Interactions that regulate the helical fold in proteins

Several factors that may contribute to the stabilization of the helical structure in proteins, detected in studies made on short synthetic peptides, have been reported. Some of them are: presence of alanine or leucine, ionic-pair bonding, stabilization of the helical dipole moment by appropriate charges at the helix N- and C-caps, and aromatic interactions of amino acids located at positions i, i + 4. An analysis of 54 helical structures from 12 proteins showed that all these stabilizing factors were also present in proteins, but the influence of any of them had a different weight, according to the distribution of the hydrophobic and hydrophilic amino acid residues in the helical sequence. The role of non-sequence depending interactions in helical stability, such as presence of disulfide bridges, or bonding of helical residues to substrate and/or cofactors, was also analysed

Active-site studies of enzymes by secondary structure prediction and by molecular modeling

Since the determination of the tertiary structure by X-ray crystallography has been achieved only for a limited number of proteins, alternative approaches are being sought. In this article, the use of secondary structure prediction and of molecular modeling is discussed. Several examples are analyzed in detail