FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2034230838> ?p ?o ?g. }

• W2034230838 endingPage "2568" @default.
• W2034230838 startingPage "2559" @default.
• W2034230838 abstract "The modified base 8-oxo-7,8-dihydro-2′-deoxyguanosine (oxoG) is a common DNA adduct produced by the oxidation of DNA by reactive oxygen species. Kinetic data reveal that DNA polymerase X (pol X) from the African swine fever virus incorporates adenine (dATP) opposite to oxoG with higher efficiency than the non-damaged G:C basepair. To help interpret the kinetic data, we perform molecular dynamics simulations of pol X/DNA complexes, in which the template base opposite to the incoming dNTP (dCTP, dATP, dGTP) is oxoG. Our results suggest that pol X accommodates the oxoGsyn:A mispair by sampling closed active conformations that mirror those observed in traditional Watson-Crick complexes. Moreover, for both the oxoGsyn:A and oxoG:C ternary complexes, conformational sampling of the polymerase follows previously described large subdomain movements, local residue motions, and active site reorganization. Interestingly, the oxoGsyn:A system exhibits superior active site geometry in comparison to the oxoG:C system. Simulations for the other mismatch basepair complexes reveal large protein subdomain movement for all systems, except for oxoG:G, which samples conformations close to the open state. In addition, active site geometry and basepairing of the template base with the incoming nucleotide, reveal distortions and misalignments that range from moderate (i.e., oxoG:Asyn) to extreme (i.e., oxoGanti/syn:G). These results agree with the available kinetic data for pol X and provide structural insights regarding the mechanism by which this polymerase can accommodate incoming nucleotides opposite oxoG. Our simulations also support the notion that α-helix E is involved both in DNA binding and active site stabilization. Our proposed mechanism by which pol X can preferentially accommodate dATP opposite template oxoG further underscores the role that enzyme dynamics and conformational sampling operate in polymerase fidelity and function." @default.
• W2034230838 created "2016-06-24" @default.
• W2034230838 creator A5003501137 @default.
• W2034230838 creator A5018933658 @default.
• W2034230838 creator A5046513501 @default.
• W2034230838 creator A5089810247 @default.
• W2034230838 creator A5090692072 @default.
• W2034230838 date "2013-12-01" @default.
• W2034230838 modified "2023-09-28" @default.
• W2034230838 title "How DNA Polymerase X Preferentially Accommodates Incoming dATP Opposite 8-Oxoguanine on the Template" @default.
• W2034230838 cites W1529812325 @default.
• W2034230838 cites W1703102103 @default.
• W2034230838 cites W1805403015 @default.
• W2034230838 cites W1965207660 @default.
• W2034230838 cites W1966302429 @default.
• W2034230838 cites W1967743969 @default.
• W2034230838 cites W1971602039 @default.
• W2034230838 cites W1976051941 @default.
• W2034230838 cites W1985346742 @default.
• W2034230838 cites W1986285943 @default.
• W2034230838 cites W1994066930 @default.
• W2034230838 cites W1997567604 @default.
• W2034230838 cites W2001014346 @default.
• W2034230838 cites W2004499709 @default.
• W2034230838 cites W2005392755 @default.
• W2034230838 cites W2006939081 @default.
• W2034230838 cites W2007696355 @default.
• W2034230838 cites W2010870003 @default.
• W2034230838 cites W2018634753 @default.
• W2034230838 cites W2027901977 @default.
• W2034230838 cites W2031882707 @default.
• W2034230838 cites W2036000659 @default.
• W2034230838 cites W2038087513 @default.
• W2034230838 cites W2038390954 @default.
• W2034230838 cites W2042426030 @default.
• W2034230838 cites W2050495185 @default.
• W2034230838 cites W2051651839 @default.
• W2034230838 cites W2052211560 @default.
• W2034230838 cites W2056094952 @default.
• W2034230838 cites W2066571699 @default.
• W2034230838 cites W2067174909 @default.
• W2034230838 cites W2074018558 @default.
• W2034230838 cites W2078972409 @default.
• W2034230838 cites W2082963155 @default.
• W2034230838 cites W2087249338 @default.
• W2034230838 cites W2089438662 @default.
• W2034230838 cites W2098208486 @default.
• W2034230838 cites W2103815459 @default.
• W2034230838 cites W2106140689 @default.
• W2034230838 cites W2109732856 @default.
• W2034230838 cites W2110223248 @default.
• W2034230838 cites W2111047099 @default.
• W2034230838 cites W2111223577 @default.
• W2034230838 cites W2113007696 @default.
• W2034230838 cites W2114447256 @default.
• W2034230838 cites W2115511934 @default.
• W2034230838 cites W2117867383 @default.
• W2034230838 cites W2118668002 @default.
• W2034230838 cites W2122421116 @default.
• W2034230838 cites W2124483575 @default.
• W2034230838 cites W2125564246 @default.
• W2034230838 cites W2127073622 @default.
• W2034230838 cites W2130233138 @default.
• W2034230838 cites W2130941491 @default.
• W2034230838 cites W2134259738 @default.
• W2034230838 cites W2139022706 @default.
• W2034230838 cites W2140126848 @default.
• W2034230838 cites W2150575470 @default.
• W2034230838 cites W2150677022 @default.
• W2034230838 cites W2150981663 @default.
• W2034230838 cites W2153053054 @default.
• W2034230838 cites W2153127802 @default.
• W2034230838 cites W2161265830 @default.
• W2034230838 cites W2171828097 @default.
• W2034230838 cites W2237046519 @default.
• W2034230838 doi "https://doi.org/10.1016/j.bpj.2013.10.014" @default.
• W2034230838 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3853083" @default.
• W2034230838 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24314086" @default.
• W2034230838 hasPublicationYear "2013" @default.
• W2034230838 type Work @default.
• W2034230838 sameAs 2034230838 @default.
• W2034230838 citedByCount "7" @default.
• W2034230838 countsByYear W20342308382015 @default.
• W2034230838 countsByYear W20342308382016 @default.
• W2034230838 countsByYear W20342308382019 @default.
• W2034230838 countsByYear W20342308382021 @default.
• W2034230838 countsByYear W20342308382022 @default.
• W2034230838 crossrefType "journal-article" @default.
• W2034230838 hasAuthorship W2034230838A5003501137 @default.
• W2034230838 hasAuthorship W2034230838A5018933658 @default.
• W2034230838 hasAuthorship W2034230838A5046513501 @default.
• W2034230838 hasAuthorship W2034230838A5089810247 @default.
• W2034230838 hasAuthorship W2034230838A5090692072 @default.
• W2034230838 hasBestOaLocation W20342308381 @default.
• W2034230838 hasConcept C104317684 @default.
• W2034230838 hasConcept C12554922 @default.
• W2034230838 hasConcept C181199279 @default.
• W2034230838 hasConcept C185581394 @default.

• next