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BioMed Research International
Volume 2015 (2015), Article ID 402536, 13 pages
http://dx.doi.org/10.1155/2015/402536
Research Article

Predicting Flavin and Nicotinamide Adenine Dinucleotide-Binding Sites in Proteins Using the Fragment Transformation Method

1Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung 40402, Taiwan
2Graduate Institute of Basic Medical Science, China Medical University, Taichung 40402, Taiwan
3Department of Information Engineering and Computer Science, Feng Chia University, Taichung 40724, Taiwan
4Master’s Program in Biomedical Informatics and Biomedical Engineering, Feng Chia University, Taichung 40724, Taiwan
5Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan

Received 16 June 2014; Accepted 21 July 2014

Academic Editor: Hao-Teng Chang

Copyright © 2015 Chih-Hao Lu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. H. M. Berman, J. Westbrook, Z. Feng et al., “The protein data bank,” Nucleic Acids Research, vol. 28, no. 1, pp. 235–242, 2000. View at Publisher · View at Google Scholar · View at Scopus
  2. A. Wilkinson, J. Day, and R. Bowater, “Bacterial DNA ligases,” Molecular Microbiology, vol. 40, no. 6, pp. 1241–1248, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Bürkle, “Physiology and pathophysiology of poly(ADP-ribosyl)ation,” BioEssays, vol. 23, no. 9, pp. 795–806, 2001. View at Publisher · View at Google Scholar · View at Scopus
  4. Q. Zhang, D. W. Piston, and R. H. Goodman, “Regulation of corepressor function by nuclear NADH,” Science, vol. 295, no. 5561, pp. 1895–1897, 2002. View at Publisher · View at Google Scholar · View at Scopus
  5. J. S. Smith and J. D. Boeke, “An unusual form of transcriptional silencing in yeast ribosomal DNA,” Genes and Development, vol. 11, no. 2, pp. 241–254, 1997. View at Publisher · View at Google Scholar · View at Scopus
  6. R. M. Anderson, K. J. Bitterman, J. G. Wood et al., “Manipulation of a nuclear NAD+ salvage pathway delays aging without altering steady-state NAD+ levels,” The Journal of Biological Chemistry, vol. 277, no. 21, pp. 18881–18890, 2002. View at Publisher · View at Google Scholar · View at Scopus
  7. J. Rutter, M. Reick, L. C. Wu, and S. L. McKnight, “Regulation of crock and NPAS2 DNA binding by the redox state of NAD cofactors,” Science, vol. 293, no. 5529, pp. 510–514, 2001. View at Publisher · View at Google Scholar · View at Scopus
  8. K. Chen, M. J. Mizianty, and L. Kurgan, “Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors,” Bioinformatics, vol. 28, no. 3, pp. 331–341, 2012. View at Publisher · View at Google Scholar · View at Scopus
  9. M. Saito, M. Go, and T. Shirai, “An empirical approach for detecting nucleotide-binding sites on proteins,” Protein Engineering, Design and Selection, vol. 19, no. 2, pp. 67–75, 2006. View at Publisher · View at Google Scholar · View at Scopus
  10. H. R. Ansari and G. P. S. Raghava, “Identification of NAD interacting residues in proteins,” BMC Bioinformatics, vol. 11, article 160, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. N. K. Mishra and G. P. S. Raghava, “Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information,” BMC Bioinformatics, vol. 11, article S48, no. 1, 2010. View at Publisher · View at Google Scholar · View at Scopus
  12. Z.-P. Liu, L.-Y. Wu, Y. Wang, X.-S. Zhang, and L. Chen, “Prediction of protein-RNA binding sites by a random forest method with combined features,” Bioinformatics, vol. 26, no. 13, pp. 1616–1622, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. L. Wang, Z. P. Liu, X. S. Zhang, and L. Chen, “Prediction of hot spots in protein interfaces using a random forest model with hybrid features,” Protein Engineering, Design and Selection, vol. 25, no. 3, pp. 119–126, 2012. View at Publisher · View at Google Scholar · View at Scopus
  14. J. S. Chauhan, N. K. Mishra, and G. P. S. Raghava, “Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information,” BMC Bioinformatics, vol. 11, article 301, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. A. Roy and Y. Zhang, “Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement,” Structure, vol. 20, no. 6, pp. 987–997, 2012. View at Publisher · View at Google Scholar · View at Scopus
  16. L. Xie and P. E. Bourne, “Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 14, pp. 5441–5446, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. J. Yang, A. Roy, and Y. Zhang, “Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment,” Bioinformatics, vol. 29, no. 20, pp. 2588–2595, 2013. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. T. Yan and W.-H. Li, “Identification of protein functional surfaces by the concept of a split pocket,” Proteins: Structure, Function and Bioinformatics, vol. 76, no. 4, pp. 959–976, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. K. A. Dill, “Dominant forces in protein folding,” Biochemistry, vol. 29, no. 31, pp. 7133–7155, 1990. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Govindarajan and R. A. Goldstein, “Evolution of model proteins on a foldability landscape,” Proteins, vol. 29, no. 4, pp. 461–466, 1997. View at Google Scholar
  21. G. Parisi and J. Echave, “Structural constraints and emergence of sequence patterns in protein evolution,” Molecular Biology and Evolution, vol. 18, no. 5, pp. 750–756, 2001. View at Publisher · View at Google Scholar · View at Scopus
