Skip to main content
SpringerLink
Log in

Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

Abstract

Different forms of carboxypeptidase proenzymes (zymogens) are observed experimentally to show different behavior: procarboxypeptidase A (proCPA, forms proCPA1 and proCPA2) exhibit some activity against small substrates, but proCPB does not. In this work, these three zymogen forms (subtypes A1, A2 and B) are investigated by means of 15-ns molecular dynamics simulations and principal component analysis to shed light on their dynamic/conformational behaviors that may be relevant to those experimental observations. The simulations revealed that proCPA (both A1 and A2) shows different conformational behavior from proCPB: the former undergoes a major conformational change (opening and closing), and the latter exhibits only a minor conformational change (remaining closed throughout the simulation). Differences center on the interface between the globular moiety of the pro-segment and the catalytic domain. Analysis of the trajectories demonstrates the importance of hydrogen bonds and salt-bridges in stabilizing the zymogen structures and shows different hydrogen-bond patterns between proCPA and proCPB: the former shows fewer strong H-bonds formed between the globular domain and the catalytic domain. The observed difference in conformational behavior between proCPA and proCPB may explain why small substrates and inhibitors can access the active sites of proCPA1 and proCPA2 but not of proCPB.

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

Similar content being viewed by others

References

  1. Aviles FX, Vendrell J, Guasch A, Coll M, Huber R (1993) Advances in metallo-procarboxypeptidases. Emerging details on the inhibition mechanism and on the activation process. Eur J Biochem 211(3):381–389

    Article  CAS  Google Scholar 

  2. Gomis-Ruth FX (2008) Structure and mechanism of metallocarboxypeptidases. Crit Rev Biochem Mol Biol 43(5):319–345

    Article  CAS  Google Scholar 

  3. Vendrell J, Aviles FX, Fricker LD (2004) Metallocarboxypeptidases. Handb Metalloproteins 3:176–189

    CAS  Google Scholar 

  4. Coll M, Guasch A, Aviles FX, Huber R (1991) Three-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity. EMBO J 10(1):1–9

    CAS  Google Scholar 

  5. Vendrell J, Querol E, Aviles FX (2000) Metallocarboxypeptidases and their protein inhibitors. Structure, function and biomedical properties. Biochim Biophys Acta, Protein Struct Mol Enzymol 1477(1–2):284–298

    Google Scholar 

  6. Garcia-Saez I, Reverter D, Vendrell J, Aviles FX, Coll M (1997) The three-dimensional structure of human procarboxypeptidase A2. Deciphering the basis of the inhibition, activation and intrinsic activity of the zymogen. EMBO J 16(23):6906–6913

    Article  CAS  Google Scholar 

  7. Khan AR, James MNG (1998) Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes. Protein Sci 7(4):815–836

    Article  CAS  Google Scholar 

  8. Lazure C (2002) The peptidase zymogen proregions: nature’s way of preventing undesired activation and proteolysis. Curr Pharm Des 8(7):511–531

    Article  CAS  Google Scholar 

  9. Guasch A, Coll M, Aviles FX, Huber R (1992) Three-dimensional structure of porcine pancreatic procarboxypeptidase A. A comparison of the A and B zymogens and their determinants for inhibition and activation. J Mol Biol 224(1):141–157

    Article  CAS  Google Scholar 

  10. Glowacki DR, Harvey JN, Mulholland AJ (2012) Taking Ockham’s razor to enzyme dynamics and catalysis. Nat Chem 4(3):169–176

    Article  CAS  Google Scholar 

  11. Pentikainen U, Pentikainen OT, Mulholland AJ (2008) Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations. Proteins 70(2):498–508

    Article  CAS  Google Scholar 

  12. Vendrell J, Guasch A, Coll M, Villegas V, Billeter M, Wider G, Huber R, Wuthrich K, Aviles FX (1992) Pancreatic procarboxypeptidases: their activation processes related to the structural features of the zymogens and activation segments. Biol Chem Hoppe-Seyler 373(7):387–392

    Article  CAS  Google Scholar 

  13. Villegas V, Vendrell J, Aviles X (1995) The activation pathway of procarboxypeptidase B from porcine pancreas: participation of the active enzyme in the proteolytic processing. Protein Sci 4(9):1792–1800

