Skip to main content
SpringerLink
Log in

Effect of external stresses on protein conformation: a computer modelling study

  • Article
  • Published:
European Biophysics Journal Aims and scope Submit manuscript

Abstract

The increasing use of digital technologies such as mobile phones has led to major health concerns about the effects of non-ionizing pulsed radiation exposure. We believe that the health implications of exposure to radiation cannot be fully understood without establishing the molecular mechanisms of biological effects of pulsed microwaves. We aim to establish methods for studying the molecular mechanisms of protein structural and energetic changes occurring due to external stresses related to non-ionizing radiation by using a combination of experimental and theoretical approaches. In this paper, we present the results from our fully atomistic simulation study of chemical and thermal stress response of a prototype protein, insulin. We performed a series of molecular dynamics simulations of insulin in solution under equilibrium conditions, under chemical stress (imitated by reducing the disulfide bonds in the protein molecule), and under short-lived thermal stress (imitated by increasing simulation temperature for up to 2 ns). The resultant protein conformational behaviour was analysed for various properties with the aim of establishing analysis routines for classification of protein unfolding pathways and associated molecular mechanisms.

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

Similar content being viewed by others

References

  • Allen MP, Tildesley DJ (1989) Computer simulation of liquids. Oxford University Press, New York

  • Badger J, Harris MR, Reynolds CD, Evans AC, Dodson EJ, Dodson GG, North ACT (1991) Structure of the pig insulin dimer in the cubic-crystal. Acta Crystallogr Sect B 47:127–136

    Article  Google Scholar 

  • Bentley G, Dodson E, Dodson G, Hodgkin D, Mercola D (1976) Structure of insulin in 4-zinc insulin. Nature 261:166–168

    CAS  PubMed  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

    PubMed  Google Scholar 

  • Bohr H, Bohr J (2000) Microwave-enhanced folding and denaturation of globular proteins. Phys Rev E 61:4310–4314

    Article  CAS  Google Scholar 

  • Brünger AT (1992) X-PLOR version 3.1, a system for X-ray crystallography and NMR. Yale University Press, New Haven

  • Chothia C, Lesk AM, Dodson GG, Hodgkin DC (1983) Transmission of conformational change in insulin. Nature 302:500–505

    CAS  PubMed  Google Scholar 

  • Ciszak E, Beals JM, Frank BH, Baker JC, Carter ND, Smith GD (1995) Role of C-terminal B-fragment residues in insulin assembly: the structure of hexameric LysB28ProB29-human insulin. Structure 3:615–622

    CAS  PubMed  Google Scholar 

  • Daniells C, Duce I, Thomas D, Sewell P, Tattersall J, de Pomerai DI (1998) Transgenic nematodes as biomonitors of microwave-induced stress. Mutat Res 399:55–64

    CAS  Google Scholar 

  • de Pomerai DI, Dawe A, Djerbib L, Allan J, Brunt G, Daniells C (2002) Growth and maturation of the nematode Caenorhabditis elegans following exposure to weak microwave fields. Enzyme Microbial Technol 30:73–79

    Article  Google Scholar 

  • Derewenda U, Derewenda Z, Dodson EJ, Dodson GG, Reynolds CD, Smith GD, Sparks C, Swenson D (1989) Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer. Nature 338:594–596

    Article  CAS  PubMed  Google Scholar 

  • Derewenda U, Derewenda Z, Dodson EJ, Dodson GG, Bing X, Markussen J (1991) X-ray analysis of the single fragment B29-A1 peptide-linked insulin molecule. A completely inactive analogue. J Mol Biol 220:425–433

    CAS  PubMed  Google Scholar 

  • Dodson EJ, Dodson GG, Hubbard RE, Reynolds CD (1983) Insulin’s structural behavior and its relation to activity. Biopolymers 22:281–291

    CAS  PubMed  Google Scholar 

  • Dong J, Wan Z, Popov M, Carey PR, Weiss MA (2003) Insulin assembly damps conformational fluctuations: Raman analysis of amide I linewidths in native states and fibrils. J Mol Biol 330:431–442

    Article  CAS  PubMed  Google Scholar 

  • Du YC, Minasian E, Tregear GW, Leach SJ (1982) Circular dichroism studies of relaxin and insulin peptide fragments. Int J Pept Protein Res 20:47–55

    CAS  PubMed  Google Scholar 

  • Falconi M, Cambria MT, Cambria A, Desideri A. (2001) Structure and stability of the insulin dimer investigated by molecular dynamics simulation. J Biomol Struct Dyn 18:761–772

    CAS  PubMed  Google Scholar 

  • French PW, Donnelan M, McKenzie DR (1997) Electromagnetic radiation at 835 MHz changes the morphology and inhibits proliferation of a human astrocytoma cell line. Bioelectrochem Bioenerget 43:13–18

    Article  CAS  Google Scholar 

  • French PW, Penny R, Laurence JA (2000) Mobile phones, heat shock proteins and cancer. Differentiation 67:93–97

