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Figure 7 | BMC Biochemistry

Figure 7

From: Insertion of a small peptide of six amino acids into the β7–β8 loop of the p51 subunit of HIV-1 reverse transcriptase perturbs the heterodimer and affects its activities

Figure 7

Molecular model of the inserted peptide in the β7–β8 loop of the p51 subunit. Molecular modeling of the extended loop was performed by the 'Loop Search' option of SYBYL version 6.5 (Tripos Associates, St. Louis, MO). A total of 100 loops, matching the Cα distances constrain between the end points of the loop residues, were obtained. The loops were examined for 'bumps' with the neighboring protein structure. Selection of the appropriate loop was based on the least root mean square deviation and maximum homology with the inserted loop sequence. A loop satisfying these criteria containing two small anti-parallel β-strands is shown in cyan. The side chains of amino acid residues of p66 are shown in green and those of p51 (wild type) are shown in orange. The side chains of interacting residues in the inserted peptide are colored violet and are indicated by their position number in parentheses. Interactions seen in the wild type loop are shown in blue dotted line while additional interactions are shown in black dotted lines.

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