A mutation data matrix for transmembrane proteins

By David C. Jones, William R. Taylor, Janet M. Thornton. 1994

The widely used Mutation Data Matrix (MDM), is an amino acid comparison matrix calculated from a study of the exchange probabilities (or odds) derived from an analysis of the evolutionary changes seen in groups of very similar proteins. In this work, a mutation data matrix is calculated for membrane spanning segments. This new mutation data matrix is found to be very different from matrices calculated from general sequence sets which are biased towards water‐soluble globular proteins, and the differences are discussed in the context of specific structural requirements of membrane spanning segments. This new matrix will help improve the accuracy of integral membrane protein sequence alignments, and could also be of use in the rational design of site directed mutagenesis experiments for this class of proteins.

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, neutral): “The ––bl , ––jtt , and ––tm options mean BLOSUM (Henikoff S and Henikoff JG 1992), JTT (Jones et al. 1992), and a transmembrane model (Jones et al. 1994), respectively.”
Domain enhanced lookup time accelerated BLAST (2012, background): “Sequence similarity searches generally perform better at detecting distantly related homologs when they use either matrices specialized for particular protein classes [3-11], or position-specific score matrices (PSSMs) [12-23].”
Amino‐Acid Properties and Consequences of Substitutions (2003, background): “…useful feature is that they can be calculated for different datasets to account for some of the protein features that effect amino acid properties, such as cellular locations (Jones et al., 1994) or different evolutionary distances (e.g. orthologues or paralogues; Henikoff and Henikoff, 1992).”
Discriminative modelling of context-specific amino acid substitution probabilities (2012, background): “Methods that infer substitution probabilities of amino acids solely from their local sequence context have the advantage that they do not require the structure of the query protein to be known (Jones et al. , 1994; Baussand et al. , 2007; Huang and Bystroff, 2006).”
Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. (2000, methodology): “Two sequences were compared in all possible frame shifts using a 100 PAM matrix derived from the Mutation Probability Matrix of Jones et al. (1994) and the maximum score was recorded as the similarity score of the pair.”
PHAT: a transmembrane-specific substitution matrix (2000, methodology): “We demonstrate that in searches on queries consisting of putative transmembrane regions, the PHAT matrix signifi cantly outperforms both the generalized matrices, BLOSUM and JTT PAM, as well as the JTT transmembrane matrix ( Jones et al., 1994 ).”