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Homology Searches Using Supersecondary Structure Code

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Protein Supersecondary Structures

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1958))

Abstract

Supersecondary structure code (SSSC), which is represented as the combination of α-helix-type (SSSC: H), β-sheet-type (SSSC: S), the other (SSSC: T), and disorder residue or C-terminal (SSSC: D) patterns, has been produced by the developed concept of Ramachandran plot, in addition, with the ω angle and with the specification of positions of torsion angles in a protein by the registration of codes for torsion angles of each amino acid peptide unit, derived from the fuzzy search of structural code homology using the template patterns 3a5c4a (SSSC: H) and 6c4a4a (SSSC: S) with conformational codes. The DSSP (Dictionary of Secondary Structure in Proteins) method assigns the secondary structure including hydrogen bond well. In contrast, supersecondary structure code is very sensitive to the supersecondary structures of proteins. In this chapter, the protocol of homology search methods, the sequence alignment using supersecondary structure code, the assignment of supersecondary structure code T, the fuzzy search using supersecondary structure code, and the exact search using supersecondary structure code are described. Supersecondary structure code is variable with the conformational change. If possible, many Protein Data Bank (PDB) data of similar main chains of proteins should be used for the homology searches. The thorough check of SSSC sequences is also useful to reveal the role of target pattern.

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References

  1. Andreeva NS, Gustchina AE (1979) On the supersecondary structure of acid proteases. Biochem Biophys Res Commun 87:32–42. https://doi.org/10.1016/0006-291x(79)91643-7

    Article  CAS  PubMed  Google Scholar 

  2. Richards FM, Kundrot CE (1988) Identification of structural motifs from protein coordinate data—secondary structure and 1st-level supersecondary structure. Proteins 3:71–84. https://doi.org/10.1002/prot.340030202

    Article  CAS  PubMed  Google Scholar 

  3. Izumi H, Wakisaka A, Nafie LA, Dukor RK (2013) Data mining of supersecondary structure homology between light chains of immunoglobulins and MHC molecules: absence of the common conformational fragment in the human IgM rheumatoid factor. J Chem Inf Model 53:584–591. https://doi.org/10.1021/ci300420d

    Article  CAS  PubMed  Google Scholar 

  4. Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7:95–99

    Article  CAS  Google Scholar 

  5. Kleywegt GJ, Jones TA (1996) Phi/psi-chology: ramachandran revisited. Structure 4:1395–1400. https://doi.org/10.1016/s0969-2126(96)00147-5

    Article  CAS  PubMed  Google Scholar 

  6. Lovell SC, Davis IW, Adrendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by C alpha geometry: phi, psi and C beta deviation. Proteins 50:437–450. https://doi.org/10.1002/prot.10286

    Article  CAS  PubMed  Google Scholar 

  7. Ho BK, Brasseur R (2005) The Ramachandran plots of glycine and pre-proline. BMC Struct Biol 5:14. https://doi.org/10.1186/1472-6807-5-14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Izumi H, Nafie LA, Dukor RK (2016) Three-dimensional chemical structure search using the conformational code for organic molecules (CCOM) program. Chirality 28:370–375. https://doi.org/10.1002/chir.22596

    Article  CAS  PubMed  Google Scholar 

  9. Touw WG, Baakman C, Black J, te Beek TAH, Krieger E, Joosten RP, Vriend G (2015) A series of PDB-related databanks for everyday needs. Nucleic Acids Res 43:D364–D368. https://doi.org/10.1093/nar/gku1028

    Article  CAS  PubMed  Google Scholar 

  10. Kabsch W, Sander C (1983) Dictionary of protein secondary structure—pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637. https://doi.org/10.1002/bip.360221211

    Article  CAS  Google Scholar 

  11. Python Software Foundation (2018) Python. https://www.python.org. Accessed 26 Jan 2018

  12. Open Bioinformatics Foundation (2018) Biopython. http://biopython.org. Accessed 26 Jan 2018

  13. Izumi H (2016) SSSC. http://researchmap.jp/muqgq8vge-2132135/#_2132135. Accessed 26 Jan 2018

  14. Izumi H (2017) SSSC analysis. http://researchmap.jp/muf10vbx5-2132135/#_2132135. Accessed 26 Jan 2018

  15. Katoh K (2013) MAFFT version 7. http://mafft.cbrc.jp/alignment/software/. Accessed 26 Jan 2018

  16. Yamada KD, Tomii K, Katoh K (2016) Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics 32:3246–3251. https://doi.org/10.1093/bioinformatics/btw412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066. https://doi.org/10.1093/nar/gkf436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Higgins D, Sievers F, Dineen D, Wilm A (2014) Clustal W/Clustal X. http://www.clustal.org/clustal2. Accessed 26 Jan 2018

  19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404

    Article  CAS  PubMed  Google Scholar 

  20. Protein Data Bank Japan (2018) PDBj. https://pdbj.org. Accessed 26 Jan 2018

  21. Molecular Organisation and Assembly in Cells (2006) Generating Ramachandran (phi/psi) plots for proteins. http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/ramachandran. Accessed 26 Jan 2018

  22. Bartolucci C, Lamba D, Grazulis S, Manakova E, Heumann H (2005) Crystal structure of wild-type chaperonin GroEL. J Mol Biol 354:940–951. https://doi.org/10.1016/j.jmb.2005.09.096

    Article  CAS  PubMed  Google Scholar 

  23. Chaudhry C, Horwich AL, Brunger AT, Adams PD (2004) Exploring the structural dynamics of the E-coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J Mol Biol 342:229–245. https://doi.org/10.1016/j.jmb.2004.07.015

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was partly supported by JSPS KAKENHI Grant Number JP16K05711. The author thanks Dr. Rina K. Dukor and Professor Laurence A. Nafie for the discussion of supersecondary structure code.

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Authors and Affiliations

  1. National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba West, Ibaraki, Japan

    Hiroshi Izumi

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  1. Hiroshi Izumi
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Correspondence to Hiroshi Izumi .

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Editors and Affiliations

  1. Department of Mathematics, Rutgers University, Piscataway, NJ, USA

    Alexander E. Kister

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Izumi, H. (2019). Homology Searches Using Supersecondary Structure Code. In: Kister, A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 1958. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9161-7_17

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  • DOI: https://doi.org/10.1007/978-1-4939-9161-7_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9160-0

  • Online ISBN: 978-1-4939-9161-7

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