Sequence substitution tables, proteins

One of the key aspects of sequence comparison is the understanding of similarity when applied to molecular sequences. There are essentially two ways of considering this simple residue identity and residue substitution. In this discussion, we consider the comparison of two protein sequences, but the process is the same for comparison of DNA or RNA sequences. The alphabet used in the comparison is just different because it is 20 for protein sequences and 4 for DNA and RNA. comparing residues at the same position in each sequence and counting up the number of identities we arrive at, a score that can be expressed as a percentage match for the pair of sequences. The alternative method compares each pair of residues and looks up a score for that pair in a substitution table or scoring matrix. The summed score across the whole se-... 

Many proteins share structural similarities due to the evolutionary process involving substitutions, insertions and deletions in amino add sequences. Consequently protein structures can be characterized according to their connnon substructures (supersecondary structures, e.g. motifs, domains). For proteins with conserved functions, the structural environments of critical active site residues are also conserved. In an attempt to better understand seqnence-structuie relationships and the underlying evolutionary processes that give rise to different fold famihes, a variety of structure classification schemes have been established. Analyses of the 3D structures archived in PDB generate various databases for the specification/search of characteristic substructures and protein structure classifications (Table 16.6). 

Table 8.6 lists the mass differences due to the substitutions of a given amino acid by another in the sequence of a peptide chain [101]. The accuracy of the molecular mass determination is critical for the success of the mutation characterization. The required accuracy depends not only on the determined molecular mass, but also on the detected substitution. Indeed, the characterization of Gln/Lys substitution needs less accurate mass measurement with a 1 kDa peptide than with a 40kDa protein. In the same way, the characterization of Gly/Trp substitution is easier than the characterization of Gln/Lys substitution. 

PAM Point Accepted Mutation. The PAM matrix is a frequency table representing substitution rates for closely related proteins at the particular evolutionary distance represented by multiple sequence alignments. 

The modified Mth RIRl, Mxe GyrA, and Ssp DnaB mini-inteins have been recently applied to the isolation of proteins with an N-terminal cysteine residues (29,30). These inteins undergo temperature- and pH-dependent C-termi-nal cleavage when the N-terminal cysteine residue of the intein is substituted with alanine (Table 2). The target protein is recombinantly expressed as a fusion protein with the C-terminal intein tag (31) (Fig. 3B). After intein splicing the protein that possesses N-terminal cysteine is generated. Moreover, such a protein can be obtained by total chemical synthesis and different chemical labels or non-canonical amino acids can be site-specifically incorporated into the sequence. 

Kelch and WD repeats consist of repeated sequence motifs with hallmark residues spaced at regular intervals (Fig. 1). In each case, only a handful of residues arc consistently conserved (bold residues in Fig. 1 sequence alignments) and even these positions can tolerate substitutions, making the identification of all repeats by sequence scanning algorithms alone difficult. In a number of cases, additional repeats present in a protein were only recognized after structural determination (Table 1). 

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