Fast Peptidyl cis−trans Isomerization within the Flexible Gly-Rich Flaps of HIV-1 Protease

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Abstract
The catalytic aspartyl protease of the HIV-1 virus is a homodimer with two flaps that control access to the active site and are known to be flexible. However, knowledge of the atomistic mechanism of the flexibility is lacking. We show that the Gly−Gly ω-bond in the glycine-rich flap tips undergoes fast cis−trans isomerization on the microsecond to millisecond time scale rather than in the usual seconds. Further study reveals that the unexpectedly fast isomerization is a direct consequence of the β-hairpin loop structure of the flap tips, which appears to be counterintuitive. After loop formation of a linear peptide containing the Gly−Gly motif, the rate of isomerization is shown to increase by many orders of magnitude.