Comparative analysis of HIV‐1 Tat variants

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Abstract
HIV‐1 Tat protein is a crucial element for viral replication; therefore, its inhibition might be exploited against the AIDS infection. To gain insights on the natural variability of this protein, we present a comparative investigation on the relationship between the primary sequences and the experimentally available three‐dimensional structures from the HIV‐1 Tat variants Z2, BRU, and MAL. Our computational tools include sequence conservation algorithms, structural analysis, electrostatic modeling, and molecular dynamics (MD) simulations. We find that two regions located between residues 10–18 and 41–52 display the highest primary sequence conservation, while the most conserved region among the available structures corresponds approximately to the segment between positions ∼44 and 50. Furthermore, in spite of their large structural divergence, Tat variants share a common mode for long‐range intramolecular interactions. Finally, the flexibility of the Z2, BRU, and MAL variants, as emerging from multinanosecond MD simulations, is rather similar. Based on this work, we conclude that the turnlike region between amino acids 44 and 50 is structurally most conserved, emerging as an important motif for pharmaceutical targeting aimed toward inhibiting Tat action. Proteins 2005.