Amino acids databases

Studying the sequences of farnesylated proteins indicated that all lipidated proteins bear a cysteine residue near the C-terminus revealing the CAAX-motif, where C is a cysteine, A stands for an aliphatic amino acid, and X can be any amino acid. Database searches resulted in more prenylated proteins, all bearing the CAAX-motif, in systems from lower eukaryotes to mammals. A closer look at the mature proteins revealed that prenylation was only the first step of processing of the CAAX-motif-encoded proteins. After transfer of the isoprene unit, the last three amino acids are cleaved proteolytically by an endoprotease and the C-terminal cysteine is carboxymethylated by a methyltransferase. ... 

Figure 2,7. Query form of Access. Database retrieval is illustrated using Query form to retrieve amino acid database with Microsoft Access.

The Protein and Bioactive Peptide Sequences (BIOPEP) is a public database (Dziuba et al., 1999) containing 707 proteins, 2123 bioactive peptides, 65 allergenic proteins with their epitopes, and 224 sensory peptides and amino acids. Databases include information such as sequence, number of amino acid residues, molecular weight, activity, and references. BIOPEP can be browsed online and the user can search for a specific sequence. 

Table 3 illustrates the data to be found in the Chemical Properties section of the Amino Acids database. 

The generation of loops is necessary because disconnected regions are often separated by a section where a few amino acids have been inserted or omitted. These are often extra loops that can be determined by several methods. One method is to perform a database search to find a similar loop and then use its geometric structure. Often, other conformation search methods are used. Manual structure building may be necessary in order to find a conformation that connects the segments. Visual inspection of the result is recommended in any case. 

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

The basic structural unit of these two-sheet p helix structures contains 18 amino acids, three in each p strand and six in each loop. A specific amino acid sequence pattern identifies this unit namely a double repeat of a nine-residue consensus sequence Gly-Gly-X-Gly-X-Asp-X-U-X where X is any amino acid and U is large, hydrophobic and frequently leucine. The first six residues form the loop and the last three form a p strand with the side chain of U involved in the hydrophobic packing of the two p sheets. The loops are stabilized by calcium ions which bind to the Asp residue (Figure S.28). This sequence pattern can be used to search for possible two-sheet p structures in databases of amino acid sequences of proteins of unknown structure. 

Figure 17.2 An example of prediction of the conformations of three CDR regions of a monoclonal antibody (top row) compared with the unrefined x-ray structure (bottom row). LI and L2 are CDR regions of the light chain, and HI is from the heavy chain. The amino acid sequences of the loop regions were modeled by comparison with the sequences of loop regions selected from a database of known antibody structures. The three-dimensional structure of two of the loop regions, LI and L2, were in good agreement with the preliminary x-ray structure, whereas HI was not. However, during later refinement of the x-ray structure errors were found in the conformations of HI, and in the refined x-ray structure this loop was found to agree with the predicted conformations. In fact, all six loop conformations were correctly predicted in this case. (From C. Chothia et al.. Science 233 755-758, 1986.)...

Homologous proteins have similar three-dimensional structures. They contain a core region, a scaffold of secondary structure elements, where the folds of the polypeptide chains are very similar. Loop regions that connect the building blocks of the scaffolds can vary considerably both in length and in structure. From a database of known immunoglobulin structures it has, nevertheless, been possible to predict successfully the conformation of hyper-variable loop regions of antibodies of known amino acid sequence. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

When the Arabidopsis Expressed Sequence Tag (EST) Database was searched with the tomato fmit Psubunit protein sequence two related cDNAs were identified (Figure 11). cDNA 2 is near full length and has been completely sequenced, cDNA 1 has also been sequenced but currently lacks approximately 100 amino acids of coding region. The two Arabidopsis cDNAs are 81% identical at the protein level and have lower identity to the protein encoded by tomato gene 1, 64 and 63% for cDNA 1 and cDNA 2, respectively. However, both cDNAs encode... 

The results of the various semi-empirical calculations on the reference structures contained within the JSCH-2005 database (134 complexes 31 hydrogen-bonded base-pairs, 32 interstrand base pairs, 54 stacked base pairs and 17 amino acid base pairs) are summarised in Table 5-10. The deviations of the various interaction energies from the reference values are displayed in Figure 5-5. As with the S22 training set, the AMI and PM3 methods generally underestimate the interactions whereas the dispersion corrected method (PM3-D) mostly over-estimates the interactions a little. Overall the PM3-D results are particularly impressive given that the method has only... 

---