title: Intrinsically disordered proteins--relation to general model expressing the active role of the water environment.
abstract: This work discusses the role of unstructured polypeptide chain fragments in shaping the protein's hydrophobic core. Based on the "fuzzy oil drop" model, which assumes an idealized distribution of hydrophobicity density described by the 3D Gaussian, we can determine which fragments make up the core and pinpoint residues whose location conflicts with theoretical predictions. We show that the structural influence of the water environment determines the positions of disordered fragments, leading to the formation of a hydrophobic core overlaid by a hydrophilic mantle. This phenomenon is further described by studying selected proteins which are known to be unstable and contain intrinsically disordered fragments. Their properties are established quantitatively, explaining the causative relation between the protein's structure and function and facilitating further comparative analyses of various structural models.
authors.affiliation: Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland.
authors.forename: Barbara
authors.initials: B
authors.lastname: Kalinowska
authors.affiliation: Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Banach
authors.affiliation: Chair of Medical Biochemistry, Medical College, Jagiellonian University, Krakow, Poland.
authors.forename: Leszek
authors.initials: L
authors.lastname: Konieczny
authors.affiliation: Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland.
authors.forename: Damian
authors.initials: D
authors.lastname: Marchewka
authors.affiliation: Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland. Electronic address: myroterm@cyf-kr.edu.pl.
authors.forename: Irena
authors.initials: I
authors.lastname: Roterman
mesh_terms: D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D008958:Models, Molecular; D014867:Water / Q000737:chemistry*
chemical_list: D064267:Intrinsically Disordered Proteins; D014867:Water
keywords: Fuzzy oil drop model; Hydrophobicity; Intrinsically disordered proteins