title: Correlated mutation analyses on super-family alignments reveal functionally important residues.
abstract: Correlated mutation analyses (CMA) on multiple sequence alignments are widely used for the prediction of the function of amino acids. The accuracy of CMA-based predictions is mainly determined by the number of sequences, by their evolutionary distances, and by the quality of the alignments. These criteria are best met in structure-based sequence alignments of large super-families. So far, CMA-techniques have mainly been employed to study the receptor interactions. The present work shows how a novel CMA tool, called Comulator, can be used to determine networks of functionally related residues in enzymes. These analyses provide leads for protein engineering studies that are directed towards modification of enzyme specificity or activity. As proof of concept, Comulator has been applied to four enzyme super-families: the isocitrate lyase/phoshoenol-pyruvate mutase super-family, the hexokinase super-family, the RmlC-like cupin super-family, and the FAD-linked oxidases super-family. In each of those cases networks of functionally related residue positions were discovered that upon mutation influenced enzyme specificity and/or activity as predicted. We conclude that CMA is a powerful tool for redesigning enzyme activity and selectivity.
authors.affiliation: Centre of Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands.
authors.forename: Remko K P
authors.initials: RK
authors.lastname: Kuipers
authors.forename: Henk-Jan
authors.initials: HJ
authors.lastname: Joosten
authors.forename: Eugene
authors.initials: E
authors.lastname: Verwiel
authors.forename: Sjoerd
authors.initials: S
authors.lastname: Paans
authors.forename: Jasper
authors.initials: J
authors.lastname: Akerboom
authors.forename: John
authors.initials: J
authors.lastname: van der Oost
authors.forename: Nicole G H
authors.initials: NG
authors.lastname: Leferink
authors.forename: Willem J H
authors.initials: WJ
authors.lastname: van Berkel
authors.forename: Gert
authors.initials: G
authors.lastname: Vriend
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Schaap
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D005956:Glucose-6-Phosphate Isomerase / Q000737:chemistry / Q000235:genetics; D006593:Hexokinase / Q000737:chemistry / Q000235:genetics; D007522:Isocitrate Lyase / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D016296:Mutagenesis; D010088:Oxidoreductases / Q000737:chemistry / Q000235:genetics; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000737:chemistry / Q000235:genetics; D017433:Protein Structure, Secondary; D012984:Software
chemical_list: D010088:Oxidoreductases; D044925:Oxidoreductases Acting on CH-CH Group Donors; C093910:galactonolactone dehydrogenase; D006593:Hexokinase; D007522:Isocitrate Lyase; D005956:Glucose-6-Phosphate Isomerase