PMC

(a) relative number of amino acids that define the two pockets; the residues that define only the experimental pocket, the overlapping ones, and those that define only the predicted pocket, are represented by the red, the green, and the blue portion of the bar, respectively; (b) comparison of the experimental (red) and predicted (blue) binding pocket of Aldose Reductase; the residues that define only the experimental pocket, the overlapping ones, and those that define only the predicted pocket, are represented in red, green, and blue, respectively; (c) comparison of the experimental (red) and predicted (blue) binding pocket of GSK-3β ; the residues that define only the experimental pocket, the overlapping ones, and those that define only the predicted pocket, are represented in red, green, and blue, respectively; (d) comparison of the experimental (red) and predicted (blue) binding pocket of Thymidine Kinase; all the residues (green) overlap.

The amino acid preferences of pocket 9 of DR0301 vary cooperatively for distinct substitutions in pocket 6. A, RBA_adj values plotted for dually substituted peptides. ■ represents values for various amino acids in pocket 9 with Glu (negatively charged) in pocket 6, represents values for various amino acids in pocket 9 with Ala (uncharged) in pocket 6, and □ represents values for various amino acids in pocket 9 with Lys (positively charged) in pocket 6. RBA_adj values are normalized for relative p6 binding affinity to reflect the effect for pocket 9 alone on amino acid preference (calculated as described in Materials and Methods). B, Coopertivity values (calculated as described in Materials and Methods) plotted for dually substituted peptides. ■ represents cooperativity values for p6Glu in conjunction with various amino acids in pocket 9. □ represents cooperativity values for p6Lys in conjunction with various amino acids in pocket 9. By definition, cooperativity values are 1 for the singly substituted p6Ala peptides.

The amino acid preferences of pocket 9 of DR0901 vary cooperatively for distinct substitutions in pocket 6. A, RBA_adj values plotted for dually substituted peptides. ■ represents values for various amino acids in pocket 9 with Asp (negatively charged) in pocket 6, □ represents values for various amino acids in pocket 9 with Ser (uncharged) in pocket 6, and represents values for various amino acids in pocket 9 with Lys (positively charged) in pocket 6. RBA_adj values are normalized for relative p6 binding affinity to reflect the effect for pocket 9 alone on amino acid preference (calculated as described in Materials and Methods). B, Coopertivity values (calculated as described in Materials and Methods) plotted for dually substituted peptides. □ represents cooperativity values for p6Ser in conjunction with various amino acids in pocket 9. represents cooperativity values for p6Lys in conjunction with various amino acids in pocket 9. By definition, cooperativity values are 1 for the singly substituted p6Asp peptides.

a) gB_CTD crystal structure and the structure of the pocket on the gB_CTD. The pocket is formed at the junction of opposing gB_CTD protomers, which are colored in wheat and light blue, with the third protomer in white. The residues that form the pocket on the gB_CTD are highlighted in colors (left panel). The residues of the outer rim of the pocket are indicated in red (right panel). b) The bottom of the pocket is made up of T814 and A851, in sky blue and green, respectively. They do not contact each other, leaving a space between them at the bottom of the pocket. c-e) Pocket mutations of T814 and A851 are hypofusogenic and were modeled in PyMOL. All three hypofusogenic mutations of T814 and A851 were predicted to fill the gB_CTD pocket as well as the space between T814 and A851 at the bottom of the pocket. f) Fusogenicity of T814 and A851 pocket mutants at 2 hr. A851V data is the same as shown in . Fusion trends were the same at 8 hr. g) Cell surface expression of pocket mutants by flow cytometry. A851V data is the same as shown in . h) Fusogenicity of mutations of the pocket rim at 2 hr. Fusion trends were the same at 8 hr. i) Cell surface expression of rim mutants. Columns show mean and error bars are SEM in all panels. *: p < 0.05, **: p < 0.01, ****: p < 0.0001 in all panels. Data in all panels are from three to six independent experiments.