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Fig. 5 | BMC Bioinformatics

Fig. 5

From: Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Fig. 5

Main results on structure-consistent alignments of natural BcII-like metallo-β-lactamases (a) and aquaporins (b). In the two panels, residues in blue and red undergo positive and negative constraints on hydrophobicity, respectively; yellow residues follow negative trends against metabolic descriptors (i.e. favoring inexpensive amino acids -no positive trends were observed); and green sites indicate residues were small volumes, small secondary structure propensities or high flexibility are preferred. The inset in panel (a) presents NMR data about slow dynamics in extended-spectrum mutants as determined by Gonzalez et al. Mol Biol Evol 2016. The structure used in panel (a) is PDB ID 1BC2 [68], with the two zinc ions in magenta, while that in panel (b) is PDB ID 1SOR [69] copied symmetrically four times to reproduce the biologically relevant tetramer. Each row of pictures in panel (a) corresponds to pairs of perpendicular views. The top picture in (b) corresponds to a view from “inside” the membrane plane, and the bottom picture is a view from above the membrane. These pictures were not rendered in the website but externally with PyMOL [66]

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BMC Bioinformatics

ISSN: 1471-2105

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