Amino acid substitution matrices models

The possibility of introducing single-site mutations in azurins enabled a detailed analysis of structure-reactivity relationships where, for example, the impact of specific amino acid substitutions on the rate of intramolecular FT could be investigated. In order to understand better the role of the polypeptide matrix separating electron donor and acceptor on FT reactivity, the structure-dependent theoretical model developed by Beratan et al. (6, 7) was employed to identify relevant ET pathways (cf. Section I.B). In this model, the total electronic coupling of a pathway is calculated as a repeated product of the couplings of the individual links. The optimal pathway connecting the two redox sites, is thus identified (cf. Eq. 5). 

The most widely used models of amino acid substitution include distance-based methods, which are based on matrixes such as PAM and BLOSUM. Again, such matrices are described fiuther in other chapters in this book. Briefly, Dayhoff s PAM 001 matrix (Dayhoff, 1979) is an empirical model that scales probabilities of change from one amino acid to another in terms of an expected 1% change between two amino acid sequences. This matrix is used to make a transition probability matrix that allows prediction of the probability of changing from one amino acid to another and also predicts equilibriiun amino acid composition. Phylogenetic distances are calculated with the assumption that the probabilities in the matrix are correct. The... 

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