This peptide is a synthetic peptide. It sequence corresponds to the major
immunogen region of the Foot-and-Mouth-Disease Virus (FMDV) serotype A variant
USA. The goal of this study is to develop a peptide that can be used as a
synthetic vaccine. For this reason the authors used a retro-inverso strategy in
order to enhance its stability in vivo.
Retro-inverso means that it was synthesized using D-residues and sequence was
inverted regarding the sequence in the protein (parent peptide - see 1bcv ).
The idea is to keep the orientations of the residues side-chains as it is in
the parent peptide. For more details about the retro-inverso peptides, the
antigenicity and immunogenicity of retro-inverso petidomimetics please see
Guichard et al. (1994) Proc. Natl.Acad. Sci. USA , 91, pp 9765-9769 Muller et
al. (1995) Peptide Research, 8 pp 138-144.

The parent peptide corresponds to the sequence 141-159 of VP1 protein of the
capsid of FMD virus. In this retro-inverso peptide the numbering of the
residues is made as following : 159 is at its N-terminal part , it correspond
to a isobutyl-malonate (LML) in order to mimic the C-terminal part of the
parent peptide; At the C-terminal part of the retro-inverso peptidomimetics
NH2-CO (CAG) was added in order to mimic the N-terminal of the parent peptide.
The Het group NH2-CO has the number 140.

All non glycine residues present a D configuration. MLEU presents a L
configuration, because it occurred less restraints violations during DYANA
calculations than the D isomer.

'LML was introduced in DYANA library as well as D-residues.' 'PHI angles of
D-residues were set in the [10,170] interval during structure calculations.'

In this peptide we found that the only the region from 151 to 159 is exhibiting
structural motifs which are untypical beta-turns. 6 betas turns were found
involving the following residues : 156-159 for 53 % of the structures, 155-158
for 30% of the structures , 153-156 for 46 % of the structures, 151-154 for 53%
of the structures, 148-151 for 30% of the structures and 145-148 (RGD) for 13 %
of the structures. The optimal fit on backbone atoms was found on the 150-158
region with a rmsd of 0.8 A.

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at http://wwpdb-remediation.rutgers.edu/downloads.html
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at http://wwpdb-remediation.rutgers.edu/downloads.html
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Solution structure of a retro-inverso peptide analogue mimicking the foot-and-mouth disease virus major antigenic site. Structural basis for its antigenic cross-reactivity with the parent peptide.

CONH2 is covalently attached to the C terminal glycine G141 by an amide linkage.

Retro-inverso analogue of G-H loop of VP1 in FMD virus

TORSION ANGLE DYNAMICS, ANNEALING, MINIMIZATION