Physical-chemical Properties Of Amino Acids Research Articles

Prediction of physical-chemical properties of amino acids from genetic code.

Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prediction for the not yet measured thermodynamical parameters of three amino acids is done.

Eukaryotic signal peptide structure/function relationships: Identification of conformational features which influence the site and efficiency of co-translational proteolytic processing by site-directed mutagenesis of human pre(Δpro)apolipoprotein A-II

Abstract The structural features which influence the efficiency and site of cleavage by eukaryotic signal peptidase have not been fully defined. Human pre(delta pro) apolipoprotein A-II is a useful model system for such an analysis. We have recently shown that a panel of mutants which have amino acids of varying physical-chemical properties substituted for the -1 residue (Ala20) of its signal peptide exhibit cleavage at one of three potential sites or, in some cases, bidirected cleavage (Folz, R. J., Nothwehr, S. F., and Gordon, J. I. (1988) J. Biol. Chem. 263, 2070-2078). In this present study, a subset of the pre(delta pro)Xaa20apoA-II mutants were used to identify conformational features, located COOH-terminal to the hydrophobic core domain, which regulate its cotranslational translocation and proteolytic processing. Proline residues were substituted at positions 13, 14, or 15 in ten of the original position 20 mutant preproteins in order to induce formation of a beta-turn structure at various positions upstream of the cleavage site. The effects of these mutations were assessed using an in vitro transcription/translation/microsome processing assay. Substitution of proline at position 13 resulted in a dramatic decrease in processing efficiency in all Xaa20 sequence contexts, while processing progressively increased when the proline was moved downstream to positions 14 and 15. Elongating the hydrophobic core of the Pro13 mutants by 1 residue reversed this effect. NH2-terminal sequence analysis of 34 co-translationally processed mutants revealed that the optimum distance between the site of proline introduction and the site of co-translational cleavage was 4-5 residues. However, this distance could be altered by the presence of certain amino acids at positions -1 and -3. The data suggest that several structural motifs NH2-terminal to residues -1 and -3 influence the location, site, and efficiency of cleavage by eukaryotic signal peptidase. These include specifically the length of the hydrophobic core, the location of beta-turns relative to the COOH terminus of this core domain, as well as the physical-chemical properties of amino acids at potential cleavage sites.

PARA-SITE: a computer algorithm for rapidly analyzing the physical-chemical properties of amino acid sequences at sites of co- and post-translational protein processing.

A new algorithm is presented which can be used to examine the physical-chemical properties of amino acids at sites of co- or post-translational processing. This algorithm has been incorporated into a computer program known as PARA-SITE. Thirty different parameters can be studied for amino acids which occupy comparable positions in naturally occurring proteins. PARA-SITE should aid in the design and interpretation of protein engineering experiments which seek to dissect structure/activity relationships.

A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids

The 20 naturally occurring amino acids are characterized by 20 variables: pKNH2, pKCOOH, pI, molecular weight, substituent van der Waals volume, seven 1H and 13C nuclear magnetic resonance shift variables, and eight hydrophobicity-hydrophilicity scales. The 20-dimensional data set is reduced to a few new dimensions by principal components analysis. The three first principal components reveal relationships between the properties of the amino acids and the genetic code. Thus the amino acids coded for by adenosine (A), uracil (U), or cytosine (C) in their second codon position (corresponding to U, A, or G in the second anticodon position) are grouped in these components. No grouping was detected for the amino acids coded for by guanine (G) in the second codon position (corresponding to C in the second anticodon position). The results show that a relationship exists between the physical-chemical properties of the amino acids and which of the A (U), U (A), or C (G) nucleotide is used in the second codon (anticodon) position. The amino acids coded for by G (C) in the second codon (anticodon) position do not participate in this relationship.