Plastocyanins

RUSTICyANIN

RUSTICyANIN

Fig. 4. Clusterization of the proteins listed in Table 1 in the sequence identity space. Each point represents a protein.

tecture. Therefore, the use of structural information is particularly relevant for the correct analysis of the differences that have arisen among these proteins during evolution.

Computed pairwise sequence identity percentages (reported in Table 2) as ID(a,b) were derived from the structure-based sequence alignments as follows:

where n is the number of identical residues in the same alignment position of proteins a and b and N is the total number of aminoacids in the shortest of the two sequences compared.

ID(a, b) values were used as sequence similarity descriptors. A distance matrix, obtained by computing distances between any two proteins a and b [^(a,b)] in sequence space, as was then used for a cluster analysis as described in detail in De Rienzo et al. (19). The resulting distribution, shown in Fig. 4, clearly highlights how the different subfamilies are clustered in different regions of sequence space and how every member of a subfamily is closer to its own cluster than to any other one.

From the sequence analyses, we can state that all the plastocyanins (both eukaryotic and cyanobacterial) and the amicyanins belong to the same cluster, in agreement with previous spectro-scopic studies results (31). Azurins and pseudoazurins define two well-separated families and the same can also be hypothesized for rusticyanin, stellacyanin, and BCP, although only one structure is known for each of these protein families, at present.

2.2. Protein Interaction Property Similarity Analysis (PIPSA)

Many problems complicate the study of the interaction properties of cupredoxins. First, different surface properties can influence the recognition and diffusion of the proteins toward their partners at different stages of the binding process. For example, whereas hydrophobic properties are important for short-range docking interactions, electrostatics are a determinant for long-range recognition and protein steering. The extent to which these properties, in particular the electrostatic interactions, are

Table 2

Pairwise Structure-Based Sequence Identity Percentages [ID(a,b)] Computed for the Oxidized Form of the Proteins in Table 1

Table 2

Pairwise Structure-Based Sequence Identity Percentages [ID(a,b)] Computed for the Oxidized Form of the Proteins in Table 1

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