The systematic approach to describing conformational rearrangements in G-quadruplexes
| Autor: | Vladimir B. Tsvetkov, Anna M. Varizhuk, Galina E. Pozmogova |
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| Rok vydání: | 2015 |
| Předmět: |
Models
Molecular 0301 basic medicine Stacking Molecular Dynamics Simulation G-quadruplex Article 03 medical and health sciences Molecular dynamics nucleic acid conformations Structural Biology Molecular Biology Chemistry DNA Original Articles General Medicine Planarity testing molecular modelling G-Quadruplexes Folding (chemistry) Crystallography 030104 developmental biology Chemical physics Nucleic Acid Conformations Nucleic Acid Conformation Computer modelling Algorithms |
| Zdroj: | Journal of Biomolecular Structure & Dynamics |
| ISSN: | 1538-0254 0739-1102 |
| DOI: | 10.1080/07391102.2015.1055303 |
| Popis: | Conformational changes in DNA G-quadruplex (GQ)-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters, which are distinct from those commonly used in DNA conformational analyses, must be introduced for adequate interpretation and, most importantly, convenient visual representation of the quadruplex modelling results. We report a set of parameters that comprehensively and systematically describe GQ geometry in dynamics. The parameters include those related to quartet planarity, quadruplex twist, and quartet stacking; they are used to quantitatively characterise various types of quadruplexes and rearrangements, such as quartet distortion/disruption or deviation/bulging of a single nucleotide from the quartet plane. Our approach to describing conformational changes in quadruplexes using the new parameters is exemplified by telomeric quadruplex rearrangement, and the benefits of applying this approach to analyse other structures are discussed. |
| Databáze: | OpenAIRE |
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