    Article  CAS  Google Scholar 

  14. Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9(9):646–652

    Article  CAS  Google Scholar 

  15. Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci USA 102(19):6679–6685

    Article  CAS  Google Scholar 

  16. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267(5612):585–590

    Article  CAS  Google Scholar 

  17. van der Kamp MW, Shaw KE, Woods CJ, Mulholland AJ (2008) Biomolecular simulation and modelling: status, progress and prospects. J R Soc Interface 5(Suppl 3):S173–190

    Article  Google Scholar 

  18. Lee VS, Tue-ngeun P, Nangola S, Kitidee K, Jitonnom J, Nimmanpipug P, Jiranusornkul S, Tayapiwatana C (2010) Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants. Mol Immunol 47(5):982–990

    Article  CAS  Google Scholar 

  19. Jitonnom J, Lomthaisong K, Lee VS (2012) Computational design of peptide inhibitor based on modifications of proregion from Plutella xylostella midgut trypsin. Chem Biol Drug Des 79(4):583–593

    Article  CAS  Google Scholar 

  20. Nimmanpipug P, Jitonnom J, Ngaojampa C, Hannongbua S, Lee VS (2007) A computational H5N1 neuraminidase model and its binding to commercial drugs. Mol Simul 33(6):487–493

    Article  CAS  Google Scholar 

  21. Jitonnom J, Mulholland AJ, Nimmanpipug P, Lee VS (2011) Hybrid QM/MM study on the deglycosylation step of chitin hydrolysis catalysed by chitinase B from Serratia marcescens. Maejo Int J Sci Technol 5(1):47–57

    CAS  Google Scholar 

  22. Jitonnom J, Lee VS, Nimmanpipug P, Rowlands HA, Mulholland AJ (2011) Quantum mechanics/molecular mechanics modeling of substrate-assisted catalysis in family 18 chitinases: conformational changes and the role of Asp142 in catalysis in ChiB. Biochemistry 50(21):4697–4711

    Article  CAS  Google Scholar 

  23. Lee VS, Kodchakorn K, Jitonnom J, Nimmanpipug P, Kongtawelert P, Premanode B (2010) Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study. J Comput Aided Mol Des 24(10):879–886

    Article  CAS  Google Scholar 

  24. Kotra LP, Cross JB, Shimura Y, Fridman R, Schlegel HB, Mobashery S (2001) Insight into the complex and dynamic process of activation of matrix metalloproteinases. J Am Chem Soc 123(13):3108–3113

    Article  CAS  Google Scholar 

  25. Perera L, Darden TA, Pedersen LG (2002) Predicted solution structure of zymogen human coagulation FVII. J Comput Chem 23(1):35–47

    Article  CAS  Google Scholar 

  26. Venkateswarlu D, Perera L, Darden T, Pedersen LG (2002) Structure and dynamics of zymogen human blood coagulation factor X. Biophys J 82(3):1190–1206

    Article  CAS  Google Scholar 

  27. Piana S, Rothlisberger U (2004) Molecular dynamics simulations of structural changes during procaspase 3 activation. Proteins Struct Funct Bioinf 55(4):932–941

    Article  CAS  Google Scholar 

  28. Zuo Z, Chen G, Zou H, Mok PC, Zhu W, Chen K, Jiang H (2007) Why does beta -secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies. Comput Biol Chem 31(3):186–195

    Article  CAS  Google Scholar 

  29. Friedman R, Caflisch A (2008) Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins Struct Funct Bioinf 73(4):814–827

    Article  CAS  Google Scholar 

  30. Friedman R, Caflisch A (2007) The protonation state of the catalytic aspartates in plasmepsin II. FEBS Lett 581(21):4120–4124

    Article  CAS  Google Scholar 

  31. Banci L, Bertini I, La Penna G (1994) The enzymatic mechanism of carboxypeptidase: a molecular dynamics study. Proteins Struct Funct Bioinf 18(2):186–197. doi:10.1002/prot.340180210

    Article  CAS  Google Scholar 

  32. Banci L, Schröder S, Kollman PA (1992) Molecular dynamics characterization of the active cavity of carboxypeptidase A and some of its inhibitor adducts. Proteins Struct Funct Bioinf 13(4):288–305. doi:10.1002/prot.340130403

    Article  CAS  Google Scholar 

  33. Makinen MW, Troyer JM, van der Werff H, Berendsen HJC, van Gunsteren WF (1989) Dynamical structure of carboxypeptidase A. J Mol Biol 207(1):201–216

