Agrobacterial, Single-Stranded DNA-Binding Protein VirE2 and Its Complexes
| Autor: | M. I. Chumakov, I. V. Volokhina, S. I. Mazilov, Yury Gusev |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
DNA
Bacterial Transfer DNA Stereochemistry In silico DNA Single-Stranded chemistry.chemical_element Molecular Dynamics Simulation Ion Channels Ti plasmid Molecular dynamics Bacterial Proteins Genetics medicine Molecular Biology chemistry.chemical_classification biology Agrobacterium tumefaciens biology.organism_classification Amino acid DNA-Binding Proteins Computational Mathematics medicine.anatomical_structure Computational Theory and Mathematics chemistry Multiprotein Complexes Modeling and Simulation Platinum Nucleus Protein Binding |
| Zdroj: | Journal of Computational Biology. 27:675-682 |
| ISSN: | 1557-8666 |
| Popis: | VirE2 from Agrobacterium tumefaciens is a single-stranded (ss) DNA-binding protein involved in delivery of ssT-DNA (single-stranded transfer DNA) from the agrobacterial Ti plasmid into the eukaryotic cell nucleus. The crystallized part of VirE2 was studied by X-ray diffraction, and the noncrystallized parts of the C- (40 amino acid residues [aars]) and N- (111 aars) termini of the protein, which are presumably disordered, were evaluated by computational methods. We did a molecular dynamics simulation of VirE2 without VirE1 and observed no large changes in domain orientation. The interaction of VirE2 with ssDNA and formation of ssDNA-VirE2 complexes in silico were studied. We also used computer-aided methods to design model complexes consisting from two- and four-subunit VirE2 proteins. We examined the implication of disordered sites in formation of two- and four-subunit VirE2 complexes. Formation of VirE2 dimers and tetramers within ssDNA-VirE2 complexes was demonstrated by computational methods. Using the Platinum program, we found that hydrophilic amino acids were predominant on the surface of the four-subunit VirE2 complex. |
| Databáze: | OpenAIRE |
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