Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation.

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Journal of Molecular Biology

• Publication date

  2008-12-31

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1016/j.jmb.2008.10.025PMID 18955064PMCID PMC2644343
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

  2020cited by this paper
• Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus

  2008cited by this paper
• Gates

  2008cited by this paper
• DNA Polymerase β Catalysis: Are Different Mechanisms Possible?

  2007cited by this paper
• Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.

  2007cited by this paper
• Protein structure prediction by all-atom free-energy refinement

  2007cited by this paper
• Interactions of the DNA polymerase X of African swine fever virus with double-stranded DNA. Functional structure of the complex.

  2007cited by this paper
• Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides

  2007cited by this paper
• Use of damaged DNA and dNTP substrates by the error-prone DNA polymerase X from African swine fever virus.

  2007cited by this paper
• Solution structures of 2 : 1 and 1 : 1 DNA polymerase–DNA complexes probed by ultracentrifugation and small-angle X-ray scattering

  2007cited by this paper
• A unified kinetic mechanism applicable to multiple DNA polymerases.

  2007cited by this paper
• Optimization Methods in Computational Chemistry

  2007cited by this paper
• DNA polymerase beta catalysis: are different mechanisms possible?

  2007cited by this paper
• Exploring the role of large conformational changes in the fidelity of DNA polymerase β

  2007cited by this paper
• Structure of purine-purine mispairs during misincorporation and extension by Escherichia coli DNA polymerase I.

  2006cited by this paper
• In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism.

  2006cited by this paper
• Contributions of an endonuclease IV homologue to DNA repair in the African swine fever virus.

  2006cited by this paper
• DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex.

  2006cited by this paper
• Remarkable sensitivity to DNA base shape in the DNA polymerase active site.

  2006cited by this paper
• Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.

  2006cited by this paper
• African Swine Fever Virus Protein pE296R Is a DNA Repair Apurinic/Apyrimidinic Endonuclease Required for Virus Growth in Swine Macrophages

  2006cited by this paper
• Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair.

  2005cited by this paper
• Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.

  2005cited by this paper
• Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity.

  2005cited by this paper
• Scalable molecular dynamics with NAMD

  2005cited by this paper
• Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase α

  2005cited by this paper
• An error-prone viral DNA ligase.

  2005cited by this paper
• Efficient and High Fidelity Incorporation of dCTP Opposite 7,8-Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4*

  2005cited by this paper
• Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly.

  2004cited by this paper
• Structural basis for the dual coding potential of 8‐oxoguanosine by a high‐fidelity DNA polymerase

  2004cited by this paper
• Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates.

  2004cited by this paper
• Substrate-induced conformational changes 1 In Silico Evidence for DNA Polymerase � ’ s Substrate – Induced Conformational Change

  2004cited by this paper
• Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing

  2004cited by this paper
• Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing.

  2004cited by this paper
• African swine fever virus proteins involved in evading host defence systems.

  2004cited by this paper
• Structures of mismatch replication errors observed in a DNA polymerase.

  2004cited by this paper
• Structural insights into the origins of DNA polymerase fidelity.

  2003cited by this paper
• DNA polymerase X of African swine fever virus: insertion fidelity on gapped DNA substrates and AP lyase activity support a role in base excision repair of viral DNA.

  2003cited by this paper
• CHARMM: The Energy Function and Its Parameterization

  2002cited by this paper
• Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus.

  2002cited by this paper
• Lesion bypass activities of human DNA polymerase mu.

  2002cited by this paper
• Swine fever: classical swine fever and African swine fever.

  2002cited by this paper
• Role of human DNA polymerase kappa as an extender in translesion synthesis.

  2002cited by this paper
• Efficiency of Correct Nucleotide Insertion Governs DNA Polymerase Fidelity*

  2002cited by this paper
• Inhibition of reverse transcription in vivo by elevated manganese ion concentration.

  2002cited by this paper
• Lesion Bypass Activities of Human DNA Polymerase μ*

  2002cited by this paper
• Role of human DNA polymerase κ as an extender in translesion synthesis

  2002cited by this paper
• Hydrogen bonding, base stacking, and steric effects in dna replication.

  2001cited by this paper
• A DNA polymerase with specificity for five base pairs.

  2001cited by this paper
• Solution structure of a viral DNA polymerase X and evidence for a mutagenic function

  2001cited by this paper
• Solution structure of a viral DNA repair polymerase

  2001cited by this paper
• DNA Structure and Aspartate 276 Influence Nucleotide Binding to Human DNA Polymerase β

  2001cited by this paper
• Eukaryotic polymerases iota and zeta act sequentially to bypass DNA lesions.

