title: Structure prediction and docking-based molecular insights of human YB-1 and nucleic acid interaction.
abstract: Y-box-binding protein 1 (YB-1), a cold shock domain protein, is one of the most conserved nucleic acid-binding proteins. The multifunctional human YB-1 is a member of a large family of proteins with an evolutionary ancient cold shock domain. The presence of a cold shock domain is a specific feature of Y-box-binding proteins and allows attributing them to a wider group of proteins containing a cold shock domain. This protein is involved in a number of cellular processes including proliferation, differentiation and stress response. The YB-1 performs its function both in the cytoplasm and in the cell nucleus. In this study, we present the structure of full-length human YB-1 protein along with investigation of their nucleic acid-binding preferential. The study also focuses on biases for particular purine and pyrimidine bases. The overall goal of this study was to model and validate full-length YB-1 protein and to compare its nucleic acid-binding studies with previous reports.
authors.affiliation: a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad 211004 , India.
authors.forename: Birendra Singh
authors.initials: BS
authors.lastname: Yadav
authors.affiliation: b Center of Bioinformatics , Nehru Science Center, Institute of Interdisciplinary Studies, University of Allahabad , Allahabad 211002 , India.
authors.forename: Swati
authors.initials: S
authors.lastname: Singh
authors.affiliation: c Department of Biotechnology , National Institute of Technology , Durgapur 713209 , India.
authors.forename: Amit Kumar
authors.initials: AK
authors.lastname: Shaw
authors.affiliation: a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad 211004 , India.
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Mani
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D017124:Conserved Sequence; D006801:Humans; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry*; D010802:Phylogeny; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D013329:Structure-Activity Relationship; D051840:Y-Box-Binding Protein 1 / Q000737:chemistry* / Q000145:classification / Q000235:genetics
chemical_list: D009696:Nucleic Acids; D051840:Y-Box-Binding Protein 1
keywords: YB-1; cold shock domain; docking; protein structure prediction