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Sequence-Based Prediction of RNA-Binding Residues in Proteins

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Prediction of Protein Secondary Structure

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1484))

Abstract

Identifying individual residues in the interfaces of protein–RNA complexes is important for understanding the molecular determinants of protein–RNA recognition and has many potential applications. Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein–RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. Step-by-step protocols for using three different web-based servers to predict RNA-binding residues are described. In addition, currently available web servers and software tools for predicting RNA-binding sites, as well as databases that contain valuable information about known protein–RNA complexes, RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. We emphasize sequence-based methods that can reliably identify interfacial residues without the requirement for structural information regarding either the RNA-binding protein or its RNA partner.

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Acknowledgments

This work was supported in part by NSF DBI0923827 to DD, by NIH GM066387 to VGH and DD, by a Presidential Initiative for Interdisciplinary Research (PIIR) award to DD from Iowa State University, and by the Edward Frymoyer Chair in Information Sciences and Technology held by VGH at Pennsylvania State University. RRW is currently supported by an appointment to the ARS-USDA Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the US Department of Energy (DOE) and USDA. ORISE is managed by ORAU under DOE contract number DE-AC05-06OR23100. We thank Carla Mann and Usha Muppirala for valuable discussions.

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Authors and Affiliations

  1. USDA-ARS, Ames, IA, 50011, USA

    Rasna R. Walia

  2. College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA

    Yasser EL-Manzalawy & Vasant G. Honavar

  3. Genetics, Development and Cell Biology Department, Iowa State University, 3112 Molecular Biology Building, Ames, IA, 50011-3650, USA

    Drena Dobbs

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  1. Rasna R. Walia
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  2. Yasser EL-Manzalawy
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  3. Vasant G. Honavar
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  4. Drena Dobbs
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Corresponding author

Correspondence to Drena Dobbs .

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Editors and Affiliations

  1. Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, Queensland, Australia

    Yaoqi Zhou

  2. Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA

    Andrzej Kloczkowski

  3. Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA

    Eshel Faraggi

  4. Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, Queensland, Australia

    Yuedong Yang

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Walia, R.R., EL-Manzalawy, Y., Honavar, V.G., Dobbs, D. (2017). Sequence-Based Prediction of RNA-Binding Residues in Proteins. In: Zhou, Y., Kloczkowski, A., Faraggi, E., Yang, Y. (eds) Prediction of Protein Secondary Structure. Methods in Molecular Biology, vol 1484. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6406-2_15

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  • DOI: https://doi.org/10.1007/978-1-4939-6406-2_15

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