Document 0169
 DOCN  M9650169
 TI    Stereochemical analysis of the antigenic tip of the V3 loop peptide of
       HIV-1 gp120.
 DT    9605
 AU    Gunasekaran K; Ramakrishnan C; Balaram P; Molecular Biophysics Unit,
       Indian Institute of Science,; Bangalore, India.
 SO    Int J Pept Protein Res. 1995 Nov;46(5):359-65. Unique Identifier :
       AIDSLINE MED/96139684
 AB    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 et 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.
 DE    Amino Acid Sequence  Antigens, Viral/*CHEMISTRY  Crystallization
       Hydrogen Bonding  HIV Envelope Protein gp120/*CHEMISTRY
       HIV-1/*CHEMISTRY  Models, Molecular  Molecular Sequence Data  *Protein
       Conformation  Protein Structure, Secondary  Support, Non-U.S. Gov't
       JOURNAL ARTICLE

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