Skip to main content
Springer Nature Link
Log in

Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-β-glucanase by molecular dynamics simulations

  • Original paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

The dependence of some molecular motions in the enzyme 1,3-1,4-β-glucanase from Bacillus licheniformis on temperature changes and the role of the calcium ion in them were explored. For this purpose, two molecular dynamics simulated trajectories along 4 ns at low (300 K) and high (325 K) temperatures were generated by the GROMOS96 package. Several structural and thermodynamic parameters were calculated, including entropy values, solvation energies, and essential dynamics (ED). In addition, thermoinactivation experiments to study the influence of the calcium ion and some residues on the activity were conducted. The results showed the release of the calcium ion, which, in turn, significantly affected the movements of loops 1, 2, and 3, as shown by essential dynamics. These movements differ at low and high temperatures and affect dramatically the activity of the enzyme, as observed by thermoinactivation studies.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Similar content being viewed by others

Abbreviations

MD:

Molecular dynamics

RF:

Reaction field

RMSD:

Root mean square deviation

ED:

Essential dynamics

References

  1. Planas A (2000) Biochim Biophys Acta 1543:361–382

    PubMed  CAS  Google Scholar 

  2. Juncosa M, Pons J, Dot T, Querol E, Planas A (1994) J Biol Chem 269:14530–14535

    PubMed  CAS  Google Scholar 

  3. Malet C, Vallés J, Bou J, Planas A (1996) J Biotechnol 48:209–219

    Article  PubMed  CAS  Google Scholar 

  4. Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon J, Davies G (1995) Proc Natl Acad Sci USA 92:7090–7094

    Article  PubMed  CAS  Google Scholar 

  5. Planas A, Juncosa M, Lloberas J, Querol E (1992) FEBS Lett 308:141–145

    Article  PubMed  CAS  Google Scholar 

  6. Welfle K, Misselwitz R, Welfle H, Politz O, Borriss R (1994) J Biomol Struct Dyn 11:1417–1424

    PubMed  CAS  Google Scholar 

  7. Welfle K, Misselwitz R, Welfle H, Politz O, Borriss R (1995) Eur J Biochem 229:726–735

    Article  PubMed  CAS  Google Scholar 

  8. Welfle K, Misselwitz R, Politz O, Borriss R, Welfle H (1996) Protein Sci 5:2255–2265

    Article  PubMed  CAS  Google Scholar 

  9. Keitel T, Meldgaard M, Heinemann U (1994) Eur J Biochem 222:203–214

    Article  PubMed  CAS  Google Scholar 

  10. Lloberas J, Querol E, Bernués J (1988) Appl Microbiol Biotechnol 29:32–38

    Article  CAS  Google Scholar 

  11. Gargallo R, Hünenberger P, Aviles F, Oliva B (2003) Protein Sci 10:2161–2172

    Article  CAS  Google Scholar 

  12. Amadei A, Linssen A, Berendsen H (1993) Proteins Struct Funct Genet 17:412–425

    Article  PubMed  CAS  Google Scholar 

  13. Yang C, Gouri S, Kuczera K (2001) J Biomol Struct Dyn 19:247–271

    PubMed  CAS  Google Scholar 

  14. van Gunsteren W, Billeter S, Eising A, Hünenberger P, Früger P, Mark A, Scott W, Tironi I (1996) Biomolecular simulation: the GROMOS96 manual and user guide. Verlag der Fachvereine, Zürich

    Google Scholar 

  15. Berendsen H, Grigera J, Straatsma T (1987) J Phys Chem 91:6269–6271

    Article  CAS  Google Scholar 

  16. Rickaert J, Ciccotti G, Berendsen H (1977) J Comput Chem 23:327–341

    Google Scholar 

  17. Tironi I, Sperb R, Smith P, van Gunsteren W (1995) J Chem Phys 102:5451–5459

    Article  CAS  Google Scholar 

  18. Hünenberger, P, van Gunsteren W (1998) J Chem Phys 108:6117–6134

    Article  Google Scholar 

  19. Gargallo R, Oliva B, Querol E, Avilés F (2000) Protein Eng 13:21–26

    Article  PubMed  CAS  Google Scholar 

  20. Richmond T (1984) J Mol Biol 176:63–89

    Article  Google Scholar 

  21. Nicholls A, Honing B (1991) J Comput Chem 12:435–440

    Article  CAS  Google Scholar 

  22. Bashford D (1997) An object-oriented programming suite for electrostatic effects in biological molecules. In: Ishikawa Y, Reynders J, Tholburn M (eds) Scientific computing in object-oriented parallel environments. Springer, Berlin Heidelberg New York, pp 233–240

    Google Scholar 

  23. Schlitter J (1993) Chem Phys Lett 215:617–621

    Article  CAS  Google Scholar 

  24. Schäfer H, Mark A, van Gunsteren W (2000) J Chem Phys 113:7809–7817

    Article  Google Scholar 

  25. Schäfer H, Daura X, Mark AE, van Gunsteren W (2001) Proteins 43:45–56

    Article  PubMed  Google Scholar 

  26. Schäfer H, Smith LJ, Mark A, van Gunsteren W (2002) Proteins 46:215–224

    Article  PubMed  CAS  Google Scholar 

  27. Sherer E, Harris S, Soliva R, Orozco M, Laughton C (1999) J Am Chem Soc 121:5981–5991

    Article  CAS  Google Scholar 

  28. Pons J, Planas A, Juncosa M, Querol E (1997) Methods Mol Biol 67:209–218

    PubMed  CAS  Google Scholar 

  29. Malet C, Viladot J, Ochoa A, Gállego B, Brosa C, Planas A (1995) Carbohydr Res 274:285–301

    Article  PubMed  CAS  Google Scholar 

  30. Mozo-Villarias A, Cedano J, Querol E (2003) Protein Eng 16:279–286

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

RG received a grant from the Spanish MEC (BQU2003-00191). BO received grants from the Fundación Ramón Areces and from the Spanish MEC (BIO2002-03609 and BIO2005-00533). EQ received grants from Ministerio de Ciencia y Tecnologia (BIO2001-264) and from the Centre de Referència de R+D de Biotecnología de la Generalitat de Catalunya.

Author information

Authors and Affiliations

  1. Department of Analytical Chemistry, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona, 08028, Spain

    Raimundo Gargallo

  2. Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain

    Juan Cedano & Enrique Querol

  3. Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Universitat de Lleida, Lleida, 25198, Spain

    Angel Mozo-Villarias

  4. Grup de Bioinformàtica Estructural (GRIB-IMIM). Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Dr. Aiguader, 80, 08003, Barcelona, Catalonia, Spain

    Baldomero Oliva

Authors
  1. Raimundo Gargallo
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Juan Cedano
    View author publications

    You can also search for this author inPubMed Google Scholar

  3. Angel Mozo-Villarias
    View author publications

    You can also search for this author inPubMed Google Scholar

  4. Enrique Querol
    View author publications

    You can also search for this author inPubMed Google Scholar

  5. Baldomero Oliva
    View author publications

    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence to Baldomero Oliva.

Additional information

The first two authors contributed equally to this work

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gargallo, R., Cedano, J., Mozo-Villarias, A. et al. Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-β-glucanase by molecular dynamics simulations. J Mol Model 12, 835–845 (2006). https://doi.org/10.1007/s00894-006-0110-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-006-0110-6

Keywords