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A mutation data matrix for transmembrane proteins
Author(s) -
Jones D.T.,
Taylor W.R.,
Thornton J.M.
Publication year - 1994
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(94)80429-x
Subject(s) - mutagenesis , context (archaeology) , matrix (chemical analysis) , mutation , sequence (biology) , membrane protein , computational biology , globular protein , transmembrane protein , protein data bank , viral matrix protein , peptide sequence , genetics , protein structure , chemistry , biology , biochemistry , membrane , gene , paleontology , receptor , chromatography
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.