Backbone folding of immunoglobulin light and heavy chains: a comparison of predicted -bend positions

Conformational properties of pairs of amino acids

Crystal structure data of 31 different globular proteins were analysed. Potentials for all 400 pairs of 20 amino acid residues in helix, extended structure, chain reversals and coil state were obtained. Analysis of these potentials showed that tripeptides of amino acid residues are not linear combinations of amino acids. The association effect of these tripeptides depends on the types of amino acids associated, the position of amino acids in the pair and the secondary structure in which the pair exists. This built-in information in tripeptides should be used in polypeptide and protein folding studies.

Reverse turns in peptides and proteins

The evidence that reverse turns frequently occur as structural components of proteins, as well as of linear and cyclic peptides, is overwhelming. This review summarizes and examines critically the experimental evidence derived from physical methods such as 1H and 13C nuclear magnetic resonance spectroscopy, spin-lattice relaxation time, circular dichroism, IR spectroscopy, and X-ray crystallography. Secondly, theoretical evidence obtained from energy calculations, which rely on empirical energy functions, and correlative methods, which rely on algorithms based on the frequency of occurrence of amino acids, is evaluated. In particular, those theoretical studies for which complementary physical studies have been completed are emphasized. Finally, examples of structure-function relationships involving reverse turns and their biological recognition are demonstrated.

Intramolecularly hydrogen-bonded peptide conformations

Over the past few years the possible occurrence of intramolecularly hydrogen-bonded structures in linear and cyclic peptides has attracted increasing attention. In this review emphasis is given to solid-state studies, particularly by X-ray diffraction and infrared absorption techniques. Conformational energy calculations are also considered. The discussion is focused both on model peptides and biological activity polypeptide molecules. The tetrapeptide system (Formula: see text), examined allows one to discuss the extended C5 structure and the various folded conformations, namely the C7 (gamma-turn), C8, C10 (beta-turn), C11, and C13 conformations. The four latter forms may include cis peptide configurations. The oxy-analogs to the C7, C10, and C13 conformations and structures containing bifurcated hydrogen bonds are also discussed. The last sections describe intramolecularly hydrogen-bonded peptide structures involving: (1) a side-chain group, (2) the N-protecting group (in synthetic model compounds), and (3) a beta-amino acid.

Location of the carbohydrate groups of ovomucoid

Tryptic glycopeptides were purified from the sialic acid-free variant of ovomucoid, O1, and its CNBr fragments. The amino acid sequences adjacent to the four major sites of carbohydrate (Carb.) attachment were: (1), Phe-Pro-Asn(Carb.)-Ala-Thr-Asp-Lys-Glu-Gly-Lys; (2), Ala-Try-Ser-Ile-Glu-Phe-Gly-Thr-Asn (Carb.)-Ile-Ser-Lys; (3), Glu, Thr-Val-Pro-Met-Asn(Carb.)-cys-Ser; (4), Ser-Ser-Tyr-Ala-Asn (Carb.)-Thr-Thr-Ser-Glu-Asp-Gly-Lys, Glycosylated Asn residues were located at position 10, between residues 49 and 60, and at positions 69 and 75, in the primary sequence. All of these carbohydrate groups contained GlcNAc, Man and Gal in the approximate molar proprotions 5:3:0.5. A further glycopeptide containing His was isolated in low yield, suggesting that some carbohydrate is attached at a fifth site. Two of the carbohydrate-attachment sites (Asn-10 and Asn-75) occur in sequences that show internal homologies. These are presumed to have evolved as a consequence of partial gene duplication. Three of the carbohydrate-attachment sites occur in similar positions to the carbohydrate groups in quail ovomucoid [Laskowski (1976) Protides Biol. Fluids Proc. Colloq. 23, in the press]. Prediction of peptide conformation from the sequence data by the method of Chou & Fasman [(1974) Biochemistry 13, 222-225] indicated that four glycosylated Asn residues in hen ovomucoid are very close to groups of amino acids that occur with high frequency in beta-turns. The possible significance of peptide-chain conformation in the attachment of carbohydrate to glycoproteins is briefly discussed.

The influence of nearest-neighbor amino acids on the conformation of the middle amino acid in proteins: comparison of predicted and experimental determination of -sheets in concanavalin A

A 20 x 20 table of tripeptides has been compiled that may be used to locate beta-sheet breaking and alpha-helix breaking residues in proteins. It is based on the definition of an alpha-helical and a beta-sheet domain on the (varphi, Psi) map based on the occurrences of alpha-helices and beta-sheets in 12 known proteins whose sequence and three-dimensional structure have been determined. Each entry in the 20 x 20 table lists three numbers, the frequency of occurrences of the middle amino acid (n) in relation to its nearest neighbors (n - 1) and (n + 1) in the alpha-helical domain, the beta-sheet domain and outside these regions. The regions between two beta-sheet-breaking residues would be permissively beta-sheet regions. The sequence of concanavalin A has been examined in this manner and of the 13 beta-strands defined by x-ray crystallography, 10 were in agreement with the permissively beta-sheet regions and, in the remaining three, beta-sheet-breaking residues were the third in one, and the third, fourth, and fifth residues in another, and the sixth residue in the third from the beginning of the beta-strands. The findings provide strong support for the role of nearest-neighboring amino acids in determining secondary structure of proteins.