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

Abstract

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

Keywords:

• biocrystallization
• molecular dynamics
• coarse-grained modeling
• DPS protein
• DPS crystals
• DNA-DPS nanoclusters

Additional information

Funding

The work was supported by the Ministry of Education and Science of Russia (project #RFMEFI61616X0070). We are grateful to Joint Supercomputer Center of the Russian Academy of Sciences for the possibilities of using MVS-100K and MVS-10P supercomputers for calculations (project #chph2). The authors thank the European synchrotron radiation facility (ESRF) for providing the possibility of conducting experiments. This work was carried out within the frameworks of the state order for ICP RAS 0082-2014-0001 (state registration #АААА-А17-117040610310-6).