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Stereochemical analysis of the antigenic tip of the V3 loop peptide of HIV-1 gp120

Gunasekaran, K. and Ramakrishnan, C and Balaram, P (1995) Stereochemical analysis of the antigenic tip of the V3 loop peptide of HIV-1 gp120. In: International Journal of Peptide & Protein Research, 46 (5). pp. 359-365.

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A novel multiple turn conformation has been observed for a segment GPGRAFY in the crystal structure of a complex of HIV-1 gp120 V3 loop peptide with the Fab fragment of a neutralizing antibody [Ghiara ct al. (1994) Science 264, 82-85]. A structural motif has been defined for the peptide segment, employing idealized backbone conformations characterized by ranges of virtual C-alpha torsion angles and bond angles. A search of 122 high-resolution protein crystal structures has permitted identification of 24 examples of similar structural motifs. Two major conformational families have been identified, which differ primarily in the conformation at residue 3. The observed conformation at residue 3 in family 1 is left-handed helical (alpha(L)) and that in family 2 is right-handed helical (alpha(R)). Of the 10 examples in family 1, 9 examples have Gly residues at position 3. Of the 12 examples in family 2, 7 examples have Asn/Asp at position 3. Computer modeling of the V3 loop tip sequence using the two backbone conformational families as starting points leads to minimum-energy conformations in which antigenically important side-chains occupy similar spatial arrangements. This stereochemical analysis of the V3 loop tip sequence suggests a rational basis for the design of synthetic analog peptides for use as viral antagonists or synthetic antigens. (C) Munksgaard 1995.

Item Type: Journal Article
Publication: International Journal of Peptide & Protein Research
Publisher: Wiley interscience
Additional Information: Copy right of this article belongs to Wiley interscience.
Keywords: β-turns, gp120, human immunodeficiency virus type 1, multiple turns, peptide conformation ,V3 loop.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 28 Apr 2010 06:10
Last Modified: 19 Sep 2010 06:00
URI: http://eprints.iisc.ac.in/id/eprint/27327

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