title: Modeling disordered protein interactions from biophysical principles.
abstract: Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Lenna X
authors.identifier: 0000-0001-7734-1784
authors.initials: LX
authors.lastname: Peterson
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.|Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America.|Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana, United States of America.
authors.forename: Amitava
authors.identifier: 0000-0002-9100-4108
authors.initials: A
authors.lastname: Roy
authors.affiliation: Department of Computer Science, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Charles
authors.initials: C
authors.lastname: Christoffer
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.|School of Pharmacy, Kitasato University, Tokyo, Japan.
authors.forename: Genki
authors.initials: G
authors.lastname: Terashi
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.|Department of Computer Science, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Daisuke
authors.identifier: 0000-0003-4091-6614
authors.initials: D
authors.lastname: Kihara
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D064267:Intrinsically Disordered Proteins / Q000737:chemistry* / Q000378:metabolism*; D051379:Mice; D008958:Models, Molecular; D011485:Protein Binding; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D064267:Intrinsically Disordered Proteins