BMB Reports

Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
권호 표지
DOI QR코드

DOI QR Code

SABA (secondary structure assignment program based on only alpha carbons): a novel pseudo center geometrical criterion for accurate assignment of protein secondary structures

  • Received : 2010.11.01
  • Accepted : 2010.12.17
  • Published : 2011.02.28
Download PDF
⟨ Previous Next ⟩

Abstract

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

Keywords

References

  1. Pauling, L., Corey, R. B. and Branson, H. R. (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. U.S.A. 37, 205-211. https://doi.org/10.1073/pnas.37.4.205
  2. Pauling, L. and Corey, R. B. (1951) The pleated sheet, a new layer configuration of polypeptide chains. Proc. Natl. Acad. Sci. U.S.A. 37, 251-256. https://doi.org/10.1073/pnas.37.5.251
  3. 28Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242. https://doi.org/10.1093/nar/28.1.235
  4. Kabsch, W. and 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
  5. Frishman, D. and Argos, P. (1995) Knowledge-based protein secondary structure assignment. Proteins 23, 566-579. https://doi.org/10.1002/prot.340230412
  6. Richards, F. M. and Kundrot, C. E. (1988) Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 3, 71-74. https://doi.org/10.1002/prot.340030202
  7. Labesse, G., Colloc'h, N., Pothier, J. and Mornon, J. P. (1997) P-SEA: a new efficient assignment of secondary structure from $C{\alpha}$ trace of proteins. Comput. Appl. Biosci. 13, 291-295.
  8. Martin, J., Letellier, G., Martin, A., Taly, J. F., Brevern, A. G. D. and Gibrat, G. F. (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol. 5, 17. https://doi.org/10.1186/1472-6807-5-17
  9. Sklenar, H., Etchebest, C. and Lavery R. (1989) Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 6, 46-60. https://doi.org/10.1002/prot.340060105
  10. King, S. M. and Johnson, W. C. (1999) Assigning secondary structure from protein coordinate data. Proteins 3, 313-320.
  11. Fodje, M. N. and Al-Karadaghi, S. (2002) Occurrence, conformational features and amino acid propensities for the $\pi$-helix. Protein Eng. 15, 353-358. https://doi.org/10.1093/protein/15.5.353
  12. Cubellis, M. V., Cailliez, F. and Lovell, S. C. (2005) Secondary structure assignment that accurately reflects physical and evolutionary characteristics. BMC Bioinformatics. 6, S8.
  13. Dupuis, F., Sadoc, J. F. and Mornon, J. P. (2004) Protein secondary structure assignment through voronoi tessellation. Proteins 55, 519-528. https://doi.org/10.1002/prot.10566
  14. Colloc’h, N., Etchebest, C., Thoreau, E., Henrissat, B. and Mornon, J. P. (1993) Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng. 6, 377-382. https://doi.org/10.1093/protein/6.4.377
  15. Zhang, W., Dunker, A. K. and Zhou, Y. (2008) Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks. Proteins 71, 61-67. https://doi.org/10.1002/prot.21654

Cited by

  1. PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements vol.35, pp.24, 2014, https://doi.org/10.1002/jcc.23683
  2. MAESTRO - multi agent stability prediction upon point mutations vol.16, pp.1, 2015, https://doi.org/10.1186/s12859-015-0548-6
  3. Protein secondary-structure description with a coarse-grained model vol.71, pp.7, 2015, https://doi.org/10.1107/S1399004715007191
  4. Protein Secondary Structure Classification Revisited: Processing DSSP Information with PSSC vol.54, pp.7, 2014, https://doi.org/10.1021/ci5000856
  5. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments vol.17, pp.3, 2016, https://doi.org/10.3390/ijms17030333