Skip to main content
SpringerLink
Log in

Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K

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

Abstract

Serine protease proteinase K, a member of the subtilisin family of enzymes, is of significant industrial, agricultural and biotechnological importance. Despite the wealth of structural information about proteinase K provided by static X-ray structures, a full understanding of the enzymatic mechanism requires further insight into the dynamic properties of this enzyme. Molecular dynamics simulations and essential dynamics (ED) analysis were performed to investigate the molecular motions in proteinase K. The results indicate that the internal core of proteinase K is relatively rigid, whereas the surface-exposed loops, most notably the substrate-binding regions, exhibit considerable conformational fluctuations. Further ED analysis reveals that the large concerted motions in the substrate-binding regions cause opening/closing of the substrate-binding pockets, thus supporting the proposed induced-fit mechanism of substrate binding. The distinct electrostatic/hydrogen-bonding interactions between Asp39 and His69 and between His69 and Ser224 within the catalytic triad lead to different thermal motions and orientations of these three catalytic residues, which can be related to their different functional roles in the catalytic process. Statistical analyses of the geometrical/functional properties as well as evolutionary conservation of the glycines in proteinase K-like proteins reveal that glycines may play an important role in determining the folding architecture and structural flexibility of this class of enzymes. Our simulation study complements the biochemical and structural studies and provides new insights into the dynamic structural basis of the functional properties of this class of enzymes.

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. 5a–c
Fig. 6a-c
Fig. 7

Similar content being viewed by others

Abbreviations

RMSD:

Root mean square deviation

MD:

Molecular dynamics

SPC:

Single point charge

NHB:

Number of hydrogen bonds

NNC:

Number of native contacts

SSE:

Number of residues in the secondary structure elements

Rg:

Radius of gyration

SASA:

Solvent accessible surface area

ED:

Essential dynamics

PSL:

Polar surface loop

References

  1. Ebeling W, Hennrich N, Klockow M, Metz H, Orth HD, Lang H (1974) Eur J Biochem 47:91–97

    Article  CAS  Google Scholar 

  2. Wiegers U, Hilz H (1971) Biochem Biophys Res Commun 44:513–519

    Article  CAS  Google Scholar 

  3. Pahler A, Banerjee A, Dattagupta JK, Fujiwara T, Lindner K, Pal GP, Suck D, Saenger W (1984) EMBO J 3:1311–1314

    CAS  Google Scholar 

  4. Wells JA, Estell DA (1988) Trends Biochem Sci 13:291–297

    Article  CAS  Google Scholar 

  5. Hilz H, Wiegers U, Adamietz P (1975) Eur J Biochem 56:103–108

    Article  CAS  Google Scholar 

  6. Shaw WV (1987) Biochem J 246:1–17

    CAS  Google Scholar 

  7. Liu SQ, Meng ZH, Yang JK, Fu YX, Zhang KQ (2007) BMC Struct Biol 7:33

    Article  CAS  Google Scholar 

  8. Pantoliano MW, Ladner RC, Bryan PN, Rollence ML, Wood JF, Poulos TL (1987) Biochemistry 26:2077–2083

    Article  CAS  Google Scholar 

  9. Siezen RJ, de Vos WM, Leunissen JA, Dijkstra BW (1991) Protein Eng 4:719–737

    Article  CAS  Google Scholar 

  10. Siezen RJ, Leunissen JAM (1997) Protein Sci 6:501–523

    Article  CAS  Google Scholar 

  11. Betzel C, Gourinath S, Kumar P, Kaur P, Perbandt M, Eschenburg S, Singh TP (2001) Biochemistry 40:3080–3088

    Article  CAS  Google Scholar 

  12. Müller A, Hinrichs W, Wolf WM, Saenger W (1994) J Biol Chem 269:23108–23111

    Google Scholar 

  13. Wolf WM, Bajorath J, Müller A, Raghunathan S, Singh TP, Hinrichs W, Saenger W (1991) J Biol Chem 266:17695–17699

    CAS  Google Scholar 

  14. Martin JR, Mulder FAA, Karimi-Nejad Y, van der Zwan J, Mariani M, Schipper D, Boelens R (1997) Structure 5:521–532

    Article  CAS  Google Scholar 

  15. Dodson G, Wlodawer A (1998) Trends Biochem Sci 23:347–352

    Article  CAS  Google Scholar 

  16. Betzel C, Pal GP, Saenger W (1988) Eur J Biochem 178:155–171

    Article  CAS  Google Scholar 

  17. Betzel C, Teplyakov AV, Harutyunyan EH, Saenger W, Wilson KS (1990) Protein Eng 3:161–172

    Article  CAS  Google Scholar 

  18. Kutzner C, van der Spoel D, Fechner M, Lindahl E, Schmitt UW, de Groot BL, Grubmuller H (2007) J Comp Chem 28:2075–2084

    Article  CAS  Google Scholar 

  19. Lindahl E, Hess B, van der Spoel D (2001) J Mol Model 7:306–317

    CAS  Google Scholar 

  20. Feenstra KA, Hess B, Berendsen HJC (1999) J Comp Chem 20:786–798

    Article  CAS  Google Scholar 

  21. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forces. Reidel, Dordrecht, pp 331–342

    Google Scholar 

  22. Berendsen HJC, Postma JPM, van Gunsteren WF, Di Nola A, Haak JR (1984) J Chem Phys 81:3684–3690

    Article  CAS  Google Scholar 

  23. Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) J Chem Phys 102:5451–5459

