Skip to main content
SpringerLink
Log in

Exploring the Role of C–H….π Interactions on the Structural Stability of Single Chain “All-Alpha” Proteins

  • Published:
Applied Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

C–H….π interactions are known to be important contributors to protein stability. In this study, we have analyzed the influence of C–H….π interactions in single chain “all-alpha” proteins. In the data set, a total of 181 C–H….π interactions were observed. The most prominent representatives are the interactions between aromatic C–H donor groups and aromatic π acceptors. Eighty-one percent of the C–H….π interactions between side chain to side chain and remaining19% of the C–H….π interactions were observed between side-chain to side-chain five-member aromatic ring. The donor atom contribution to C–H….π interactions was mainly from Phe, Tyr, and Trp residues. The acceptor atom contribution to C–H….π interactions was mainly from Phe, Tyr, Trp, and His. The highest percentage of C–H….π interactions were observed form Phe residue. The secondary structure preference analysis of all C–H….π interacting residues showed that Phe, Tyr, Trp, and His preferred to be in helix. Long-range C–H….π interactions are the predominant type of interactions in single chain all-alpha proteins data set. All the C–H….π interactions forming residues in the data set preferred to be in the buried region. Seventy-three percent of the donor residues and 65% of the acceptor residues are highly conserved.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  1. Tamres, M. (1952). Journal of the American Chemical Society, 74, 3375–3378. doi:10.1021/ja01133a047.

    Article  CAS  Google Scholar 

  2. Reeves, L. W., & Schneider, W. G. (1957). Canadian Journal of Chemistry, 35, 251–261. doi:10.1139/v57-036.

    Article  CAS  Google Scholar 

  3. Nishio, M., Hirota, M., & Umezawa, Y. (Eds.) (1998). New York: Wiley.

  4. Matsui, I., Matsui, E., Sakai, Y., Kikuchi, H., Kawarabayasi, Y., Ura, H., et al. (2000). The Journal of Biological Chemistry, 275, 4871–4879. doi:10.1074/jbc.275.7.4871.

    Article  CAS  Google Scholar 

  5. Chakrabarti, P., & Samanta, U. (1995). Journal of Molecular Biology, 251, 9–14. doi:10.1006/jmbi.1995.0411.

    Article  CAS  Google Scholar 

  6. Umezawa, Y., & Nishio, M. (1998). Bioorganic & Medicinal Chemistry, 6, 493–504. doi:10.1016/S0968-0896(98)00002-9.

    Article  CAS  Google Scholar 

  7. Muraki, M., Harata, K., Sugita, N., & Sato, K. I. (2000). Biochemistry, 39, 292–299. doi:10.1021/bi991402q.

    Article  CAS  Google Scholar 

  8. Umezawa, Y., & Nishio, M. (1998). Bioorganic & Medicinal Chemistry, 6, 2507–2515. doi:10.1016/S0968-0896(98)80024-2.

    Article  CAS  Google Scholar 

  9. Jabs, A., Weiss, M. S., & Hilgenfeld, R. (1999). Journal of Molecular Biology, 286, 291–304. doi:10.1006/jmbi.1998.2459.

    Article  CAS  Google Scholar 

  10. Shimohigashi, Y., Maeda, I., Nose, T., Ikesue, K., Sakamoto, H., Ogawa, Y., et al. (1996). Journal of the Chemical Society, 1, 2479–2485.

    Google Scholar 

  11. Shimohigashi, Y., Nose, T., Yamauchi, Y., & Maeda, I. (1999). Biopolymers, 51, 9–17. doi:10.1002/(SICI)1097-0282(1999)51:1<9::AID-BIP3>3.0.CO;2-5.

    Article  CAS  Google Scholar 

  12. Steiner, T. (2002). Angewandte Chemie International Edition in English, 41, 48–76. doi:10.1002/1521-3773(20020104)41:1<48::AID-ANIE48>3.0.CO;2-U.

    Article  CAS  Google Scholar 

  13. Steiner, T., & Koellner, G. J. (2001). Journal of Molecular Biology, 305, 535–557. doi:10.1006/jmbi.2000.4301.

    Article  CAS  Google Scholar 

  14. Meyer, E. A., Castellano, R. K., & Diederich, F. (2003). Angewandte Chemie International Edition in English, 42, 1210–1250. doi:10.1002/anie.200390319.

