Structure and conformation of linear peptides

The geometries of the 20 genetically encoded amino acids were optimized at the restricted Hartree-Fock level of theory using the 6-31+G* basis set. A detailed comparison showed the calculated geometries to be in excellent agreement with those determined by X-ray crystallography. The study demonstrated that the geometric parameters for the main-chain group and for the bonds and common functional groups of the side-chains exhibit a high degree of transferability among the members of this set of molecules. This geometric transferability is a necessary prerequisite for the corresponding transferability of their electron density distributions and hence of their bond and atomic properties. The transferability of the electron distributions will be demonstrated and exploited in the following paper of this series, which uses the topology of the electron density to define an atom within the quantum theory of atoms in molecules. Particular features of the geometries of the amino acids are discussed. It has been shown, for example, how the apparent anomaly of the Calpha-N bond length in a peptide being shorter than in the charged species Calpha-NH3+ is resolved when the charge separation is gauged by the differences in the charges of the Calpha and N atoms as opposed to the use of formal charges. A compilation of literature sources on experimental geometries covering each member of the 20 amino acids is presented. A set of rules for labeling the atoms and bonds, complementing the generally accepted IUPAC-IUB rules, is proposed to uniquely identify every atom and bond in the amino acids.

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Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Matta

Bader

2002

Proteins

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Molecular structure of l-lysyl-l-tyrosyl-l-serine acetate

Verdaguer¹,

Fita

Subirana

1990

International Journal of Biological Macromolecules

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Head‐to‐tail sequences and other patterns of peptide aggregation in the solid state

Suresh

Vijayan

1985

International Journal of Peptide and Protein Research

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Encouraged by the results of our earlier study on the occurrence and the geometrical features of head‐to‐tail sequences involving amino acids, which have been suggested to be of probable relevance to prebiotic polymerisation, the available crystal structures of unprotected peptides have been analysed with a view to investigating head‐to‐tail sequences and other patterns of peptide aggregation in the solid state. The number of available dipeptide structures is large enough to permit meaningful conclusions. The dipeptide molecules in the crystal structures can be broadly classified as extended or folded depending upon their conformations. The basic elements of dipeptide aggregation are different types of head‐to‐tail sequences and sequences involving hydrogen bonds with the peptide nitrogen atom as the donor, generated by periodic translations and 21 screw axes. Using these basic elements and the known geometrical preferences of hydrogen bonds, it is possible to construct several plausible idealized patterns, mostly two‐dimensional, of dipeptide aggregation for extended as well as folded molecules. The patterns observed in crystal structures are in substantial agreement with these idealized patterns. Infinite hydrogen‐bonded sequences of the type observed in dipeptide structures remain the basic elements of aggregation in the structures of higher peptides also. The present analysis shows that peptide aggregation in the solid state is controlled primarily by interactions involving main chain atoms. Also, despite the increased molecular flexibility of peptides in comparison with amino acids and the presence of additional hydrogen bonding groups in them, head‐to‐tail sequences remain the most important intrinsic feature not only of amino acid aggregation but of peptide aggregation as well.

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Structure and conformation of linear peptides

Cited by 5 publications

References 5 publications

Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries

Molecular structure of l-lysyl-l-tyrosyl-l-serine acetate

Head‐to‐tail sequences and other patterns of peptide aggregation in the solid state

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