Amino acids constellations

Rather than using an amino acid sequence to search SWISS-PROT, AACompI-dent of ExPASy Proteomic tools (http //www.expasy.ch/tools/) uses the amino acid composition of an unknown protein to identify known proteins of the same composition. The program requires the desired amino acid composition, the pi and molecular weight of the protein (if known), the appropriate taxonomic class, and any special keywords. The user must select from one of six amino acid constellations that influence how the analysis is performed. For each sequence in the database, the algorithm computes a score based on the difference in compositions between the sequence and the query composition. The results, returned by e-mail, are organized as three ranked lists. Because the computed scores are a measure of difference, a score of zero implies that there is exact correspondence between the query compo-... 

A constellation of genes code for PBPs of varying amino acid sequences and functionalities. PBPs occur as free-standing polypeptides and as protein fusions. This combinatorial system of structural modules results in a large increase in diversity. 

A binding site in a receptor or enzyme protein is seen as a constellation of amino acid side chains and peptide bonds in the backbone. The spatial... 

The error and yield values from each participant were used to obtain overall averages across participants. A constellation of 16 amino acids, which excluded Cys and Trp, was used for all calculations. 

Figure 4. ExPASy Scores for tpis rabit When Data Were Submitted without or with Data from a Calibration Protein. Amino acid analysis data were submitted to the ExPASy site using the 16 residue Constellation 2 with (empty bars), and without (filled bars), known protein (calibrant) data furnished by the participants. The chart shows rank assigned to tpis rabit (SwissProt data base) for selected sites (a) Sites (n = 14) where accompanying data improved rank of tpis rabit. (b) Sites (n = 11) where including calibration data degraded the rank obtained for the query protein. For 16 sites (not shown), there was no change in rank of rabbit tpis with the inclusion of calibration data (see Table IV). Rank values above 10 are truncated.

The catalytic site in RmL was identified originally from the location of the known lipase/esterase consensus sequence G-X-S-X-G (Brenner, 1988) containing the nucleophilic serine (Ser-144). This amino acid was found to be involved in a hydrogen-bonded constellation also including His-257 and Asp-203. Overall this hydrogen-bonding network is very reminiscent of the catalytic triad of serine proteinases. However, in contrast to proteinases, the triad is concealed under a short helix, the lid, and is therefore inaccessible to solvent. 

The discovery of catalytic triads in lipases and in related esterases, such as acetylcholinesterase (AChE) (Sussman et al., 1991) and cutinase (Martinez et al., 1992), revived interest in this otherwise well-known constellation of amino acids (like GcL, the AChE triad includes a glutamate). It should also be remembered that there are other functionally... 

It is well established that the same three-dimensional scaffolding in proteins often carries constellations of amino acids with diverse enzymatic functions. A classic example is the large family of a/jS, or TIM, barrel enzymes (Farber and Petsko, 1990 Lesk et ai, 1989). It appears that lipases are no exception to date five other hydrolases with similar overall tertiary folds have been identified. They are AChE from Torpedo calif arnica (Sussman et al., 1991) dienelactone hydrolase, a thiol hydrolase, from Pseudomonas sp. B13 (Pathak and Ollis, 1990 Pathak et al, 1991) haloalkane dehalogenase, with a hitherto unknown catalytic mechanism, from Xanthobacter autotrophicus (Franken et al, 1991) wheat serine carboxypeptidase II (Liao et al, 1992) and a cutinase from Fusa-rium solani (Martinez et al, 1992). Table I gives some selected physical and crystallographic data for these proteins. They all share a similar overall topology, described by Ollis et al (1992) as the a/jS hydrolase... 

Comparative studies on homologous proteins show a high conservation of the structural fold and constellation of amino acid side chains at the active site. The best example is that of the serine proteinase family of trypsin, chymotrypsin, elastase and protease A from Streptomyces griseus (see, for example, reference 97) (Fig. 10). 

Another possibility is to search for constellations of amino acids that can confirm a similar function even when the proteins containing them adopt completely different folds. Probably the best known example of this type of similarity is the serine protease catalytic triad (Ser, His, Asp), which occurs in at least 10 different folds. Several approaches have been developed to search for these, including PINTS [42] (http //pints.embl.de), the Catalytic Site Adas [43] (http //www.ebi.ac.uk/thomton-srv/databases/CSA), and Spasm/Rigor [44]. For some protein structures these similarities can be very illuminating as to function by either finding a convergendy evolved site on a new fold [45] or confirming a prediction of function based on a weak similarity to a known fold [46,47]. 

IFN-P shares 29% amino acid homology with IFN-a and has been used in the treatment of multiple sclerosis. Type 1 interferons (a and P) differ from Type II interferons (y) in biochemical properties, biological function, and receptor specificity. Side effects common to both classes of interferons include chills, fever, rigors, headache, myalgia s, hypotension, nausea, vomiting, anorexia, constipation, fatigue, neutropenia, and elevated transaminases. This constellation of symptoms frequently results in mild to moderate hypotension and volume depletion and could potentially contribute to prerenal azotemia or acute tubular necrosis. 

The importance of optimal distance for proton transfer has been emphasized by work on triose-phosphate isomerase. An essential base, Glu-16S, has been replaced by Asp, effectively increasing the bond distance for proton transfer by 1 A (50). The rates of the enzyme-catalyzed enolization steps are reduced 1000-fold (50) relative to wild type. Although the mutant is impaired, its activity is still substantial considering that the wild-type enzyme accelerates the reaction 10 -fold relative to acetate ion in solution. Attempts to select for second-site revertants which restore catalytic activity have met with only modest success (51, 52), but they begin to address the important questions pertaining to the evolution of the optimal geometry of the constellation of amino acids around the active site. 

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