"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.

Incorporating the cognate instead of non-cognate substrates is crucial for DNA polymerase function. Here we analyze molecular dynamics simulations of DNA polymerase μ (pol μ) bound to different non-cognate incoming nucleotides including A:dCTP, A:dGTP, A(syn):dGTP, A:dATP, A(syn):dATP, T:dCTP, and T...

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Autores principales:	Yunlang Li, Tamar Schlick
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/ea07e4f250b04c5cb99b417d32033cee
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spelling	oai:doaj.org-article:ea07e4f250b04c5cb99b417d32033cee2021-11-18T05:52:08Z"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.1553-734X1553-735810.1371/journal.pcbi.1003074https://doaj.org/article/ea07e4f250b04c5cb99b417d32033cee2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23717197/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Incorporating the cognate instead of non-cognate substrates is crucial for DNA polymerase function. Here we analyze molecular dynamics simulations of DNA polymerase μ (pol μ) bound to different non-cognate incoming nucleotides including A:dCTP, A:dGTP, A(syn):dGTP, A:dATP, A(syn):dATP, T:dCTP, and T:dGTP to study the structure-function relationships involved with aberrant base pairs in the conformational pathway; while a pol μ complex with the A:dTTP base pair is available, no solved non-cognate structures are available. We observe distinct differences of the non-cognate systems compared to the cognate system. Specifically, the motions of active-site residue His329 and Asp330 distort the active site, and Trp436, Gln440, Glu443 and Arg444 tend to tighten the nucleotide-binding pocket when non-cognate nucleotides are bound; the latter effect may further lead to an altered electrostatic potential within the active site. That most of these "gate-keeper" residues are located farther apart from the upstream primer in pol μ, compared to other X family members, also suggests an interesting relation to pol μ's ability to incorporate nucleotides when the upstream primer is not paired. By examining the correlated motions within pol μ complexes, we also observe different patterns of correlations between non-cognate systems and the cognate system, especially decreased interactions between the incoming nucleotides and the nucleotide-binding pocket. Altered correlated motions in non-cognate systems agree with our recently proposed hybrid conformational selection/induced-fit models. Taken together, our studies propose the following order for difficulty of non-cognate system insertions by pol μ: T:dGTP<A(syn):dATP<T:dCTP<A:dGTP<A(syn):dGTP<A:dCTP<A:dATP. This sequence agrees with available kinetic data for non-cognate nucleotide insertions, with the exception of A:dGTP, which may be more sensitive to the template sequence. The structures and conformational aspects predicted here are experimentally testable.Yunlang LiTamar SchlickPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 5, p e1003074 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Yunlang Li Tamar Schlick "Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.
description	Incorporating the cognate instead of non-cognate substrates is crucial for DNA polymerase function. Here we analyze molecular dynamics simulations of DNA polymerase μ (pol μ) bound to different non-cognate incoming nucleotides including A:dCTP, A:dGTP, A(syn):dGTP, A:dATP, A(syn):dATP, T:dCTP, and T:dGTP to study the structure-function relationships involved with aberrant base pairs in the conformational pathway; while a pol μ complex with the A:dTTP base pair is available, no solved non-cognate structures are available. We observe distinct differences of the non-cognate systems compared to the cognate system. Specifically, the motions of active-site residue His329 and Asp330 distort the active site, and Trp436, Gln440, Glu443 and Arg444 tend to tighten the nucleotide-binding pocket when non-cognate nucleotides are bound; the latter effect may further lead to an altered electrostatic potential within the active site. That most of these "gate-keeper" residues are located farther apart from the upstream primer in pol μ, compared to other X family members, also suggests an interesting relation to pol μ's ability to incorporate nucleotides when the upstream primer is not paired. By examining the correlated motions within pol μ complexes, we also observe different patterns of correlations between non-cognate systems and the cognate system, especially decreased interactions between the incoming nucleotides and the nucleotide-binding pocket. Altered correlated motions in non-cognate systems agree with our recently proposed hybrid conformational selection/induced-fit models. Taken together, our studies propose the following order for difficulty of non-cognate system insertions by pol μ: T:dGTP<A(syn):dATP<T:dCTP<A:dGTP<A(syn):dGTP<A:dCTP<A:dATP. This sequence agrees with available kinetic data for non-cognate nucleotide insertions, with the exception of A:dGTP, which may be more sensitive to the template sequence. The structures and conformational aspects predicted here are experimentally testable.
format	article
author	Yunlang Li Tamar Schlick
author_facet	Yunlang Li Tamar Schlick
author_sort	Yunlang Li
title	"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.
title_short	"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.
title_full	"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.
title_fullStr	"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.
title_full_unstemmed	"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.
title_sort	"gate-keeper" residues and active-site rearrangements in dna polymerase μ help discriminate non-cognate nucleotides.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/ea07e4f250b04c5cb99b417d32033cee
work_keys_str_mv	AT yunlangli gatekeeperresiduesandactivesiterearrangementsindnapolymerasemhelpdiscriminatenoncognatenucleotides AT tamarschlick gatekeeperresiduesandactivesiterearrangementsindnapolymerasemhelpdiscriminatenoncognatenucleotides
_version_	1718424763013005312

"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides.

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