Structural and energetic consequences of oxidation of d(ApGpGpGpTpT) telomere repeat unit in complex with TRF1 protein.
Identifieur interne : 001E17 ( PubMed/Checkpoint ); précédent : 001E16; suivant : 001E18Structural 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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pubmed:20464436Le document en format XML
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<term>Séquence nucléotidique</term>
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<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>
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<Abstract><AbstractText>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.</AbstractText>
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<Reference><Citation>Phys Chem Chem Phys. 2005 Apr 21;7(8):1624-6</Citation>
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