Abstract 844: RNA binding domains of nucleolin exhibit specificity in driving nucleolin-miRNA interactions: An in silico modeling and RNA-protein docking study

Abstract

Abstract Nucleolin (NCL) is a stress responsive multifunctional RNA binding protein (RBP) that plays important roles in gene transcription and RNA metabolism. NCL levels and similarly many of NCL RNA targets are dysregulated in multiple human cancers. NCL- RNA interactions are driven by its four RNA binding domains (RBDs). Despite the myriad NCL functions that involve its RNA-binding properties, the mechanisms driving these interactions are poorly understood. Partial three-dimensional structural information available on NCL RBDs in the RCSB PDB database, is not sufficient to provide a comprehensive understanding of NCL- RNA interactions. To get a better insight into RNA binding specificity for its diverse targets, we have built upon the existing NCL-RBDs structures to generate multiple combinations of RBDs in tandem, using in silico modeling approaches. In this study, we analyze NCL-miRNA interactions in depth with a focus on a subset of miRNAs that are implicated in breast cancer. Using both template-based and ab initio approaches, we have generated complete and robust structural models of all 4 NCL RBDs in tandem and in combinations of two different RBDs in sequence. All models were then tested using a variety of structural quality evaluation programs. Models with top validation scores were used in RNA-protein docking algorithms and assessed for interaction with specific miRNA. Our docking analyses have generated a comprehensive map of the miRNA-NCL protein interface sites for each individual miRNA and consistently predict specific RBDs in NCL-miRNA binding. We have also identified critical residues on the NCL-RBDs that may drive the miRNA binding in an RBD-type specific manner. Our results corroborate previous studies on RBDs from other RBPs. Structural information derived from this study provides a valuable perspective for future experiments. Identification of consensus on RNA binding motifs on NCL RBDs is critical in elucidating RNA target specificity by NCL. Computational analyses provide time and cost-effective benefits over experimental techniques; the in silico predictions are important in designing rational experiments for the future investigations confirming the NCL-miRNA interactions. Our study provides the foundational steps for establishing consensus motifs on NCL-RBDs that potentially direct RNA target specificity. Targeting these specific binding sites will provide new approaches to regulate NCL functions in gene expression during tumorigenesis. Citation Format: Avdar San, Anjana Saxena, Shaneen Singh. RNA binding domains of nucleolin exhibit specificity in driving nucleolin-miRNA interactions: An in silico modeling and RNA-protein docking study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 844.