Proteins context

Campagne, F. and Weinstein, H. (1999) Schematic representation of residue-based protein context-dependent data an application to transmembrane proteins. J. Mol. Graph. Model 17,207-213. 

Fig. 14. Localization of homologous modules in the HAD superfamily in representative larger protein contexts as described in the text. Gray-stippled regions represent the HAD superfamily homologs.

Another frequently used global information that covers protein context is the residue frequencies. The composition is often calibrated with that from the database as in Gamier et al. (1996), where only observed frequencies of amino acids and amino acid pairs are used for protein secondary structure prediction. 

The molecular basis for the evolution of distinct kdr mutations in different insects and arachnids remains unclear. Assuming that the pyrethroid binding site(s) (and/or the pyrethroid response domain) is composed of multiple amino acid residues, there are two ways by which different mutations can be selected in different insects and arachnids. First, the random mutation hypothesis mutation in any pyrethroid binding site/response domain affects pyrethroid toxicity without impacting normal sodium channel functional properties. Thus, selection of different mutations in different insects and arachnids is purely random. Second, the nonrandom mutation hypothesis mutation in any pyrethroid binding site/response domain affects pyrethroid toxicity, but some mutations also drastically alter normal sodium channel functional properties in one species, but not in another, presumably because of different sodium channel backbone sequences. That is, there may be severe fimess costs for some mutations, if placed out of their native protein context. 

VI. The Recognition of Specific CaaX Motifs is Influenced by Protein Context... 

Figure 3.55. Alternative Conformations of a Peptide Sequence. Many sequences can adopt alternative conformations in different proteins. Here the sequence VDLLKN shown in red assumes an a helix in one protein context (left) and a P strand in another (right).

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