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. 2014 Dec 16;54(2):422–433. doi: 10.1021/bi501088e

Figure 4.

Figure 4

(A) Superposition of the “flap” region of PRG48T/L89M-SQV (cyan/orange) and PRWT-SQV (silver). Monomer A is indicated by cyan/silver and Monomer B colored in orange/silver. PRG48T/L89M-SQV residues are rendered as dark red sticks and PRWT-SQV as silver sticks. Vdw interactions and distances are shown in red for PRG48T/L89M-SQV and gray for PRWT-SQV. Repositioning of the flap of monomer B of PRG48T/L89M-SQV is stabilized by new vdw interactions between Phe53′ and Thre48′. There is an increase in distance between the side chains of Ile54 and Gly51′ in PRG48T/L89M-SQV compared to PRWT-SQV resulting in a loss of a vdw interaction between the flaps of monomer A and B in PRG48T/L89M-SQV. Vdw contacts are also lost between Gly51 and Gly52′ and between between Ile50 and Thre48′ in PRG48T/L89M-SQV. (B) The root mean squared fluctuations of the Cα atoms of PRWT-SQV and PRG48T/L89M-SQV. The average structure of the ensemble was used as the reference. The differences between the RMSF values of the PRWT-SQV and PRG48T/L89M-SQV were calculated. A positive number indicates that a particular residue of PRWT-SQV fluctuates more than PRG48T/L89M-SQV and vice versa. (C) ΔRMSF values in (B) mapped onto PR illustrating where the largest differences between PRWT-SQV and PRG48T/L89M-SQV occur. (Red signifies residues that are less flexible in PRG48T/L89M-SQV compared to PRWT-SQV. Yellow signifies residues that are more flexible in the PRG48T/L89M-SQV relative to PRWT-SQV.