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Flap opening in HIV-1 protease simulated by ‘activated’ molecular dynamics

Abstract

We have used an ‘activated’ molecular dynamics approach to simulate flap opening in HIV-1 protease. An initial impulse for flap opening was provided by applying harmonic constraints to non-flap residues. After an initial ‘melting’ phase, the two β-hairpin structures that constitute the flaps opened to a 25 Å gap within 200 ps of simulation. Analysis of backbone torsion angles suggests that flap opening is related to conformational changes at Lys 45, Met 46, Gly 52 and Phe 53. In contrast, similar molecular dynamics simulations on the M461 mutant, which is associated with drug resistance, indicates that this mutation stabilizes the flaps in a closed conformation.

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