Appropriate cellular localization plays a key role in regulating protein functions. Active traffic of macromolecules across the nuclear membrane through the nuclear pore complex (NPC) is mediated primarily by members of the Karyopherin 2 family (Kap2), which bind their transport substrates through distinct nuclear localization or export signals (NLSs or NESs). The long term objectives of the applicant are to understand the recognition mechanisms and functional programs for each Kap2 pathway. This project focuses on the most prominent export- Kap2 CRM1. CRM1 is the nuclear export receptor for hundreds of macromolecules with diverse functions, and hence is an important regulator of many cellular processes. This proposal describes a computational/bioinformatics project to compile an up-to-date LR-NES database and develop a structure- and sequence-based LR-NES prediction program. The first goal of this project is to compile a LR-NES database that will include most of the experimentally validated natural and synthetic LR-NES containing proteins published in the literature. The information will be stored in a MySQL database and be made available through the Internet. Each entry will include the detailed information for the protein regarding its export properties, such as the functional export signal, critical residues required for export, determined or predicted secondary structure of the export signal, etc. The second goal of this project is to develop a structure- and sequence-based LR-NES prediction algorithm. The consensus sequence of LR-NESs is diverse, vague, and prevalent. As a result, the only available predictor of LR-NES, which is based on sequence alone, is only marginally useful. This project seeks to use the structural requirements obtained from the newly available crystal structure of CRM1 bound to a LR-NES- containing cargo to filter the LR-NES sequence patterns and thereby greatly increase the prediction accuracy. The project will provide insights into how different NESs interacts with CRM1 and aid in the development of future therapeutics (inhibitors and gene targeting agents) targeted at the CRM1 export pathway to control various disease states including cancer and viral replications.
This proposal describes a bioinformatics project to compile a database and a prediction program for the leucine-rich nuclear export signals recognized by CRM1, which is a nuclear export receptor for hundreds of proteins with diverse functions. The results of the project will provide insights into how different nuclear export signals interact with CRM1 and thereby aid in the development of future therapeutics targeted at the CRM1 export pathway to control various diseases including cancer, cardiac hypertrophy, dengue fever and AIDS.
| Xu, Darui; Marquis, Kara; Pei, Jimin et al. (2015) LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins. Bioinformatics 31:1357-65 |
| Xu, Darui; Farmer, Alicia; Collett, Garen et al. (2012) Sequence and structural analyses of nuclear export signals in the NESdb database. Mol Biol Cell 23:3677-93 |
| Xu, Darui; Grishin, Nick V; Chook, Yuh Min (2012) NESdb: a database of NES-containing CRM1 cargoes. Mol Biol Cell 23:3673-6 |
