variants G118V and R149I Affects Substate Binding and Catalysis

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Fluorescently labeled human apurinic/apyrimidinic endonuclease APE1 reveals effects of DNA polymerase β on the APE1-DNA interaction

Artemiy S. Bakman et al.

Summary: The base excision repair (BER) pathway involves a step-by-step process in which DNA glycosylases and AP endonucleases work together to repair damaged DNA. This study aimed to verify the passing-the-baton model of DNA intermediates transfer between enzymes by creating an experimental system. The findings of the study confirm that Pol beta plays a key role in coordinating the activities of APE1 and Pol beta in the initial steps of BER.

DNA REPAIR (2023)

Review Biochemistry & Molecular Biology

The Role of Natural Polymorphic Variants of DNA Polymerase β in DNA Repair

Olga A. Kladova et al.

Summary: This review summarizes the in silico prediction of the effects of Pol beta SNPs on DNA repair efficacy, available data on cancers associated with Pol beta SNPs, and experimentally tested variants of Pol beta. Amino acid substitutions in Pol beta can affect the maintenance of the enzyme's structure, interactions with DNA, catalytic activity, and the attachment of nucleotide triphosphate.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Chemistry, Physical

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

Mario S. Valdes-Tresanco et al.

Summary: gmx_MMPBSA is a new tool for performing end-state free energy calculations from GROMACS molecular dynamics trajectories, offering various options including binding free energy calculations with different solvation models, stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Additionally, promising methodologies for calculating relative binding free energies have been implemented.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Biochemistry & Molecular Biology

Lysines in the lyase active site of DNA polymerase β destabilize nonspecific DNA binding, facilitating searching and DNA gap recognition

Michael J. Howard et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2020)

Article Environmental Sciences

Loss of DNA polymerase induces cellular senescence

Aqila A. Ahmed et al.

ENVIRONMENTAL AND MOLECULAR MUTAGENESIS (2018)

Article Genetics & Heredity

Initiating base excision repair in chromatin

Erin E. Kennedy et al.

DNA REPAIR (2018)

Article Biochemistry & Molecular Biology

The nature of the DNA substrate influences pre-catalytic conformational changes of DNA polymerase

Ji Huang et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2018)

Article Oncology

DNA Polymerase Beta Germline Variant Confers Cellular Response to Cisplatin Therapy

Antonia A. Nemec et al.

MOLECULAR CANCER RESEARCH (2017)

Article Biochemistry & Molecular Biology

Modulating the DNA polymerase β reaction equilibrium to dissect the reverse reaction

David D. Shock et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Chemistry, Physical

Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model

Yang Jiang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Chemistry, Multidisciplinary

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy

Lili Duan et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)

Article Chemistry, Physical

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Marie Zgarbova et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Review Biotechnology & Applied Microbiology

Oxidatively induced DNA damage and its repair in cancer

Miral Dizdaroglu

MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH (2015)

Article Biochemistry & Molecular Biology

Structure and Mechanism of DNA Polymerase β

William A. Beard et al.

BIOCHEMISTRY (2014)

Article Biochemistry & Molecular Biology

Observing a DNA Polymerase Choose Right from Wrong

Bret D. Freudenthal et al.

Article Chemistry, Physical

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties

Christian L. Wennberg et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Cell Biology

Base Excision Repair

Hans E. Krokan et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2013)

Article Chemistry, Physical

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

Bill R. Miller et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Biochemistry & Molecular Biology

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

Zheng Yang et al.

JOURNAL OF STRUCTURAL BIOLOGY (2012)

Review Multidisciplinary Sciences

The DNA damage response and cancer therapy

Christopher J. Lord et al.

NATURE (2012)

Review Genetics & Heredity

Nucleotide excision repair: new tricks with old bricks

Irene Kamileri et al.

TRENDS IN GENETICS (2012)

Article Chemistry, Multidisciplinary

A Simple Spreadsheet Program To Simulate and Analyze the Far-UV Circular Dichroism Spectra of Proteins

Luciano A. Abriata

JOURNAL OF CHEMICAL EDUCATION (2011)

Article Oncology

A study of pyrimidine base damage in relation to oxidative stress and cancer

H. Iijima et al.

BRITISH JOURNAL OF CANCER (2009)

Article Biochemistry & Molecular Biology

The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding

Drew L. Murphy et al.

BIOCHEMISTRY (2008)

Article Biochemistry & Molecular Biology

The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient

Shibani Dalal et al.

NUCLEIC ACIDS RESEARCH (2008)

Review Multidisciplinary Sciences

Base-excision repair of oxidative DNA damage

Sheila S. David et al.

NATURE (2007)

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Biochemistry & Molecular Biology

Magnesium-induced assembly of a complete DNA polymerase catalytic complex

VK Batra et al.

STRUCTURE (2006)

Article Biochemistry & Molecular Biology

Base excision repair in nucleosome substrates

I Jagannathan et al.

CHROMOSOME RESEARCH (2006)

Article Biochemistry & Molecular Biology

Reduced DNA gap repair in aging rat neuronal extracts and its restoration by DNA polymerase β and DNA-ligase

TH Krishna et al.

JOURNAL OF NEUROCHEMISTRY (2005)

Article Oncology

DNA repair activity for oxidative damage and risk of lung cancer

T Paz-Elizur et al.

JOURNAL OF THE NATIONAL CANCER INSTITUTE (2003)

Article Chemistry, Multidisciplinary

Development of polyphosphate parameters for use with the AMBER force field

KL Meagher et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)

Review Biochemistry & Molecular Biology

Oxidative DNA damage: mechanisms, mutation, and disease

MS Cooke et al.

FASEB JOURNAL (2003)

Article Pharmacology & Pharmacy

Oxy radicals, lipid peroxidation and DNA damage

LJ Marnett

TOXICOLOGY (2002)

Article Biochemistry & Molecular Biology

Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase β

CA Dunlap et al.

BIOCHEMISTRY (2002)