Internal water bridge and antiparallel sheet in the structure of benzyloxycarbonyl-<scp>L</scp>-alanyl-<scp>D</scp>-phenylalanyl-<scp>L</scp>-proline monohydrate

Nair, C.M.K.; Nagaraj, Ramakrishnan; Ramaprasad, S.; Balaram, P.; Vijayan, M.

doi:10.1107/s0567740881003646

Acta Crystallogr Sect B

1981

DOI: 10.1107/s0567740881003646

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Internal water bridge and antiparallel sheet in the structure of benzyloxycarbonyl-L-alanyl-D-phenylalanyl-L-proline monohydrate

C.M.K. Nair¹,

Ramakrishnan Nagaraj²,

S. Ramaprasad³

et al.

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Cited by 9 publications

(1 citation statement)

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“…Such internal bridges involving one water molecule have been observed before in short peptides (e.g. Nair, Nagaraj, Ramaprasad, Balaram & Vijayan, 1981;Aubry, Vitoux, Boussard & Marraud, 1981;Toniolo et al, 1987) but two-membered water bridges connecting adjacent residues, like that in the present structure, are less usual.…”

mentioning

confidence: 77%

Incipient type II β-turn, internal water bridge and head-to-tail sequence in the structure of tri-α-aminoisobutyric acid dihydrate

Jayashree¹,

Suresh²,

Vijayan³

et al. 1987

Acta Crystallogr C

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mentioning

confidence: 77%

Incipient type II β-turn, internal water bridge and head-to-tail sequence in the structure of tri-α-aminoisobutyric acid dihydrate

Jayashree¹,

Suresh²,

Vijayan³

et al. 1987

Acta Crystallogr C

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Conformational studies of heterochiral peptides with diastereoisomeric residues: Crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo‐isoleucine

et al. 1995

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The x-ray diffraction analyses of three N- and C-terminally blocked L,D dipeptides, namely t-Boc-D-Leu-L-Leu-OMe (1), t-Boc-L-Ile-D-aIle-OMe (2), and t-Boc-D-aIle-L-Ile-OMe (3) containing enantiomeric or diastereomeric amino acid residues have been carried out. The structures were determined by direct methods and refined anisotropically to final Rf actors of 0.077, 0.058, and 0.072 for (1), (2), and (3), respectively. Peptides 1-3 all assume a similar U-shaped structure with phi and psi torsion angles corresponding to one of the possible calculated minimum energy regions (regions E and G for L residues, and F*, D* and H* for D residues). The peptide backbones of 1-3 are almost superimposable [provided that the appropriate inversion of the chiral centers of (2) is made]. Side-chain conformations of Leu residues in peptide (1) are g- (tg-) for the L-Leu residue and the mirrored g+ (tg+) for the D-Leu residue; however, in peptides (2) and (3) the conformations of the isoconfigurational side chains of the Ile or allo-Ile residues are (g-t) t and (tg+) t for the L-Ile and the D-allo-Ile moieties, respectively. In all cases, these conformations correspond to the more populated conformers of beta-branched residues statistically found in crystal structures of small peptides. The results seem to indicate that, at least in short peptides with enantiomeric or diastereoisomeric residues, the change in chirality in the main-chain atoms perturbs the backbone conformation to a lesser extent and the side chain conformation to a greater extent.

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Calibration of effective van der Waals atomic contact radii for proteins and peptides

1987

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Effective van der Waals radii were calibrated in such a way that molecular models built from standard bond lengths and bond angles reproduced the amino acid conformations observed by crystallography in proteins and peptides. The calibrations were based on the comparison of the Ramachandran plots prepared from high-resolution X-ray data of proteins and peptides with the allowed phi, psi torsional angle space for the dipeptide molecular models. The calibrated radii are useful as criteria with which to filter energetically improbable conformations in molecular modeling studies of proteins and peptides.

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Internal water bridge and antiparallel sheet in the structure of benzyloxycarbonyl-L-alanyl-D-phenylalanyl-L-proline monohydrate

Cited by 9 publications

References 5 publications

Incipient type II β-turn, internal water bridge and head-to-tail sequence in the structure of tri-α-aminoisobutyric acid dihydrate

Incipient type II β-turn, internal water bridge and head-to-tail sequence in the structure of tri-α-aminoisobutyric acid dihydrate

Conformational studies of heterochiral peptides with diastereoisomeric residues: Crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo‐isoleucine

Calibration of effective van der Waals atomic contact radii for proteins and peptides

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