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Order Ortervirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
The current combination of the order members was justified by the structure of their polymerase/reverse transcriptase proteins that are sharing a common origin. The polymerase proteins are similar in structure and include aspartic protease (retroviral aspartyl protease) and an integrase belonging to the DDE recombinase superfamily. They also share similar capsid and nucleocapsid proteins/domains (Krupovic and Koonin 2017). Moreover, belpaoviruses, metaviruses, pseudoviruses, and retroviruses have some other important features in common (Krupovic et al. 2018).
Gaussian accelerated molecular dynamics for elucidation of drug pathways
Published in Expert Opinion on Drug Discovery, 2018
Apurba Bhattarai, Yinglong Miao
The HIV protease is an important target for drug design to treat HIV infection [50,56]. It is a retroviral aspartyl protease with two glycine rich flaps. The two flaps play a key role in gating access of ligands to the protein active site. In X-ray crystal structures, the two flaps adopt a semi-open conformation in the ligand-free (apo) form of the protein, but a closed conformation in the ligand-bound (holo) protein [57,58],(Figure 2(a)). In addition, the protein flaps are able to sample an open conformational state [59]. Recently, Huang et al. investigated ligand binding to the HIV protease through long timescale MD simulations, which revealed important insights into the ligand binding mechanism [56]. However, in a 14 µs Anton cMD simulation, the sampling ligand XK263 (a cyclic urea inhibitor) could not reach the protein active site with a minimum root-mean-square deviation (RMSD) of 5.73 Å compared with the X-ray conformation.