title: Systematic analysis of tropomodulin/tropomyosin interactions uncovers fine-tuned binding specificity of intrinsically disordered proteins.
abstract: An intriguing regulatory mechanism is the ability of some proteins to recognize their binding partners in an isoform-specific manner. In this study we undertook a systematic analysis of the specificity of the tropomodulin (Tmod) interaction with tropomyosin (TM) to show that affinities of different Tmod isoforms to TM are isoform-dependent. Intrinsic disorder predictions, alignment of sequences, and circular dichroism were utilized to establish a structural basis for these isoform-specific interactions. The affinity of model peptides derived from the N-terminus of different TM isoforms to protein fragments that correspond to the two TM-binding sites of different Tmod isoforms were analyzed. Several residues were determined to be responsible for the isoform-dependent differences in affinity. We suggest that changing a set of residues rather than a single residue is needed to alter the binding affinity of one isoform to mimic the affinity of another isoform. The general intrinsic disorder predictor, PONDR® VLXT, was shown to be a useful tool for analyzing regions involved in isoform-specific binding and for predicting the residues important for isoform differences in binding. Knowing the residues responsible for isoform-specific affinity creates a tool suitable for studying the influence of Tmod/TM interactions on sarcomere assembly in muscle cells or actin dynamics in non-muscle cells.
authors.affiliation: Department of Biochemistry and Molecular Biology, Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA. vuversky@iupui.edu
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Uversky
authors.forename: Samar P
authors.initials: SP
authors.lastname: Shah
authors.forename: Yulia
authors.initials: Y
authors.lastname: Gritsyna
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Hitchcock-DeGregori
authors.forename: Alla S
authors.initials: AS
authors.lastname: Kostyukova
mesh_terms: D001665:Binding Sites; D002942:Circular Dichroism; D006801:Humans; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D051348:Tropomodulin / Q000235:genetics / Q000378:metabolism*; D014335:Tropomyosin / Q000235:genetics / Q000378:metabolism*
chemical_list: D020033:Protein Isoforms; D051348:Tropomodulin; D014335:Tropomyosin