Estimation of peptide hormone noncovalent binding site functionality from frequencies of interaction of amino acid side chains in proteins

Making sense from antisense: a review of experimental data and developing ideas on sense--antisense peptide recognition

Peptides encoded in the antisense strand of DNA have been predicted and found experimentally to bind to sense peptides and proteins with significant selectivity and affinity. Such sense--antisense peptide recognition has been observed in many systems, most often by detecting binding between immobilized and soluble interaction partners. Data obtained so far on sequence and solvent dependence of interaction support a hydrophobic-hydrophilic (amphipathic) model of peptide recognition. Nonetheless, the mechanistic understanding of this type of molecular recognition remains incomplete. Improving this understanding likely will require expanding the types of characteristics measured for sense--antisense peptide complexes and hence the types of analytical methods applied to such interactions. Understanding the mechanism of sense--antisense peptide recognition also may provide insights into mechanisms of native (sense) peptide and protein interactions and protein folding. Such insight may be helpful to learn how to design macromolecular recognition agents in technology for separation, diagnostics and therapeutics.

The influence of side chain structures on the residue-residue associations in globular proteins

The relationship between the physical make-up of the side chain structure of an amino acid and its capacity to associate with other side chains in the crystalline state of protein molecules has been investigated by a linear regression study. Relevant inter- and intra-molecular forces and steric factors are taken to represent the side chain structure, while the observed atom-atom interactions in a set of protein crystals are taken to represent the residue-residue association potentials. Correlation equations are set up in such a way that, (i) the dependence of the association potential of a residue on the side chain structures of associating residues, and (ii) the dependence of the association potential of a residue on its own side chain structure are brought out separately. The results show definite quantitative relationships in each of the above two views. Particularly, the behaviour of the charged residues is highly correlated to the structural make of their side chains. It is demonstrated how and to what extent the effects of associating/preferring residues are taken care of when they associate with a certain kind of residue in the protein environment.

Role of hydrophobicity in protein structure is overestimated

Some microcalorimetrically measured and theoretically calculated thermodynamic interaction coefficients of amino acid compounds in aqueous and peptidic systems have been collected, and are reported here. They indicate that although hydrophobicity contributes to the stability of the native structure of proteins, its influence on their exact configuration is limited.