Amino acids, adjacent

Subtilisins are serine proteases of broad specificity, although the order of preference for the PI residue (the amino acid adjacent to the site of cleavage in the substrate) varies from one species to the next. Subtilisins from Bacillus licheni-formis and Bacillus amyloliquefaciens differ in protein sequence by 31% and show a factor of 10-60 variation in substrate specificity. For 19 residues that are... 

Cat heps in C, dipeptidyl transferase, dipeptidyl amino peptidase I. Isoln from beef spleen Tallan el al, J. Biot. Chem. 194, 793 (1952) de la Haba et al, ibid. 234, 316 0 959)-Hydrolyzes dipeptidyl amides or esters bearing a free a-amino (or a-imino) group in the N-terminal position, esp. those containing an aromatic amino acid adjacent to the free a -amino group Planta, Gruber, Biochtm. Biophys. Acta 53, 443 (1961) Wurz et al. Biochemistry 1, 19 (1962). Enhances the proteolysis of prothrombin to thrombin and thus plays an important role in blood dotting Purcell, Barnhart, flio-chim. Biophys. Acta 78, 800 (1963),... 

In spite of the fact that succinic dehydrogenase has been known to exist for half a century and that many laboratories have attempted to study its mode of action, little is known of its mode of regulation. The 23 amino acids adjacent to the flavin have been sequenced. 

Randic (2012) introduced a novel approach to the problem of protein alignments. It is based on superposition of amino acid adjacent matrices of a pair of proteins, which have been modified to record the sequential order of amino acids. 

Let us introduce the amino acid adjacency matrix (AAA matrix) [24] as a tool of graphical bioinformatics. This is a 20 x 20 matrix, the rows and columns of which belong to 20 natural amino acids, which have been ordered as follows ... 

AAA matrices have been fonnd of interest for characterization of segments of proteins and whole proteins in their comparative studies. Invariants of the AAA matrix have been nsed for characterization of proteins. As we will see in the next section, 20-component vectors based on the differences in rows and colnmns of the AAA matrix were nsed in nenral network analysis for characterization of transmembrane regions of ND6 proteins in order to discriminate between transmembrane and non-transmembrane regions of ND6 proteins [25]. In another stndy, El-Lakkani and El-Sherif [26] presented a 3-D amino acid adjacency matrix nsed on nine ND5 proteins of different species and found high correlation between their results in comparison with results obtained with ClustalW program [27]. Similarly, independently invariants from amino acid adjacency matrix and decagonal isometric matrix were also constructed and similarly nsed in neural network analysis. 

The two matrix representations of the protein segments, the amino acid adjacency matrix and the decagonal isometries matrix, are derived from the sequence information alone. As has been demonstrated, mathematical descriptors, dependent on the sequence information alone, have successfully revealed the underlying characteristics and patterns of given sequences. Their numerical nature also makes them easier to incorporate into a mathematical model. In addition, as has been well illustrated in chemical graph theory, when considering characterization of molecules, one can... 

One of the present authors arrived at the exact solution of the protein alignment problem [34] by modifying the amino acid adjacency matrix [24]. The amino acid adjacency matrix (AAA), as mentioned before, is a 20 x 20 matrix, in which each row and column belong to one of the 20 natural amino acids. The matrix elanent (AAA)ij counts how many times in the primary sequence of a protein is amino acid i followed by amino acid j. The 20 amino acids have been ordered as follows ... 

The AAA matrix for theND6 human protein of Table 13.9 is shown in Matrix 13.3. The first row of the amino acid adjacency matrix for the ND6 human protein thus is... 

It registers the presence of the pairs AR, AG, AI, and AW occurring once and the pairs AL and AM occurring twice in the primary sequence of the ND6 human protein. The zeros indicate that in the sequence of this protein there are no adjacent amino acids AA, AN, AD, AC, AQ, and so on. Similarly, the first row of the amino acid adjacency matrix for the ND6 protein of mouse, the second protein of Table 13.9, is... 

In the case of the AAA matrix, in order to recover the lost information on the location of individual amino acids in the sequence of proteins, one should record the sequential numbers of adjacent amino acids rather than their abundance. This is possible by modifying the amino acid adjacency matrix and using the sequential labels of amino acids as input so that the resulting matrix has full information on protein sequences. The so-modified AAA matrix allows, if required, reconstruction of the protein sequence. Observe that now the matrix elements are not numbers, but sets of numbers, the special case of which are numbers that can also be viewed... 

Amino acid adjacency matrices, which in addition to the information on abundance of individual amino acids also give the count of successive pairs of amino acids, are accompanied by some loss of information, in the view that information on the location of various pairs is not known. A remedy for this loss of information is to record the locations of pairs of adjacent amino acids rather than just their occurrence. In this way, the AAA matrix of Matrix 13.13 has a new form shown in Matrix 13.4, in which we show only the portion of the matrix involving elements G-V. The modified AAA matrix shown in Matrix 13.5 is associated with the sequence of the first 45 amino acids of the human ND6 protein. Observe the elements (G, L) and (G, F) that have in the corresponding AAA matrix the abundance count 2, are now replaced by two sequential numbers. Although many matrix elements of the modified AAA matrix may remain to be single numbers, in general, the elements of the modified AAA matrix are not numbers, but sets, that is, collections of numbers. In Matrix 13.5, we show the same portion of the AAA matrix for the second protein of Table 13.10. 

Full program (Appendix 16), which prints as output (i) the sequential numbers of all amino acid adjacent pairs for the pair of proteins considered, and (ii) the sequential numbers for amino acids having the same sequential shift (differences in sequential locations). 

M. Randid, M. Novic, and M. Vracko, On novel representation of proteins based on amino acid adjacency matrix, SAR QSAR Environ. Res. 19 (2008) 339-349. 

A. El-Lakkani and S. El-Sherif, Similarity analysis of protein sequences based on 2D and 3D amino acid adjacency matrices, Chem. Phys. Lett. 590 (2013) 192-195. 

The eukaryotic homolog of the HTH motif consists of two apparent amphi-pathic helices (60—90 amino acids) connected by a short loop of 10—25 amino acids, thus more appropriately called HLH (47—49). The eukaryotic HLH is physically larger than the prokaryotic counterpart HTH motif. Most significantly, unlike HTH proteins, the actual DNA-binding motif of the HLH proteins is a stretch of about 13 basic amino acids adjacent to the HLH whose main role... 

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