title: In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces.
abstract: We provide first large scale analysis of the peculiarities of surface areas of 5658 dissimilar (below 50% sequence similarity) proteins with known 3D-structures that bind to proteins, DNA or RNAs. We show here that area of the protein surface is highly correlated with the protein length. The size of the interface surface is only modestly correlated with the protein size, except for RNA-binding proteins where larger proteins are characterized by larger interfaces. Disordered proteins with disordered interfaces are characterized by significantly larger per-residue areas of their surfaces and interfaces when compared to the structured proteins. These result are applicable for proteins involved in interaction with DNA, RNA, and proteins and suggest that disordered proteins and binding regions are less compact and more likely to assume extended shape. We demonstrate that disordered protein binding residues in the interfaces of disordered proteins drive the increase in the per residue area of these interfaces. Our results can be used to predict in silico whether a given protomer from the DNA, RNA or protein complex is likely to be disordered in its unbound form.
authors: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, PR China.
authors: Zhonghua
authors: Z
authors: Wu
authors: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, PR China.
authors: Gang
authors: G
authors: Hu
authors: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, PR China.
authors: Jianyi
authors: J
authors: Yang
authors: Center for Applied Mathematics, Tianjin University, Tianjin, PR China.
authors: Zhenling
authors: Z
authors: Peng
authors: Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation. Electronic address: vuversky@health.usf.edu.
authors: Vladimir N
authors: VN
authors: Uversky
authors: Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. Electronic address: lkurgan@ece.ualberta.ca.
authors: Lukasz
authors: L
authors: Kurgan
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D064267:Intrinsically Disordered Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D015203:Reproducibility of Results; D013499:Surface Properties
chemical_list: D064267:Intrinsically Disordered Proteins; D046912:Multiprotein Complexes; D012313:RNA; D004247:DNA
keywords: Binding interface; Binding surface; Intrinsic disorder; Protein–DNA interaction; Protein–RNA interaction; Protein–protein interaction