Computers

  2010 MAR 25 - (VerticalNews.com) -- "HIV-1 protease is a crucial enzyme for the life cycle of the human immunodeficiency virus, the retrovirus that triggers AIDS. It is well documented that HIV-1 protease mediates the cleavage of Gag, Gag-Pol, and Nef precursor polyproteins and is highly selective concerning the set of 12 different amino acid sequences that cleaves," researchers in Oporto, Portugal report.

  "However, the governing principles and physical parameters, which determine substrate recognition and specificity, remain poorly understood despite the many speculative proposals that abound in the literature. In fact, it has been difficult so far to circumvent the fact that protease's substrates share little sequence identity and lack an obvious consensus binding motif. We have used microsecond time scale MD simulations to quantitatively show that some sequences of the polyprotein Gag-Pol that are not cleaved (nonsubstrates) have in fact a higher affinity to the active site of HIV-1 protease than a substrate; i.e., recognition is not governed by affinity to the active site," wrote M.A.S. Perez and colleagues, University of Porto ...read more

  2010 MAR 18 - (VerticalNews.com) -- According to a study from Edmonton, Canada, "We present a computational exploration of five- and six-coordinate Ni(II) and vanadyl porphyrins, including prediction of UV-vis spectroscopic behavior and metalloporphyrin structure as well as determination of a binding energy threshold between strongly bound complexes that have been isolated as single crystals and weakly bound ones that we detect by visible absorption spectroscopy. The excited states are calculated using the tandem of the time-dependent density functional theory (TD-DFT) and the conductor-like polarizable continuum model (CPCM). ...read more

  2010 MAR 4 - (VerticalNews.com) -- According to a study from London, the United Kingdom, "The formation of carbonyl sulphide, OCS, is investigated computationally on a model carbonaceous grain surface (coronene) using density functional theory. Four reaction pathways for the formation of OCS are investigated: formation from CO + S (on both the singlet and the triplet surfaces) and CO + HS, and formation from CS + O (again on both the singlet and the triplet surfaces) and CS + OH. ...read more