  2000cited by this paper
• Eukaryotic polymerases ι and ζ act sequentially to bypass DNA lesions

  2000cited by this paper
• Structural design of a eukaryotic DNA repair polymerase: DNA polymerase beta.

  2000cited by this paper
• Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases.

  2000cited by this paper
• On the truncation of long-range electrostatic interactions in DNA.

  2000cited by this paper
• Suppression of spontaneous mutagenesis in human cells by DNA base excision-repair.

  2000cited by this paper
• All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

  2000cited by this paper
• DNA Polymerases: Structural Diversity and Common Mechanisms*

  1999cited by this paper
• DNA repair mechanisms for the recognition and removal of damaged DNA bases.

  1999cited by this paper
• Encyclopedia of virology

  1999cited by this paper
• AFRICAN SWINE FEVER VIRUS (ASFARVIRIDAE)

  1999cited by this paper
• Mammalian base excision repair and DNA polymerase beta.

  1998cited by this paper
• Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation

  1998cited by this paper
• Encyclopedia of computational chemistry

  1998cited by this paper
• The mechanism of action of T7 DNA polymerase.

  1998cited by this paper
• Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

  1997cited by this paper
• Characterization of an African Swine Fever Virus 20-kDa DNA Polymerase Involved in DNA Repair*

  1997cited by this paper
• A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity.

  1997cited by this paper
• Oxidative Decay of DNA*

  1997cited by this paper
• VMD: visual molecular dynamics.

  1996cited by this paper
• Requirement of mammalian DNA polymerase-beta in base-excision repair.

  1996cited by this paper
• Analysis of the complete nucleotide sequence of African swine fever virus.

  1995cited by this paper
• The Key–Lock Theory and the Induced Fit Theory

  1995cited by this paper
• A unified polymerase mechanism for nonhomologous DNA and RNA polymerases.

  1994cited by this paper
• Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

  1993cited by this paper
• Structural basis for the 3′‐5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.

  1991cited by this paper
• An attempt to unify the structure of polymerases.

  1990cited by this paper
• Genetic diversity of African swine fever virus isolates from soft ticks (Ornithodoros moubata) inhabiting warthog burrows in Zambia.

  1988cited by this paper
• Monoclonal antibodies of African swine fever virus: antigenic differences among field virus isolates and viruses passaged in cell culture

  1986cited by this paper
• African swine fever virus.

  1985cited by this paper
• The persistence of African swine fever in Africa and the Mediterranean

  1984cited by this paper
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

  1983cited by this paper
• Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes

  1977cited by this paper

• Structural basis for DNA replication by the African swine fever virus polymerase

  2025cites this paper
• Genetic Variations of African Swine Fever Virus: Major Challenges and Prospects

  2024cites this paper
• Current research progress on the viral immune evasion mechanisms of African swine fever virus

  2024cites this paper
• Genome Plasticity of African Swine Fever Virus: Implications for Diagnostics and Live-Attenuated Vaccines

  2022cites this paper
• Comparative Analysis of Full Genome Sequences of African Swine Fever Virus Isolates Taken from Wild Boars in Russia in 2019

  2021cites this paper
• Insights into DNA polymerase δ’s mechanism for accurate DNA replication

  2019cites this paper
• Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia

  2018cites this paper
• Conformational flexibility and base-pairing tendency of the tobacco carcinogen O6-[4-oxo-4-(3-pyridyl)butyl]guanine.

  2017cites this paper
• Fidelity of Nucleotide Incorporation by the RNA-Dependent RNA Polymerase from Poliovirus.

  2016cites this paper
• How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation.

  2014cites this paper
• Is the DPT tautomerization of the long A·G Watson–Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question

  2014cites this paper
• Does the G·G*syn DNA mismatch containing canonical and rare tautomers of the guanine tautomerise through the DPT? A QM/QTAIM microstructural study

  2014cites this paper
• How DNA polymerases catalyze DNA replication, repair, and mutation.

  2014cites this paper
• Atomistic nature of the DPT tautomerisation of the biologically important C·C* DNA base mispair containing amino and imino tautomers of cytosine: a QM and QTAIM approach.

  2013cites this paper
• How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template.

  2013cites this paper
• Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches

  2013cites this paper
• “Gate-keeper” Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides

  2013cites this paper
• Computational Simulation Strategies for Analysis of Multisubunit RNA Polymerases

  2013cites this paper
• Molecular Machines DNA Polymerases Structure , Function , and Modeling

  2011cites this paper
• Effect of Watson-Crick and Hoogsteen base pairing on the conformational stability of C8-phenoxyl-2'-deoxyguanosine adducts.

  2010cites this paper
• Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates.

  2009cites this paper