Structural and energetic consequences of oxidation of d(ApGpGpGpTpT) telomere repeat unit in complex with TRF1 protein.
Identifieur interne : 002607 ( Main/Exploration ); précédent : 002606; suivant : 002608Structural and energetic consequences of oxidation of d(ApGpGpGpTpT) telomere repeat unit in complex with TRF1 protein.
Auteurs : Piotr Cysewski [Pologne] ; Przemysław CzeleSource :
- Journal of molecular modeling [ 0948-5023 ] ; 2010.
Descripteurs français
- KwdFr :
- Analyse de régression, Conformation moléculaire, Données de séquences moléculaires, Liaison aux protéines, Oxydoréduction, Protéine-1 se liant aux répétitions télomériques (), Protéine-1 se liant aux répétitions télomériques (métabolisme), Purines (métabolisme), Séquence nucléotidique, Séquences répétées d'acides nucléiques (génétique), Thermodynamique, Télomère (), Télomère (génétique), Télomère (métabolisme).
- MESH :
- génétique : Séquences répétées d'acides nucléiques, Télomère.
- métabolisme : Protéine-1 se liant aux répétitions télomériques, Purines, Télomère.
- Analyse de régression, Conformation moléculaire, Données de séquences moléculaires, Liaison aux protéines, Oxydoréduction, Protéine-1 se liant aux répétitions télomériques, Séquence nucléotidique, Thermodynamique, Télomère.
English descriptors
- KwdEn :
- Base Sequence, Molecular Conformation, Molecular Sequence Data, Oxidation-Reduction, Protein Binding, Purines (metabolism), Regression Analysis, Repetitive Sequences, Nucleic Acid (genetics), Telomere (chemistry), Telomere (genetics), Telomere (metabolism), Telomeric Repeat Binding Protein 1 (chemistry), Telomeric Repeat Binding Protein 1 (metabolism), Thermodynamics.
- MESH :
- chemical , chemistry : Telomeric Repeat Binding Protein 1.
- chemical , metabolism : Purines, Telomeric Repeat Binding Protein 1.
- chemistry : Telomere.
- genetics : Repetitive Sequences, Nucleic Acid, Telomere.
- metabolism : Telomere.
- Base Sequence, Molecular Conformation, Molecular Sequence Data, Oxidation-Reduction, Protein Binding, Regression Analysis, Thermodynamics.
Abstract
The configuration hyperspace of canonical and oxidized 14-mers of B-DNA comprising telomere repeat units d(ApGpGpGpTpT) was sampled over 40 ns via molecular dynamic (MD) simulations. The energetic and structural consequences of TRF1 binding to telomere B-DNA were compared with non-complexed systems. Energetic properties of analyzed pairs, di- and tri-nucleotide steps occurring in central telomere repeat unit were estimated by means of advanced quantum chemistry computations including not only BSSE corrections, electron correlation contributions but also non-negligible many-body terms. These data along with bases pair and base step parameters distributions allow for quantization of consequences of oxidation and/or TRF1 binding to telomere repeat units. Occurrence of 8-oxoguanine in central telomeric triad (CTT) is the source of high stiffness if compared to non-modified oligomer. The origin of this property comes from significantly alteration of intermolecular interactions introduced by 8-oxoguanine. The increased stability observed for base-base interactions are accumulated and characterizes also di- and tri-nucleotides. The observed changes in the intermolecular interactions originate from structural alterations imposed by TRF1 binding to canonical and oxidized telomere B-DNA. First and most direct consequence of TRF1 binding to oxidized telomere repeat unit is alteration of shift-slide correlations if compared to canonical system. This in turn leads to large differences in purine-purine overlapping in oxidized structures. Thus, oxidized telomere B-DNA double strands are sensitive to interactions with protein ligands and numerous structural and energetic changes are imposed on base pairs forming CTT.
DOI: 10.1007/s00894-010-0730-8
PubMed: 20464436
Affiliations:
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xml:lang="en">Structural and energetic consequences of oxidation of d(ApGpGpGpTpT) telomere repeat unit in complex with TRF1 protein.</title><author><name sortKey="Cysewski, Piotr" sort="Cysewski, Piotr" uniqKey="Cysewski P" first="Piotr" last="Cysewski">Piotr Cysewski</name><affiliation wicri:level="1"><nlm:affiliation>Physical Chemistry Department, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950, Bydgoszcz, Poland. piotr.cysewski@cm.umk.pl</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Physical Chemistry Department, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950, Bydgoszcz</wicri:regionArea><wicri:noRegion>Bydgoszcz</wicri:noRegion></affiliation></author><author><name sortKey="Czele, Przemyslaw" sort="Czele, Przemyslaw" uniqKey="Czele P" first="Przemysław" last="Czele">Przemysław Czele</name></author></analytic><series><title level="j">Journal of molecular modeling</title><idno 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télomériques ()</term><term>Protéine-1 se liant aux répétitions télomériques (métabolisme)</term><term>Purines (métabolisme)</term><term>Séquence nucléotidique</term><term>Séquences répétées d'acides nucléiques (génétique)</term><term>Thermodynamique</term><term>Télomère ()</term><term>Télomère (génétique)</term><term>Télomère (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Telomeric Repeat Binding Protein 1</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Purines</term><term>Telomeric Repeat Binding Protein 1</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Telomere</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Repetitive Sequences, Nucleic Acid</term><term>Telomere</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Séquences répétées d'acides 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nucléotidique</term><term>Thermodynamique</term><term>Télomère</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The configuration hyperspace of canonical and oxidized 14-mers of B-DNA comprising telomere repeat units d(ApGpGpGpTpT) was sampled over 40 ns via molecular dynamic (MD) simulations. The energetic and structural consequences of TRF1 binding to telomere B-DNA were compared with non-complexed systems. Energetic properties of analyzed pairs, di- and tri-nucleotide steps occurring in central telomere repeat unit were estimated by means of advanced quantum chemistry computations including not only BSSE corrections, electron correlation contributions but also non-negligible many-body terms. These data along with bases pair and base step parameters distributions allow for quantization of consequences of oxidation and/or TRF1 binding to telomere repeat units. Occurrence of 8-oxoguanine in central telomeric triad (CTT) is the source of high stiffness if compared to non-modified oligomer. The origin of this property comes from significantly alteration of intermolecular interactions introduced by 8-oxoguanine. The increased stability observed for base-base interactions are accumulated and characterizes also di- and tri-nucleotides. The observed changes in the intermolecular interactions originate from structural alterations imposed by TRF1 binding to canonical and oxidized telomere B-DNA. First and most direct consequence of TRF1 binding to oxidized telomere repeat unit is alteration of shift-slide correlations if compared to canonical system. This in turn leads to large differences in purine-purine overlapping in oxidized structures. Thus, oxidized telomere B-DNA double strands are sensitive to interactions with protein ligands and numerous structural and energetic changes are imposed on base pairs forming CTT.</div></front></TEI><affiliations><list><country><li>Pologne</li></country></list><tree><noCountry><name sortKey="Czele, Przemyslaw" sort="Czele, Przemyslaw" uniqKey="Czele P" first="Przemysław" last="Czele">Przemysław Czele</name></noCountry><country name="Pologne"><noRegion><name sortKey="Cysewski, Piotr" sort="Cysewski, Piotr" uniqKey="Cysewski P" first="Piotr" last="Cysewski">Piotr Cysewski</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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