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Rationalisation of the differences between APOBEC3G structures from crystallography and NMR studies by molecular dynamics simulations.

Autore F, Bergeron JR, Malim MH, Fraternali F, Huthoff H - PLoS ONE (2010)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.

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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Related in: MedlinePlus

Water binding sites in the β1-β2 sheet as determined by MD solvent density analysis.Water molecules that bridge the backbone of the β1-β2 sheet are indicated in red and their interactions with amino acid residues are indicated with black dotted lines. The water-mediated interactions between the backbone of the residues V224 and Y222 in β1 and L235, Q237 and R238 in β2 are shown for: (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. (F) Representation of the water molecules observed in the electron density map of the crystal structure XRAY2-2K3A.
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pone-0011515-g007: Water binding sites in the β1-β2 sheet as determined by MD solvent density analysis.Water molecules that bridge the backbone of the β1-β2 sheet are indicated in red and their interactions with amino acid residues are indicated with black dotted lines. The water-mediated interactions between the backbone of the residues V224 and Y222 in β1 and L235, Q237 and R238 in β2 are shown for: (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. (F) Representation of the water molecules observed in the electron density map of the crystal structure XRAY2-2K3A.

Mentions: We next set out to investigate interactions of the β1-β2 sheet with the solvent during the A3G C-CDA simulations by means of MD solvent density analysis [38]. In particular, we analysed the persistence of water molecules at the β1-β2 region by generating MD hydration maps (MDHS) for the XRAY1, XRAY2-2K3A, NMR1-2K3A, NMR2 and NMR3-2K3A structures (Figure 7). In this type of simulation, the protein structure is restrained to remain rigid, while allowing the water molecules to reach equilibrium solvation around the protein [38]. In this manner, sites within the protein structure that are particularly prone to interact with water can be identified. Because the protein structure is restrained to remain rigid, we did not include structures with in silico generated sequences in this analysis.


Rationalisation of the differences between APOBEC3G structures from crystallography and NMR studies by molecular dynamics simulations.

Autore F, Bergeron JR, Malim MH, Fraternali F, Huthoff H - PLoS ONE (2010)

Water binding sites in the β1-β2 sheet as determined by MD solvent density analysis.Water molecules that bridge the backbone of the β1-β2 sheet are indicated in red and their interactions with amino acid residues are indicated with black dotted lines. The water-mediated interactions between the backbone of the residues V224 and Y222 in β1 and L235, Q237 and R238 in β2 are shown for: (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. (F) Representation of the water molecules observed in the electron density map of the crystal structure XRAY2-2K3A.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2902501&req=5

pone-0011515-g007: Water binding sites in the β1-β2 sheet as determined by MD solvent density analysis.Water molecules that bridge the backbone of the β1-β2 sheet are indicated in red and their interactions with amino acid residues are indicated with black dotted lines. The water-mediated interactions between the backbone of the residues V224 and Y222 in β1 and L235, Q237 and R238 in β2 are shown for: (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. (F) Representation of the water molecules observed in the electron density map of the crystal structure XRAY2-2K3A.
Mentions: We next set out to investigate interactions of the β1-β2 sheet with the solvent during the A3G C-CDA simulations by means of MD solvent density analysis [38]. In particular, we analysed the persistence of water molecules at the β1-β2 region by generating MD hydration maps (MDHS) for the XRAY1, XRAY2-2K3A, NMR1-2K3A, NMR2 and NMR3-2K3A structures (Figure 7). In this type of simulation, the protein structure is restrained to remain rigid, while allowing the water molecules to reach equilibrium solvation around the protein [38]. In this manner, sites within the protein structure that are particularly prone to interact with water can be identified. Because the protein structure is restrained to remain rigid, we did not include structures with in silico generated sequences in this analysis.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.

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.

Show MeSH
Related in: MedlinePlus