title: Solution structure and backbone dynamics of human Raf-1 kinase inhibitor protein.
abstract: Human Raf-1 kinase inhibitor protein (hRKIP) is a small multi-functional protein of 187 residues. It contains a conserved pocket, which binds a wide range of ligands from various small molecules to distinct proteins. To provide a structural basis for the ligand diversity of RKIP, we herein determined the solution structure of hRKIP, and analyzed its structural dynamics. In solution, hRKIP mainly comprises two antiparallel β sheets, two α helices and two 3₁₀ helices. NMR dynamic analysis reveals that the overall structure of hRKIP is rigid, but its C-terminal helix which is close to the ligand-binding site is mobile. In addition, residues around the ligand-binding pocket exhibit significant conformational exchange on the μs-ms timescale. Conformational flexibility may allow the ligand-binding pocket and the C-terminal helix to adopt various conformations to interact with different substrates. This work may shed light on the underlying molecular mechanisms of how hRKIP recognizes and binds diverse substrate ligands.
authors.affiliation: The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
authors.forename: Chenyun
authors.initials: C
authors.lastname: Guo
authors.forename: Cuiying
authors.initials: C
authors.lastname: Yi
authors.forename: Yu
authors.initials: Y
authors.lastname: Peng
authors.forename: Yi
authors.initials: Y
authors.lastname: Wen
authors.forename: Donghai
authors.initials: D
authors.lastname: Lin
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D049488:Phosphatidylethanolamine Binding Protein / Q000737:chemistry* / Q000648:ultrastructure*; D011485:Protein Binding; D011487:Protein Conformation; D019908:Proto-Oncogene Proteins c-raf / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: C511482:PEBP1 protein, human; D049488:Phosphatidylethanolamine Binding Protein; D019908:Proto-Oncogene Proteins c-raf
keywords: FMN; G-protein coupled receptor; GDP; GPCR; GTP; HSQC; Human Raf-1 kinase inhibitor protein (hRKIP); Ligand-binding pocket; MAPK; Model-free analysis; NF-κB; NMR; NOE; NOESY; PE; Protein dynamics; R(1); R(2); R(ex); RKIP; RMSD; Raf-1 kinase inhibitor protein; S(2); Solution structure; conformational exchange rate; flavin mononucleotide; guanosine di-phosphate; guanosine tri-phosphate; heteronuclear singular quantum correlation; longitudinal relaxation rate; mitogen-activated protein kinase; nuclear factor-kappa B; nuclear overhauser effect; nuclear overhauser enhancement spectroscopy; o-phosphorylethanolamine; order parameters; root-mean-square deviation; transverse relaxation rate