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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

Time evolution of the secondary structure elements during MD simulations.Positions of secondary structure elements α1, β1 and β2 are indicated on the y-axis and the simulation time in nanoseconds is indicated on the x-axis. Simulations labelled with an asterisk contain in silico created mutations. Colours indicate secondary structure elements at a given time point as determined by DSSP classification; α-helices in blue; β-sheets in red; turns in yellow; bends in green.
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pone-0011515-g005: Time evolution of the secondary structure elements during MD simulations.Positions of secondary structure elements α1, β1 and β2 are indicated on the y-axis and the simulation time in nanoseconds is indicated on the x-axis. Simulations labelled with an asterisk contain in silico created mutations. Colours indicate secondary structure elements at a given time point as determined by DSSP classification; α-helices in blue; β-sheets in red; turns in yellow; bends in green.

Mentions: To determine in more detail the conformational changes of the β2 strand, the stability of the secondary structure elements during each of the simulations was examined. We did this by plotting elements of defined secondary structure for each amino acid against the simulated time (Figure 5, Figure S3 and Figure S4). This confirmed that the starting conformation of the β2 strand from the crystal structures remained predominantly stable throughout the simulations, although temporal closing and opening of the bulge in the simulations XRAY2-2K3A and XRAY2* was observed. Simulations with the NMR structures showed a more dynamical behaviour in the sense that folding of the β2 strand was generally improved, and in some instances was periodically disrupted and reformed (Figure 5 and Figure S3). In particular, the NMR2-2K3A* and NMR3-2K3A simulations showed the most dramatic stabilization and ordering of the β2-strand, and NMR2 and NMR3* showed appreciable partial increases in formation of β2. For NMR1* and NMR1-2K3A we observed minor increases in formation of β2. These changes in the β2 region do not appear to influence other secondary structure elements (Figure S4), indicating that conformational changes leading to the formation of a more ordered β2-strand are compatible with the rest of the A3G C-CDA structure.


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)

Time evolution of the secondary structure elements during MD simulations.Positions of secondary structure elements α1, β1 and β2 are indicated on the y-axis and the simulation time in nanoseconds is indicated on the x-axis. Simulations labelled with an asterisk contain in silico created mutations. Colours indicate secondary structure elements at a given time point as determined by DSSP classification; α-helices in blue; β-sheets in red; turns in yellow; bends in green.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011515-g005: Time evolution of the secondary structure elements during MD simulations.Positions of secondary structure elements α1, β1 and β2 are indicated on the y-axis and the simulation time in nanoseconds is indicated on the x-axis. Simulations labelled with an asterisk contain in silico created mutations. Colours indicate secondary structure elements at a given time point as determined by DSSP classification; α-helices in blue; β-sheets in red; turns in yellow; bends in green.
Mentions: To determine in more detail the conformational changes of the β2 strand, the stability of the secondary structure elements during each of the simulations was examined. We did this by plotting elements of defined secondary structure for each amino acid against the simulated time (Figure 5, Figure S3 and Figure S4). This confirmed that the starting conformation of the β2 strand from the crystal structures remained predominantly stable throughout the simulations, although temporal closing and opening of the bulge in the simulations XRAY2-2K3A and XRAY2* was observed. Simulations with the NMR structures showed a more dynamical behaviour in the sense that folding of the β2 strand was generally improved, and in some instances was periodically disrupted and reformed (Figure 5 and Figure S3). In particular, the NMR2-2K3A* and NMR3-2K3A simulations showed the most dramatic stabilization and ordering of the β2-strand, and NMR2 and NMR3* showed appreciable partial increases in formation of β2. For NMR1* and NMR1-2K3A we observed minor increases in formation of β2. These changes in the β2 region do not appear to influence other secondary structure elements (Figure S4), indicating that conformational changes leading to the formation of a more ordered β2-strand are compatible with the rest of the A3G C-CDA structure.

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