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Computer evaluation of VirE2 protein complexes for ssDNA transfer ability
Irina Volokhina1, Yury Gusev1, Svyatoslav Mazilov1
1Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov 410049, Russia.
Computational Biology and Chemistry
|February 27, 2017
Summary
Agrobacterium VirE2 proteins may form membrane pores to deliver DNA into plant cells. Computer simulations suggest a two-subunit complex might gate, but four-subunit complexes showed no pore changes.
Area of Science:
- Molecular Biology
- Biophysics
- Computational Biology
Background:
- Agrobacterium tumefaciens transfers single-stranded DNA (ssDNA) from its Ti plasmid into plant chromosomes.
- The mechanism of ssDNA transport across plant cell membranes is not fully understood.
- VirE2 proteins are hypothesized to form membrane pores for ssDNA-VirD2-VirE2 complex translocation.
Purpose of the Study:
- To computationally simulate the pore-forming capacity of VirE2 proteins.
- To evaluate the conformational dynamics of VirE2 complexes.
Main Methods:
- Molecular dynamics simulations.
- Normal modes analysis.
- Simulation of two- and four-subunit VirE2 complexes.
Main Results:
- No significant domain reorientation was observed in two- and four-subunit VirE2 complexes within 1 ns simulations.
- A potential ion channel-like gating mechanism was proposed for the two-subunit VirE2 complex.
- No conformational changes were predicted within the pore of the four-subunit VirE2 complex.
Conclusions:
- The study provides insights into the potential pore-forming ability of VirE2 proteins.
- A two-subunit VirE2 complex may exhibit gating behavior, facilitating DNA transfer.
- Further research is needed to elucidate the precise role of VirE2 in DNA translocation.
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