ArticlePloS one2010
Rationalisation of the differences between APOBEC3G structures from crystallography and NMR studies by molecular dynamics simulations.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Exploring putative drug properties associated with TNF-alpha inhibition and identification of potential targets in cardiovascular disease using machine learning-assisted QSAR modeling and virtual reverse pharmacology approach.Molecular diversity · 2024Article
- Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA.Nucleic acids research · 2019Article
- AID and Apobec3G haphazard deamination and mutational diversity.Cellular and molecular life sciences : CMLS · 2013Review
- Mapping the Vif-A3G interaction using peptide arrays: a basis for anti-HIV lead peptides.Bioorganic & medicinal chemistry · 2013Article
- Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F.Nature communications · 2013Article
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- Article
- Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation.Biology · 2012Article
- Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.Journal of chemical theory and computation · 2012Article
- Molecular dynamics simulation in virus research.Frontiers in microbiology · 2012Article
- Mutator effects and mutation signatures of editing deaminases produced in bacteria and yeast.Biochemistry. Biokhimiia · 2011Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The human APOBEC3G (A3G) protein is a cellular polynucleotide cytidine deaminase that acts as a host restriction factor of retroviruses, including HIV-1 and various transposable elements. Recently, three NMR and two crystal structures of the catalytic deaminase domain of A3G have been reported, but these are in disagreement over the conformation of a terminal beta-strand, beta2, as well as the identification of a putative DNA binding site. We here report molecular dynamics simulations with all of the solved A3G catalytic domain structures, taking into account solubility enhancing mutations that were introduced during derivation of three out of the five structures. In the course of these simulations, we observed a general trend towards increased definition of the beta2 strand for those structures that have a distorted starting conformation of beta2. Solvent density maps around the protein as calculated from MD simulations indicated that this distortion is dependent on preferential hydration of residues within the beta2 strand. We also demonstrate that the identification of a pre-defined DNA binding site is prevented by the inherent flexibility of loops that determine access to the deaminase catalytic core. We discuss the implications of our analyses for the as yet unresolved structure of the full-length A3G protein and its biological functions with regard to hypermutation of DNA.
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Registered trials
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