A new paper using ACEMD has been published in JACS under the title Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase stemming from a collaboration between University College London (UK) and Universitat Pompeu Fabra (Spain) researchers.
In this work researchers unveiled previously undescribed closed conformations in drug-bound HIV-1 RT which suggesting that “allosteric modulation is effected via the alteration of the kinetic landscape of conformational transitions upon drug-binding”. In the publication researchers also state that “a more detailed understanding of the mechanism of NNRTI inhibition and the effect of binding upon domain motion could aid the design of more effective inhibitors and help identify novel allosteric sites.”
The work was performed through an ensemble molecular dynamics strategy using ACEMD and aggregate simulation time of ~0.6 µs.
D. W. Wright, S. K. Sadiq, G. De Fabritiis, P. V. Coveney, Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase, J. Am. Chem. Soc., 2012, 134 (31), 12885–12888. http://pubs.acs.org/doi/abs/10.1021/ja301565k