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An Antiparallel ß-Sheet And A ß-Turn Characterize The Structure Of Antiviral Hiv-1 Peptide T140, As Revealed By 2d Nmr And Md Simulations.

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The polyphemusins present in the hemocytes of the horsechoe crab and their structurally modified analogs have been shown to exhibit activity against HIV-1. Among the many variants, T22 ([Tyr5,12, Lys7]-polyphemusin II), and its shorter and more potent analog, T140 [Arg1-Arg-2-Nal-Cys-Tyr5- Arg-Lys-D-Lys-Pro-Tyr10-Arg-Cit-Cys-Arg14] (Polyphemusin II-derived peptide), affect the HIV-cell fusion process and inhibit the T-cell line-tropic (T-tropic) HIV-1 infection. Conformational studies of polyphemusin II derived peptide have been carried out by 1H and 13C 2D-NMR and MD simulations in water and HFA (40%). The NMR parameters of chemical shift, temperature coefficients of the NH chemical shifts, 3JNHa coupling constants and the pattern of nOe's were used to deduce the structural characteristics. Solution structures were generated using dihedral and distance restraints by MD simulations. The structures are characterized by a dominant family possessing an anti-parallel β-pleated sheet that is constrained by the disulphide bridge between Cys4 and Cys13. The two strands of the β-sheet are joined by a Type II' β-turn spanning the residues Lys7-D-Lys8-Pro9-Tyr10. This conformation is present in both water and HFA. The only difference in the two structures is that the β-strands are more cohesive in HFA being firmly held by H-bonds. The solution structures generated from MD simulations were refined by MARDIGRAS to R-factors of 0.44 and 0.57 in water and HFA respectively. The conformation deduced for T140 is very similar to that reported for T22 and is thought to be associated with their anti HIV activity.
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Keywords: antiparallel; hiv-1; md simulations; t140

Document Type: Review Article

Affiliations: Dept. of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Mumbai 400 098, India (2) Tata Institute of Fundamental Research, Homi Bhabha Road, Navy Nagar Colaba, Mumbai 400 005, India.

Publication date: 2003-08-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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