Template-Based Modeling of Protein-RNA Interactions.
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.
School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei, China.
Jinfang
J
Zheng
Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, United States of America.
Petras J
PJ
Kundrotas
Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, United States of America.
Ilya A
IA
Vakser
School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei, China.
Shiyong
0000-0001-7986-5178
S
Liu
D000595:Amino Acid Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D012984:Software
D016601:RNA-Binding Proteins; D012313:RNA
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