    Article  CAS  Google Scholar 

  15. Martis, R. L., Singh, S. K., Michael Gromiha, M., & Santhosh, C. (2008). Journal of Theoretical Biology, 250, 655–662. doi:10.1016/j.jtbi.2007.10.024.

    Article  CAS  Google Scholar 

  16. Berman, H. M., Westbrook, J. Z., Feng, G., Gillilandm, T. N., Bhat, H., Weissig, I. N., et al. (2000). Nucleic Acids Research, 28, 235–242. doi:10.1093/nar/28.1.235.

    Article  CAS  Google Scholar 

  17. Conte, L. L., Ailey, B., Hubbard, T. J. P., Brenner, S. E., Murzin, A. G., & Chothia, C. (2000). Nucleic Acids Research, 28, 257–259. doi:10.1093/nar/28.1.257.

    Article  Google Scholar 

  18. Tiwari, A., & Panigrahi, S. K. (2007). In Silico Biology, 7, 0057.

    Google Scholar 

  19. Babu, M. M. (2003). Nucleic Acids Research, 31, 3345–3348. doi:10.1093/nar/gkg528.

    Article  CAS  Google Scholar 

  20. Kabsch, W., & Sander, C. (1983). Biopolymers, 22, 2577–2637. doi:10.1002/bip. 360221211.

    Article  CAS  Google Scholar 

  21. Gilis, D., & Rooman, M. (1996). Journal of Molecular Biology, 257, 1112–1126. doi:10.1006/jmbi.1996.0226.

    Article  CAS  Google Scholar 

  22. Gilis, D., & Rooman, M. (1997). Journal of Molecular Biology, 272, 276–290. doi:10.1006/jmbi.1997.1237.

    Article  CAS  Google Scholar 

  23. Gromiha, M. M., & Selvaraj, S. (1997). Journal of Biological Physics, 23, 151–162. doi:10.1023/A:1004981409616.

    Article  CAS  Google Scholar 

  24. Gromiha, M. M., Santhosh, C., & Ahmed, S. (2004). International Journal of Biological Macromolecules, 34, 203–211. doi:10.1016/j.ijbiomac.2004.04.003.

    Article  CAS  Google Scholar 

  25. Selvaraj, S., & Gromiha, M. M. (2003). Biophysical Journal, 84, 1919–1925. doi:10.1016/S0006-3495(03)75000-0.

    Article  CAS  Google Scholar 

  26. Gromiha, M. M., & Selvaraj, S. (2004). Progress in Biophysics and Molecular Biology, 86, 235–277. doi:10.1016/j.pbiomolbio.2003.09.003.

    Article  CAS  Google Scholar 

  27. Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor, D., Martz, E., et al. (2003). Bioinformatics (Oxford, England), 19, 163–164. doi:10.1093/bioinformatics/19.1.163.

    Article  CAS  Google Scholar 

  28. Boeckman, B., Bairoch, A., Apweiler, R., Blatter, M. C., Estreicher, A., Gasteiger, E., et al. (2003). Nucleic Acids Research, 31, 365–370. doi:10.1093/nar/gkg095.

    Article  Google Scholar 

  29. Brandl, M., Weiss, M. S., Jabs, A., Sühnel, J., & Hilgenfeld, R. (2001). Journal of Molecular Biology, 307, 357–377. doi:10.1006/jmbi.2000.4473.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank the management of Vellore Institute of Technology for providing the facilities to carry out this work. The authors also thank the reviewers for their suggestions in the improvement of this manuscript.

Author information

Authors and Affiliations

  1. School of Biotechnology, Chemical and Biomedical Engineering, Bioinformatics Division, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India

    V. Shanthi, K. Ramanathan & Rao Sethumadhavan

Authors
  1. V. Shanthi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. K. Ramanathan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rao Sethumadhavan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rao Sethumadhavan.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shanthi, V., Ramanathan, K. & Sethumadhavan, R. Exploring the Role of C–H….π Interactions on the Structural Stability of Single Chain “All-Alpha” Proteins. Appl Biochem Biotechnol 160, 1473–1483 (2010). https://doi.org/10.1007/s12010-009-8584-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12010-009-8584-1

Keywords

Search

Navigation