RNA-binding residues prediction using structural features

BackgroundRNA-protein complexes play an essential role in many biological processes. To explore potential functions of RNA-protein complexes, it’s important to identify RNA-binding residues in proteins.ResultsIn this work, we propose a set of new structural features for RNA-binding residue prediction. A set of template patches are first extracted from RNA-binding interfaces. To construct structural features for a residue, we compare its surrounding patches with each template patch and use the accumulated distances as its structural features. These new features provide sufficient structural information of surrounding surface of a residue and they can be used to measure the structural similarity between the surface surrounding two residues. The new structural features, together with other sequence features, are used to predict RNA-binding residues using ensemble learning technique.ConclusionsThe experimental results reveal the effectiveness of the proposed structural features. In addition, the clustering results on template patches exhibit distinct structural patterns of RNA-binding sites, although the sequences of template patches in the same cluster are not conserved. We speculate that RNAs may have structure preferences when binding with proteins.

[1]  Liangjiang Wang,et al.  BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences , 2006, Nucleic Acids Res..

[2]  Oliviero Carugo,et al.  CX, an algorithm that identifies protruding atoms in proteins , 2002, Bioinform..

[3]  K. S. Arun,et al.  Least-Squares Fitting of Two 3-D Point Sets , 1987, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[4]  Yu Zong Chen,et al.  Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. , 2004, RNA.

[5]  N. Go,et al.  Amino acid residue doublet propensity in the protein–RNA interface and its application to RNA interface prediction , 2006, Nucleic acids research.

[6]  J. Bujnicki,et al.  Computational methods for prediction of protein-RNA interactions. , 2012, Journal of structural biology.

[7]  R. Bock.  Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. , 2000, Biochimie.

[8]  Rasna R. Walia,et al.  RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins , 2014, PloS one.

[9]  Igor B. Kuznetsov,et al.  DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins , 2007, Bioinform..

[10]  J. Pelletier,et al.  High-throughput assays probing protein-RNA interactions of eukaryotic translation initiation factors. , 2009, Analytical biochemistry.

[11]  Haruki Nakamura,et al.  PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences , 2010, Nucleic Acids Res..

[12]  Yu-dong Cai,et al.  Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. , 2003, Biochimica et biophysica acta.

[13]  R. Polikar,et al.  Ensemble based systems in decision making , 2006, IEEE Circuits and Systems Magazine.

[14]  Jae-Hyung Lee,et al.  Genetics, Development and Cell Biology Publications Genetics, Development and Cell Biology Rnabindr: a Server for Analyzing and Predicting Rna-binding Sites in Proteins Rnabindr: a Server for Analyzing and Predicting Rna-binding Sites in Proteins , 2022 .

[15]  Lior Rokach,et al.  Ensemble-based classifiers , 2010, Artificial Intelligence Review.

[16]  Yael Mandel-Gutfreund,et al.  Classifying RNA-Binding Proteins Based on Electrostatic Properties , 2008, PLoS Comput. Biol..

[17]  Satoru Miyano,et al.  A neural network method for identification of RNA-interacting residues in protein. , 2004, Genome informatics. International Conference on Genome Informatics.

[18]  Huan‐Xiang Zhou,et al.  Prediction of protein interaction sites from sequence profile and residue neighbor list , 2001, Proteins.

[19]  Vasant Honavar,et al.  PRIDB: a protein–RNA interface database , 2010, Nucleic Acids Res..

[20]  Zheng Yuan,et al.  Exploiting structural and topological information to improve prediction of RNA-protein binding sites , 2009, BMC Bioinformatics.

[21]  R. Graham,et al.  Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry , 2008, Nucleic acids research.

[22]  Vasant Honavar,et al.  Struct-NB: predicting protein-RNA binding sites using structural features , 2010, Int. J. Data Min. Bioinform..

[23]  Yaoqi Zhou,et al.  Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets , 2010, Nucleic acids research.

[24]  Shandar Ahmad,et al.  PSSM-based prediction of DNA binding sites in proteins , 2005, BMC Bioinformatics.

[25]  Jonathan J. Ellis,et al.  Protein–RNA interactions: Structural analysis and functional classes , 2006, Proteins.

[26]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[27]  S. Jones,et al.  Protein-RNA interactions: a structural analysis. , 2001, Nucleic acids research.

[28]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[29]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[30]  Harry F Noller,et al.  RNA Structure: Reading the Ribosome , 2005, Science.

[31]  Zhi-Ping Liu,et al.  Prediction of protein-RNA binding sites by a random forest method with combined features , 2010, Bioinform..

[32]  Melissa S Jurica,et al.  Pre-mRNA splicing: awash in a sea of proteins. , 2003, Molecular cell.

[33]  Vasant G Honavar,et al.  Prediction of RNA binding sites in proteins from amino acid sequence. , 2006, RNA.

[34]  M. Lewis,et al.  Fractal surfaces of proteins. , 1985, Science.

[35]  Ling Jing,et al.  Predicting DNA- and RNA-binding proteins from sequences with kernel methods. , 2009, Journal of theoretical biology.

[36]  Yael Mandel-Gutfreund,et al.  Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces , 2007, Nucleic Acids Res..

[37]  J. Keene.  RNA regulons: coordination of post-transcriptional events , 2007, Nature Reviews Genetics.

[38]  S. Gerstberger,et al.  A census of human RNA-binding proteins , 2014, Nature Reviews Genetics.

[39]  Gajendra P.S. Raghava,et al.  Prediction of RNA binding sites in a protein using SVM and PSSM profile , 2008, Proteins.

[40]  Seungwoo Hwang,et al.  Using evolutionary and structural information to predict DNA‐binding sites on DNA‐binding proteins , 2006, Proteins.

[41]  Magnar Bjørås,et al.  Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA , 2003, Nature.

[42]  T. Glisovic,et al.  RNA‐binding proteins and post‐transcriptional gene regulation , 2008, FEBS letters.

[43]  Jack Y. Yang,et al.  BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features , 2010, BMC Syst. Biol..

[44]  D. Lejeune,et al.  Protein–nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure , 2005, Proteins.