Limits...
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.

Show MeSH

Related in: MedlinePlus

Charge distribution over the A3G C-CDA surface.Comparison of the electrostatic surface of the starting structures with the representative structures from the clustering analysis of the MD simulations. The potential is ranged from −10κT (red) to +10κT (blue). (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. Dotted lines in (A) and (D) indicate the proposed orientation of DNA binding grooves.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2902501&req=5

pone-0011515-g008: Charge distribution over the A3G C-CDA surface.Comparison of the electrostatic surface of the starting structures with the representative structures from the clustering analysis of the MD simulations. The potential is ranged from −10κT (red) to +10κT (blue). (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. Dotted lines in (A) and (D) indicate the proposed orientation of DNA binding grooves.

Mentions: We next analysed the structures of the C-CDA domain of A3G to determine whether a DNA binding site near the deaminase catalytic core could be identified. We already indicated that the positioning of putative DNA binding grooves and the identification of residues that interact with the DNA substrate differs widely between the crystallography and NMR studies. In particular, entirely different putative DNA binding grooves were proposed based on the A3G C-CDA NMR1-2K3A structure and the XRAY1 crystal structure [34](see the initial structures in Figure 8A and 8D, respectively). Curiously, the XRAY2-2K3A and NMR3-2K3A show a surface area with grooves that is similar to XRAY1, whereas NMR2 most closely resembles the groove proposed for the NMR1-2K3A structure (Figure 8). Furthermore, the charge distribution over the surface of the protein is different in each of the reported structures.


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)

Charge distribution over the A3G C-CDA surface.Comparison of the electrostatic surface of the starting structures with the representative structures from the clustering analysis of the MD simulations. The potential is ranged from −10κT (red) to +10κT (blue). (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. Dotted lines in (A) and (D) indicate the proposed orientation of DNA binding grooves.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011515-g008: Charge distribution over the A3G C-CDA surface.Comparison of the electrostatic surface of the starting structures with the representative structures from the clustering analysis of the MD simulations. The potential is ranged from −10κT (red) to +10κT (blue). (A) NMR1-2K3A; (B) NMR2; (C) NMR3-2K3A; (D) XRAY1 and (E) XRAY2-2K3A. Dotted lines in (A) and (D) indicate the proposed orientation of DNA binding grooves.
Mentions: We next analysed the structures of the C-CDA domain of A3G to determine whether a DNA binding site near the deaminase catalytic core could be identified. We already indicated that the positioning of putative DNA binding grooves and the identification of residues that interact with the DNA substrate differs widely between the crystallography and NMR studies. In particular, entirely different putative DNA binding grooves were proposed based on the A3G C-CDA NMR1-2K3A structure and the XRAY1 crystal structure [34](see the initial structures in Figure 8A and 8D, respectively). Curiously, the XRAY2-2K3A and NMR3-2K3A show a surface area with grooves that is similar to XRAY1, whereas NMR2 most closely resembles the groove proposed for the NMR1-2K3A structure (Figure 8). Furthermore, the charge distribution over the surface of the protein is different in each of the reported structures.

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