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.

Keywords:

• YB-1
• protein structure prediction
• cold shock domain
• docking

Acknowledgements

BSY is thankful to DST, New Delhi, for a fellowship. SS is thankful to UGC, New Delhi, for a fellowship. AKS is thankful to TEQIP II training stipend from MNNIT, Allahabad. AM is thankful to a project grant from SERB, New Delhi.