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Rationalisation of the Differences between APOBEC3G Structures from Crystallography and NMR Studies by Molecular Dynamics Simulations

Figure 3

Alignment of the β1-β2 region from A2 and A3 proteins.

Amino acid sequence alignment of the β1-β2 region from the human A2 and A3 proteins as generated with T-coffee, with the most conserved residues indicated by grey shading. The positions of β1 and β2 as present in the A2 crystal structure are indicated by arrows above the alignment. H-bonds between back-bone atoms in the β1-β2 sheet of A2 are indicated with red lines. Purple lines indicate H-bonds shared by the two crystal structures of the A3G C-CDA domain. The following H-bonds indicated by purple lines are also present in the NMR structures: L220-L242 in NMR1-2K3A and NMR3-2K3A; Y222-G240 in all NMR structures. Green lines indicate H-bonds unique to XRAY1 and blue lines indicate H-bonds observed in XRAY2-2K3A. Except for the absence of H-bonds between Y225-L235 in NMR2 and H228-T231 in NMR3-2K3A, H-bonds indicated by blue lines are also present in the NMR structures.

Figure 3

doi: https://doi.org/10.1371/journal.pone.0011515.g003