Other Correlations Amino-acids

An effective method for localizing causes of redox potentials is to plot the total backbone and side chain contributions to ( ) per residue for homologous proteins as functions of the residue number using a consensus sequence, with insertions treated by summing the contribution of the entire insertion as one residue. The results for homologous proteins should be examined for differences in the contributions to ( ) per residue that correlate with observed redox potential differences. These differences can then be correlated with any other sequence-redox potential data for proteins that lack crystal or NMR structures. In addition, any sequences of homologous proteins that lack both redox potentials and structures should be examined, because residues important in defining the redox potential are likely to have semi-sequence conservation of a few key amino acid types. 

Remember that, by convention, the NH2 group of each amino acid is written at the left the COOH group is at the right Other reagents split the chain at different points. By correlating the results of different hydrolysis experiments, it is possible to deduce the primary structure of the protein (or polypeptide). Example 23.10 shows how this is done in a particularly simple case. 

Natural mutation of amino acids in the core of a protein can stabilize the same fold with different complementary amino acid types, but they can also cause a different fold of that particular portion. If the sequence identity is lower than 30% it is much more difficult to identify a homologous structure. Other strategies like secondary structure predictions combined with knowledge-based rules about reciprocal exchange of residues are necessary. If there is a reliable assumption for common fold then it is possible to identify intra- and intermolecular interacting residues by search for correlated complementary mutations of residues by correlated mutation analysis, CMA (see e.g., http //www.fmp-berlin.de/SSFA). 

Since these investigations could be carried out only in the crystalline state, the question of the dynamics of the triple-helix formation and of the correlation of its stability with the amino acid sequence could be answered only with the help of other methods working in solution. 

The importance of lipophilicity to bitterness has been well established, both directly and indirectly. The importance of partitioning effects in bitterness perception has been stressed by Rubin and coworkers, and Gardner demonstrated that the threshold concentration of bitter amino acids and peptides correlates very well with molecular connectivity (which is generally regarded as a steric parameter, but is correlated with the octanol-water partition coefficient ). Studies on the surface pressure in monolayers of lipids from bovine, circumvallate papillae also indicated that there is a very good correlation between the concentration of a bitter compound that is necessary in order to give an increase in the surface pressure with the taste threshold in humans. These results and the observations of others suggested that the ability of bitter compounds to penetrate cell membranes is an important factor in bitterness perception. 

In addition to the enzyme s amino acid sequence, other parameters can affect the outcome of a biocatalytic process. For instance, a similar outcome in the aforementioned DERA-catalyzed statin synthesis was achieved by process improvements [21]. Using a thermostable variant of DERA (thermostability generally correlates well with tolerance to high concentrations of organic reagents or cosolvents), and fed-batch conditions, an efficient process that overcame sensitivity to high concentrations of chloroacetaldehyde was developed. 

Although the correlation between structural properties of aromatic hydrocarbons and their carcinogenic properties proved to be much more complicated than was hoped, this type of calculation opened the door to the application of quantum chemistry to biological systems. The calculations are applied not only to cancer-related problems, but also to the study of amino acids, peptides, nucleotides, and other than anti-cancer therapeutic agents. 

To study the role of lysine residues in susceptibility to formalin fixation, the amino acid composition of immunoreactive peptides (to various monoclonal antibodies) was studied. Each peptide was evaluated to determine if immu-noreactivity was lost after formalin fixation. Formalin sensitivity was correlated with the peptides amino acid composition. The first step in the method is biopanning from a peptide combinatorial library with a monoclonal antibody. The peptides that bind to the antibody were tested for their sensitivity to formalin fixation. Some peptides remain immunoreactive whereas others do not. The peptides were then sequenced to look for differences between those that were sensitive to formaldehyde versus those that were not. The goal was to find whether there is a particular amino acid that is present in formalin-sensitive epitopes but absent in formalin-resistant epitopes, or vice versa. An advantage of this approach is that it is open-ended, without excluding any amino acids. 

Protein content of dehulled Trapper field peas is negatively correlated with the amino acids threonine, cystine, glycine, alanine, methionine, and lysine and positively correlated with glutamic acid and arginine (8). Holt and Sosulski (19) obtained similar correlations with Century field peas for all amino acids except glutamic acid. Other investigators (20) also found that sulfur amino acids (cys, met) are negatively correlated with protein content. 

---