Design of peptides with alpha,beta-dehydro residues: synthesis, crystal structure and molecular conformation of N-Boc-L-Ile-deltaPhe-L-Trp-OCH3. 1998

R Vijayaraghavan, and P Kumar, and S Dey, and T P Singh
Department of Biophysics, All India Institute of Medical Sciences, New Delhi.

The dehydro-peptide Boc-L-Ile-deltaPhe-L-Trp-OCH3 was synthesized by the azlactone method in the solution phase. The peptide was crystallized from methanol in an orthorhombic space group P2(1)2(1)2(1)with a = 10.777(2), b = 11.224(2), c = 26.627(10) A. The structure was determined by direct methods and refined to an R value of 0.069 for 3093 observed reflections [I > or = 2delta(I)]. The peptide failed to adopt a folded conformation with backbone torsion angles: phi1 = 90.8(8)degrees, psi1 = -151.6(6)degrees, phi2 = 89.0(8)degrees, psi2 = 15.9(9)degrees, phi3 = 165.7(7)degrees, psi3T = -166.0(7)degrees . A general rule derived from earlier studies indicates that a three-peptide unit sequence with a deltaPhe at the (i + 2) position adopts a beta-turn II conformation. Because the branched beta-carbon residues such as valine and isoleucine have strong conformational preferences, they combine with the deltaPhe residue differently to generate a unique set of conformations in such peptides. The presence of beta-branched residues simultaneously at both (i + 1) and (i + 3) positions induces unfolded conformations in tetrapeptides, but a beta-branched residue substituted only at (i + 3) position can not prevent the formation of a folded beta-turn II conformation. On the other hand, the present structure shows that a beta-branched residue substituted at the (i + 1) position prevents the formation of a beta-turn II conformation. These observations indicate that a beta-branched residue at the (i + 1) position prevents a folded conformation whereas it cannot generate the same degree of effect from the (i + 3) position. This may be because of the trans disposition of the planar deltaPhe side-chain with respect to the C=O group in the residue. The molecules are packed in an anti-parallel manner to generate N2-H2...O2 (-x, y -1/2, -z + 3/2) and N3epsilon1-H3epsilon1 ...O1(-X, y -1/2, -z + 3/2) hydrogen bonds.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D010455 Peptides Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are considered to be larger versions of peptides that can form into complex structures such as ENZYMES and RECEPTORS. Peptide,Polypeptide,Polypeptides
D010649 Phenylalanine An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE. Endorphenyl,L-Phenylalanine,Phenylalanine, L-Isomer,L-Isomer Phenylalanine,Phenylalanine, L Isomer
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D003461 Crystallography The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Crystallographies

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