    Article  CAS  Google Scholar 

  34. Chiche L, Heitz A, Padilla A, Le-Nguyen D, Castro B (1993) Solution conformation of a synthetic bis-headed inhibitor of trypsin and carboxypeptidase A: new structural alignment between the squash inhibitors and the potato carboxypeptidase inhibitor. Protein Eng 6(7):675–682

    Article  CAS  Google Scholar 

  35. Bayés A, Sonnenschein A, Daura X, Vendrell J, Aviles FX (2003) Procarboxypeptidase A from the insect pest Helicoverpa armigera and its derived enzyme. Eur J Biochem 270(14):3026–3035

    Article  Google Scholar 

  36. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER version 9. University of California, San Francisco

    Google Scholar 

  37. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16):1999–2012

    Article  CAS  Google Scholar 

  38. Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graphics 8(1):52–56, 29

    Google Scholar 

  39. Stote RH, Karplus M (1995) Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins Struct Funct Genet 23(1):12–31

    Article  CAS  Google Scholar 

  40. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935

    Article  CAS  Google Scholar 

  41. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 98(12):10089–10092

    Article  CAS  Google Scholar 

  42. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23(3):327–341

    Article  CAS  Google Scholar 

  43. Berendsen HJC, Postma JPM, Van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81(8):3684–3690

    Article  CAS  Google Scholar 

  44. Baker EN, Hubbard RE (1984) Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 44(2):97–179

    Article  CAS  Google Scholar 

  45. Daidone I, Amadei A (2012) Essential dynamics: foundation and applications. Wiley Interdiscip Rev Comput Mol Sci. doi:10.1002/wcms.1099

    Google Scholar 

  46. Amadei A, Linssen AB, Berendsen HJ (1993) Essential dynamics of proteins. Proteins 17(4):412–425

    Article  CAS  Google Scholar 

  47. Haider S, Parkinson GN, Neidle S (2008) Molecular dynamics and principal components analysis of human telomeric quadruplex multimers. Biophys J 95(1):296–311

    Article  CAS  Google Scholar 

  48. Falconi M, Biocca S, Novelli G, Desideri A (2007) Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant. BMC Struct Biol 7(1):73

    Article  Google Scholar 

  49. Meyer T, Ferrer-Costa C, Perez A, Rueda M, Bidon-Chanal A, Luque FJ, Laughton CA, Orozco M (2006) Essential dynamics: a tool for efficient trajectory compression and management. J Chem Theory Comput 2(2):251–258

    Article  CAS  Google Scholar 

  50. Hadfield AT, Mulholland AJ (1999) Active-site dynamics of ASADH—A bacterial biosynthetic enzyme. Int J Quantum Chem 73(2):137–146

    Article  CAS  Google Scholar 

  51. Gargallo R, Hünenberger PH, Avilés FX, Oliva B (2003) Molecular dynamics simulation of highly charged proteins: Comparison of the particle–particle particle-mesh and reaction field methods for the calculation of electrostatic interactions. Protein Sci 12(10):2161–2172

    Article  CAS  Google Scholar 

  52. Mátrai J, Jonckheer A, Joris E, Krüger P, Carpenter E, Tuszynski J, De Maeyer M, Engelborghs Y (2008) Exploration of the activation pathway of Δα-Chymotrypsin with molecular dynamics simulations and correlation with kinetic experiments. Eur Biophys J 38(1):13–23. doi:10.1007/s00249-008-0348-2

    Article  Google Scholar 

  53. Mujika JI, Lopez X, Mulholland AJ (2012) Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations. Org Biomol Chem 10(6):1207–1218. doi:10.1039/c1ob06444d

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was financially supported by the National Research Council of Thailand. We would like to thank the Advanced Computing Research Centre, University of Bristol (see http://www.bris.ac.uk/acrc/) for providing the computational facilities of this work. AJM is an EPSRC Leadership Fellow (grant number EP/G007705/1).

Author information

Authors and Affiliations

  1. Department of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand

    Jitrayut Jitonnom

  2. Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK

    Adrian J. Mulholland

Authors
  1. Jitrayut Jitonnom
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adrian J. Mulholland
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jitrayut Jitonnom.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 2.32 mb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jitonnom, J., Mulholland, A.J. Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity. Theor Chem Acc 131, 1224 (2012). https://doi.org/10.1007/s00214-012-1224-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00214-012-1224-9

Keywords

Search

Navigation