    Article  CAS  Google Scholar 

  24. Hess B, Bekker H, Berendsen HJC, Fraaije J (1997) J Comp Chem 18:1463–1472

    Article  CAS  Google Scholar 

  25. Kabsch W, Sander C (1983) Biopolymers 22:2577–2637

    Article  CAS  Google Scholar 

  26. Amadei A, Linssen ABM, Berendsen HJC (1993) Proteins 17:412–425

    Article  CAS  Google Scholar 

  27. Balsera MA, Wriggers W, Oono Y, Schulten K (1996) J Phys Chem 100:2567–2572

    Article  CAS  Google Scholar 

  28. Hayward S, Berendsen HJC (1998) Proteins 30:144–154

    Article  CAS  Google Scholar 

  29. Altschul SF, Madden TL, Schaffer AA (1997) Nucleic Acids Res 25:3389–3402

    Article  CAS  Google Scholar 

  30. Subramaniam S (1998) Proteins 32:1–2

    Article  CAS  Google Scholar 

  31. Thompson JD, Higgins DG, Gibson TJ (1994) Nucleic Acids Res 22:4673–4680

    Article  CAS  Google Scholar 

  32. Peters GH, Frimurer TM, Andersen JN, Olsen H (1999) Biophys J 77:505–515

    Article  CAS  Google Scholar 

  33. Vreede J, van der Horst MA, Hellingwerf KJ, Grielaard W, van Aalten DMF (2003) J Biol Chem 278:18434–18439

    Article  CAS  Google Scholar 

  34. van Aalten DMF, Haker A, Hendriks J, Hellingwerf KJ, Joshua-Tor L, Crielaard W (2002) J Biol Chem 277:6463–6468

    Article  CAS  Google Scholar 

  35. Horn JR, Ramaswamy S, Murphy KP (2003) J Mol Biol 331:497–508

    Article  CAS  Google Scholar 

  36. Sobek H, Hecht HJ, Aehle W, Schomburg D (1992) J Mol Biol 228:108–117

    Article  CAS  Google Scholar 

  37. Dauberman JL, Ganshaw G, Simpson C, Graycar TP, McGinnis S, Bott R (1994) Acta Cryst D 50:650–656

    Article  CAS  Google Scholar 

  38. Koshland DEJ (1958) Proc Natl Acad Sci USA 44:98–104

    Article  CAS  Google Scholar 

  39. Nishihira J, Tachikawa H (1996) J Theor Biol 196:513–519

    Article  Google Scholar 

  40. Moult J, Sussman F, James MNG (1985) J Mol Biol 182:555–566

    Article  CAS  Google Scholar 

  41. Dauter Z, Betzel C, Genov N, Pipon N, Wilson KS (1991) Acta Cryst B 47:707–730

    Article  Google Scholar 

  42. Rypniewski WR, Dambmann C, von der Osten C, Dauter M, Wilson KS (1995) Acta Cryst D 51:73–84

    Article  CAS  Google Scholar 

  43. van Aalten DMF, Findlay JBC, Amadei A, Berendsen HJC (1996) Protein Eng 8:1129–1135

    Article  Google Scholar 

  44. Mello LV, de Groot BL, Li S, Jedrzejas MJ (2002) J Biol Chem 277:36678–36688

    Article  CAS  Google Scholar 

  45. Barrett CP, Noble ME (2005) J Biol Chem 280:13993–14005

    Article  CAS  Google Scholar 

  46. Liu SQ, Liu CQ, Fu YX (2007) J Mol Graphics Model 26:306–318

    Article  CAS  Google Scholar 

  47. Liu SQ, Liu SX, Fu YX (2008) J Mol Model 14:857–870

    Article  CAS  Google Scholar 

  48. Jancso A, Szent-Györgyi AG (1994) Proc Natl Acad Sci USA 91:8762–8766

    Article  CAS  Google Scholar 

  49. Vermersch PS, Tesmer JJG, Lemon DD, Quiocho FA (1990) J Biol Chem 265:16592–16630

    CAS  Google Scholar 

Download references

Acknowledgments

We thank the High Performance Computer Center in Yunnan University for computational support. This work was funded by the National Natural Science Foundation of China (approved numbers 30630003 and 30860011) and partially supported by grants from Yunnan Province (2006C008M, 2007C163M, 07Z10756, 2007PY-22 and 08Y0026) and Innovation Group Project from Yunnan University (KL070002).

Author information

Authors and Affiliations

  1. Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, Yunnan, P. R. China

    Shu-Qun Liu, Yun-Xin Fu & Ke-Qin Zhang

  2. Department of Cardiology, No. 1 Affiliated Hospital, Kunming Medical College, Kunming, 650032, Yunnan, P. R. China

    Zhao-Hui Meng

  3. Human Genetics Center, School of Public Health, University of Texas, 1400 Herman Pressler, E453, Houston, TX, 77025, USA

    Yun-Xin Fu

Authors
  1. Shu-Qun Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhao-Hui Meng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yun-Xin Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ke-Qin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yun-Xin Fu or Ke-Qin Zhang.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

894_2009_518_MOESM1_ESM.mpg

Supplementary material 1: Animation1.mpg. Large concerted motion of proteinase K described by eigenvector 1. The α helices, β strands and loops/links are colored red, yellow and green, respectively (MPG 817 kb)

894_2009_518_MOESM2_ESM.mpg

Supplementary material 2: Animation2.mpg. Large concerted motion of proteinase K described by eigenvector 2. The α helices, β strands and loops/links are colored red, yellow and green, respectively (MPG 792 kb)

894_2009_518_MOESM3_ESM.mpg

Supplementary material 3: Animation3.mpg. Large concerted motion of proteinase K described by eigenvector 3. The α helices, β strands and loops/links are colored red, yellow and green, respectively (MPG 662 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, SQ., Meng, ZH., Fu, YX. et al. Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K. J Mol Model 16, 17–28 (2010). https://doi.org/10.1007/s00894-009-0518-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-009-0518-x

Keywords

Search

Navigation