title: Recurrence quantification analysis in structure-function relationships of proteins: an overview of a general methodology applied to the case of TEM-1 beta-lactamase.
abstract: Protein structure-function relationships have been increasingly scrutinized by a variety of correlational and information theoretic measures. In an effort to extend this methodology, a technique originally developed in non-linear science, recurrence quantification analysis, was combined with traditional principal components analysis to study a large number (56) of TEM-1 beta-lactamase mutants. The hydrophobicity profiles corresponding to the primary structure of 13 naturally occurring mutations partially impairing function, together with 43 artificial non-tolerated mutations were subjected to discriminant analysis, derived from the results of recurrence quantification analysis, coupled to a principal exponents extraction. Eleven (85%) of the naturally occurring mutants and 36 (84%) of the artificial mutants were correctly classified (p < 0.0001). We conclude that this technique may be useful in protein engineering and, in general, in structure-function studies of biopolymers.
authors.affiliation: Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612, USA.
authors.forename: J P
authors.initials: JP
authors.lastname: Zbilut
authors.forename: A
authors.initials: A
authors.lastname: Giuliani
authors.forename: C L
authors.initials: CL
authors.lastname: Webber
authors.forename: A
authors.initials: A
authors.lastname: Colosimo
mesh_terms: D000595:Amino Acid Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D008433:Mathematics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009154:Mutation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D001618:beta-Lactamases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D001618:beta-Lactamases; C034413:beta-lactamase TEM-1