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Interaction of deoxyribonucleic acid with deoxyribonucleic acid-binding protein from starved cells: cluster formation and crystal growing as a model of initial stages of nucleoid biocrystallization.
Tereshkin, Eduard; Tereshkina, Ksenia; Loiko, Natalia; Chulichkov, Alexei; Kovalenko, Vladislav; Krupyanskii, Yurii.
Afiliación
  • Tereshkin E; a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia.
  • Tereshkina K; a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia.
  • Loiko N; a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia.
  • Chulichkov A; b Laboratory of Viability of Microorganisms, Research Center of Biotechnology , Russian Academy of Sciences , Moscow , Russia.
  • Kovalenko V; a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia.
  • Krupyanskii Y; a Department of Matter Structure , Semenov Institute of Chemical Physics of Russian Academy of Sciences , Moscow , Russia.
J Biomol Struct Dyn ; 37(10): 2600-2607, 2019 07.
Article en En | MEDLINE | ID: mdl-30033848
The paper represents the study of interaction between deoxyribonucleic acid (DNA) and deoxyribonucleic acid-binding protein from starved cells (DPS) cluster formation and crystal growing within a cell. This study is a part of the project that includes European Synchrotron Radiation Facility (ESRF) investigations of in vivo and in vitro nanocrystallization processes of Escherichia coli (E. coli) nucleoid under stress condition combined with theoretical molecular dynamics approaches. Nucleoid biocrystallization is an adaptive mechanism of bacterial cells under stress. It is poorly understood at the present time. Understanding crystal formation process is a very important for molecular biology, pharmacology and other areas. In the simulation part the coarse-grained modeling of various combinations of the following molecules was used: DPS proteins (from 1 to 108 DPS dodecamers in simulation box), short DNA fragments with a length of 24 base pairs (b.p., from 1 to 100 DNA fragments in simulation box) and a part of pBluescript SK(+) plasmide with a length of 161 b.p., in the presence of ions. We defined structural, energetic and dynamic properties of DPS-DPS and DPS-DNA complexes in clusters and crystals that allow us to predict crystal formation and the structure of these crystals in experimental systems.  Communicated by Ramaswamy H. Sarma.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN / Proteínas de Unión al ADN / Simulación de Dinámica Molecular / Simulación del Acoplamiento Molecular Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Revista: J Biomol Struct Dyn Año: 2019 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN / Proteínas de Unión al ADN / Simulación de Dinámica Molecular / Simulación del Acoplamiento Molecular Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Revista: J Biomol Struct Dyn Año: 2019 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Reino Unido