ABSTRACT
Theoretical conformational analysis of dodecapeptide "loop" of one of four domains of CaM is carried out. It's shown that one of the lowest energy conformations of the "loop" can bring about together E(i)- and F(i)-hands till van-der-waals contacts. Predominance and advantages of the calculated conformations are discussed in connection with structural organization of the domains and their capability to bind Ca(2+)-ions. The proposed "alpha-hairpin" structure of the domains is a part of a supersecondary structure of globular lobe of CaM.
Subject(s)
Calmodulin/metabolism , Protein Structure, Secondary , Amino Acid Sequence , Molecular Sequence DataABSTRACT
Several peptides of the tachykinin family are reviewed. Special attention is spared to mammalian tachykinins as peptide neurotransmitters. Conformational possibilities of the tachykinins are considered in connection with their ability to interact with specific receptors. The results of theoretical and experimental studies suggest a significant identity of spatial structures of the tachykinins and explain the absence of the strict specificity in tachykinin-receptor interactions.
Subject(s)
Receptors, Neurotransmitter/metabolism , Tachykinins/metabolism , Amino Acid Sequence , Animals , Molecular Sequence Data , Protein Conformation , Receptors, Tachykinin , Tachykinins/chemistryABSTRACT
Theoretical conformational analysis of C-terminal fragments of tachykinin peptides with a common amino acid sequence Asx-Xaa-Phe-Yaa-Gly-Leu-Met-NH2 suggested the conformational states to be independent of the nature of Xaa and Yaa residues. It is shown that among plausible spatial forms of the C-terminal fragments an alpha-helix with the hydrophobic coat consisted of identically oriented side chains is energetically the most stable structure. The preference of this conformation for tachykinins functioning is discussed.
Subject(s)
Tachykinins/chemistry , Amino Acid Sequence , Molecular Sequence Data , Protein Conformation , Structure-Activity RelationshipABSTRACT
Theoretical conformational analysis of N-terminal fragments of the title peptides has been carried out using the potential energy calculations. The number of conformational states for each fragment is very limited, and they are easily interconverted. Since these fragments cannot form alpha-helises, it is unlikely that upon binding of tachikinins to their receptors, their N-terminal fragments could overcome the hydrophobic barrier of the cell membrane's lipid belayer.
Subject(s)
Tachykinins/chemistry , Amino Acid Sequence , Lipid Bilayers , Molecular Sequence Data , Physalaemin/analogs & derivatives , Physalaemin/chemistry , Protein Conformation , Substance P/chemistryABSTRACT
The stereochemical conditions of the enzymatic process of carbohydrate chain addition to the amino acid sequence are reviewed. A particular attention is given to the process of N-glycosylation, which was studied by the method of theoretical conformational analysis.
Subject(s)
Carbohydrate Conformation , Carbohydrates/chemistry , Amino Acid Sequence , Glycosylation , Molecular Sequence DataABSTRACT
Theoretical conformational analysis of oligopeptides CH3CO-Asn-X-Thr-NHCH3 (X = Gly, Ala, Pro), modelling N-glycosylation site, and their glycosylated derivatives CH3CO-(GlcNAc beta 1-4GlcNAc beta 1) Asn-X-Thr-NHCH3 has been carried out. Active conformations of the site are found, corresponding to structural prerequisities of N-glycosylation: Asn residue's position in beta-turn and hydrogen bond formation between side chains of Asn and Thr/Ser residues. In this case the L conformation of the central residue X is most probable. Since Pro residue does not possess this conformation, sequences with X = Pro are not glycosylated. It is shown that glycosylation of the above-mentioned sites is accompanied by reorientation of the Asn residue's side chains.
Subject(s)
Glycoproteins/analysis , Amino Acid Sequence , Asparagine , Glycolipids/analysis , Glycosylation , Models, Molecular , Molecular Sequence Data , Protein Conformation , Serine , ThreonineABSTRACT
Theoretical conformational analysis of O-glycosylated polypeptide chain has been carried out. It is shown that formation of a regular structure is possible, in which the peptide backbone is covered by a layer of well-packed carbohydrate side chains. A beta-barrel is proposed as the spatial model of blood group-specific glycoproteins; it consists of glycosylated beta-hairpins, which interact if they are sterically close. In this beta-barrel the peptide backbone forms an inner "tunnel" which is isolated by the compact carbohydrate coat.