  22. C. H. Lu, Y. S. Lin, Y. C. Chen, C. S. Yu, S. Y. Chang, and J. K. Hwang, “The fragment transformation method to detect the protein structural motifs,” Proteins: Structure, Function and Genetics, vol. 63, no. 3, pp. 636–643, 2006. View at Publisher · View at Google Scholar · View at Scopus
  23. L. Schrodinger, The PyMOL Molecular Graphics System, Version 1.3r1, 2010.
  24. U. Dengler, K. Niefind, M. Kieß, and D. Schomburg, “Crystal structure of a ternary complex of D-2-hydroxy-isocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 Å resolution,” Journal of Molecular Biology, vol. 267, no. 3, pp. 640–660, 1997. View at Publisher · View at Google Scholar · View at Scopus
  25. E. Gross, C. S. Sevier, A. Vala, C. A. Kaiser, and D. Fass, “A new FAD-binding fold and intersubunit disulfide shuttle in the thiol oxidase Erv2p,” Nature Structural Biology, vol. 9, no. 1, pp. 61–67, 2002. View at Publisher · View at Google Scholar · View at Scopus
  26. S. V. Antonyuk, R. W. Strange, M. J. Ellis et al., “Structure of d-lactate dehydrogenase from Aquifex aeolicus complexed with NAD+ and lactic acid (or pyruvate),” Acta Crystallographica F: Structural Biology and Crystallization Communications, vol. 65, part 12, pp. 1209–1213, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. C. K. Wu, T. A. Dailey, H. A. Dailey, B. C. Wang, and J. P. Rose, “The crystal structure of augmenter of liver regeneration: a mammalian FAD-dependent sulfhydryl oxidase,” Protein Science, vol. 12, no. 5, pp. 1109–1118, 2003. View at Publisher · View at Google Scholar · View at Scopus
  28. J. R. Thompson, J. K. Bell, J. Bratt, G. A. Grant, and L. J. Banaszak, “Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase,” Biochemistry, vol. 44, no. 15, pp. 5763–5773, 2005. View at Publisher · View at Google Scholar · View at Scopus
  29. M. Nardini, S. Spanò, C. Cericola et al., “CtBP/BARS: a dual-function protein involved in transcription co-repression and Golgi membrane fission,” EMBO Journal, vol. 22, no. 12, pp. 3122–3130, 2003. View at Publisher · View at Google Scholar · View at Scopus
  30. R. Kort, H. Komori, S. I. Adachi, K. Miki, and A. Eker, “DNA apophotolyase from Anacystis nidulans: 1.8 Å structure, 8-HDF reconstitution and X-ray-induced FAD reduction,” Acta Crystallographica Section D: Biological Crystallography, vol. 60, no. 7, pp. 1205–1213, 2004. View at Publisher · View at Google Scholar · View at Scopus
  31. Y. Huang, R. Baxter, B. S. Smith, C. L. Partch, C. L. Colbert, and J. Deisenhofer, “Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 47, pp. 17701–17706, 2006. View at Publisher · View at Google Scholar · View at Scopus
  32. J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, and H. M. Holden, “Molecular basis for severe epimerase deficiency galactosemia. X-ray structure of the human V94M-substituted UDP-galactose 4-epimerase,” The Journal of Biological Chemistry, vol. 276, no. 23, pp. 20617–20623, 2001. View at Publisher · View at Google Scholar · View at Scopus
  33. C. A. Brautigam, B. S. Smith, Z. Ma et al., “Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 33, pp. 12142–12147, 2004. View at Publisher · View at Google Scholar · View at Scopus
  34. H. Komori, R. Masui, S. Kuramitsu et al., “Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 24, pp. 13560–13565, 2001. View at Publisher · View at Google Scholar · View at Scopus
  35. F. Todone, M. A. Vanoni, A. Mozzarelli et al., “Active site plasticity in D-amino acid oxidase: a crystallographic analysis,” Biochemistry, vol. 36, no. 19, pp. 5853–5860, 1997. View at Publisher · View at Google Scholar · View at Scopus
  36. I. F. Sevrioukova, H. Li, and T. L. Poulos, “Crystal structure of putidaredoxin reductase from Pseudomonas putida, the final structural component of the cytochrome P450cam monooxygenase,” Journal of Molecular Biology, vol. 336, no. 4, pp. 889–902, 2004. View at Publisher · View at Google Scholar · View at Scopus
  37. S. Y. Song, Y. B. Xu, Z. J. Lin, and C. L. Tsou, “Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor,” Journal of Molecular Biology, vol. 287, no. 4, pp. 719–725, 1999. View at Publisher · View at Google Scholar · View at Scopus
  38. L. Pollegioni, K. Diederichs, G. Molla et al., “Yeast D-amino acid oxidase: structural basis of its catalytic properties,” Journal of Molecular Biology, vol. 324, no. 3, pp. 535–546, 2002. View at Publisher · View at Google Scholar · View at Scopus
  39. E. C. Settembre, P. C. Dorrestein, J. H. Park, A. M. Augustine, T. P. Begley, and S. E. Ealick, “Structural and mechanistic studies on thiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis,” Biochemistry, vol. 42, no. 10, pp. 2971–2981, 2003. View at Publisher · View at Google Scholar · View at Scopus
  40. J. Yang, A. Roy, and Y. Zhang, “BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions,” Nucleic Acids Research, vol. 41, no. 1, pp. D1096–D1103, 2013. View at Publisher · View at Google Scholar · View at Scopus
  41. S. Henikoff and J. G. Henikoff, “Amino acid substitution matrices from protein blocks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 22, pp. 10915–10919, 1992. View at Publisher · View at Google Scholar · View at Scopus
  42. W. Kabsch and C. Sander, “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features,” Biopolymers, vol. 22, no. 12, pp. 2577–2637, 1983. View at Publisher · View at Google Scholar · View at Scopus
  43. J. C. Gower and G. J. S. Ross, “Minimum spanning trees and single-linkage cluster analysis,” Journal of the Royal Statistical Society, vol. 18, no. 1, article 11, 1969. View at Google Scholar