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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
Variable internal flexibility characterizes the helical capsid formed by agrobacterium VirE2 protein on
Tanmay A M Bharat1, David Zbaida, Miriam Eisenstein
1Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel.
Structure (London, England : 1993)
|June 18, 2013
Summary
Agrobacterium tumefaciens VirE2 protein binds single-stranded DNA (ssDNA), forming a T-complex. Structural analysis reveals a rigid assembly with local flexibility, crucial for gene transfer mechanisms.
Area of Science:
- Molecular Biology
- Structural Biology
- Microbiology
Background:
- Agrobacterium tumefaciens is a key plant pathogen known for its gene transfer capabilities.
- The bacterium secretes VirE2, a single-stranded DNA (ssDNA)-binding protein essential for transforming eukaryotic hosts.
- VirE2 plays a role in adapting bacterial conjugation mechanisms for plant transformation.
Purpose of the Study:
- To elucidate the three-dimensional structure of the VirE2-ssDNA complex.
- To understand the structural constraints and flexibility of the VirE2 protein within the complex.
- To investigate how VirE2 structure facilitates sequence-independent DNA binding.
Main Methods:
- Cryo-electron microscopy (cryo-EM) for 3D reconstruction.
- Iterative helical real-space reconstruction techniques.
- Computational modeling, chemical modifications, mass spectrometry, and electron paramagnetic resonance (EPR).
Main Results:
- A solenoidal shell (T-complex) structure of the VirE2-ssDNA complex was determined.
- The N-terminal domain of VirE2 is tightly constrained, while the C-terminus is weakly constrained.
- The overall quaternary structure is rigid but exhibits local flexibility.
Conclusions:
- The rigid yet locally flexible structure of the VirE2-ssDNA complex is critical for its function.
- This structural adaptability likely enables VirE2 to accommodate various DNA substrates without sequence specificity.
- Understanding VirE2 structure provides insights into bacterial conjugation and plant transformation processes.
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