    Article  Google Scholar 

  • Hawkins B, Cross K, Craik D (1995) Solution structure of the B-fragment of insulin as determined by 1H NMR spectroscopy. Comparison with the crystal structure of the insulin hexamer and with the solution structure of the insulin monomer. Int J Pept Protein Res 46:424–433

    CAS  PubMed  Google Scholar 

  • Hertz HG (1973) In: Franks F (ed) Water—a comprehensive treatise, vol 3. Plenum Press, New York, pp 301–399

  • Hua QX, Weiss MA (1991) Comparative 2D NMR studies of human insulin and des-pentapeptide insulin: sequential resonance assignment and implications for protein dynamics and receptor recognition. Biochemistry 30:5505–5515

    CAS  PubMed  Google Scholar 

  • Hua QX, Shoelson SE, Kochoyan M, Weiss MA (1991) Receptor binding redefined by a structural switch in a mutant human insulin. Nature 354:238–241

    Article  CAS  PubMed  Google Scholar 

  • Hua QX, Shoelson SE, Inouye K, Weiss MA (1993a) Paradoxical structure and function in a mutant human insulin associated with diabetes mellitus. Proc Natl Acad Sci USA 90:582–586

    CAS  PubMed  Google Scholar 

  • Hua QX, Ladbury JE, Weiss MA (1993b) Dynamics of a monomeric insulin analogue: testing the molten-globule hypothesis. Biochemistry 32:1433–1442

    CAS  PubMed  Google Scholar 

  • Hua QX, Nakagawa SH, Jia W, Hu SQ, Chu YC, Katsoyannis PG, Weiss MA (2001) Hierarchical protein folding: asymmetric unfolding of an insulin analogue lacking the A7-B7 interfragment disulfide bridge. Biochemistry 40:12299–12311

    Article  CAS  PubMed  Google Scholar 

  • Hua QX, Jia W, Frank BH, Phillips NF, Weiss MA (2002) A protein caught in a kinetic trap: structures and stabilities of insulin disulfide isomers. Biochemistry 41:14700–14715

    Article  CAS  PubMed  Google Scholar 

  • Humphrey W, Dalke A, Schulten K (1996) VMD – visual molecular dynamics. J Mol Graph 14:33–38

    CAS  PubMed  Google Scholar 

  • InsightII User Guide (1996) Molecular Simulations, San Diego, Calif

  • Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K (1999) NAMD2: Greater scalability for parallel molecular dynamics. J Comput Phys 151:283–312

    Article  Google Scholar 

  • Kazmirski SL, Daggett V (1998) Simulations of the structural and dynamical properties of denatured proteins: the “molten coil” state of bovine pancreatic trypsin inhibitor. J Mol Biol 277:487–506

    Article  CAS  PubMed  Google Scholar 

  • Kazmirski SL, Li A, Daggett V (1999) Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. J Mol Biol 290:283–304

    Article  CAS  PubMed  Google Scholar 

  • Kruger P, Strassburger W, Wollmer A, van Gunsteren WF, Dodson GG (1987) The simulated dynamics of the insulin monomer and their relationship to the molecule’s structure. Eur Biophys J 14:449–459

    CAS  PubMed  Google Scholar 

  • Laurence JA, French PW, Lindner RA, McKenzie DR (2000) Biological effects of electromagnetic fields – mechanism for the effects of pulsed microwave radiation on protein conformation. J Theor Biol 206:291–298

    CAS  PubMed  Google Scholar 

  • Leach AR (2001) Molecular modelling – principles and applications, 2nd edn. Prentice-Hall, Harlow, UK

  • Li A, Daggett V (1996) Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol 257:412–429

    Article  CAS  PubMed  Google Scholar 

  • Li A, Daggett V (1998) Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J Mol Biol 275:677–694

    Article  CAS  PubMed  Google Scholar 

  • Ludvigsen S, Olsen HB, Kaarsholm NC (1998) A structural switch in a mutant insulin exposes key residues for receptor binding. J Mol Biol 279:1–7

    Article  CAS  PubMed  Google Scholar 

  • MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616

    Article  CAS  Google Scholar 

  • Mark AE, Berendsen HJ, van Gunsteren WF (1991) Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study. Biochemistry 30:10866–10872

    CAS  PubMed  Google Scholar 

  • Mayor U, Johnson CM, Daggett V, Fersht AR (2000) Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci USA 97:13518–13522

    Article  CAS  PubMed  Google Scholar 

  • Mirmira RG, Nakagawa SH, Tager HS (1991) Importance of the character and configuration of residues B24, B25, and B26 in insulin-receptor interactions. J Biol Chem 266:1428–1436

    CAS  PubMed  Google Scholar 

  • O’Donohue MF, Burgess AW, Walkinshaw MD, Treutlein HR (1995) Modeling conformational changes in cyclosporin A. Protein Sci 4:2191–2202

    CAS  PubMed  Google Scholar 

  • O’Donohue M, Minasian E, Leach SJ, Burgess AW, Treutlein HR (2000) PEPCAT – a new tool for conformational analysis of peptides. J Comput Chem 21:446–461

    Article  CAS  Google Scholar 

  • Olsen HB, Ludvigsen S, Kaarsholm NC (1996) Solution structure of an engineered insulin monomer at neutral pH. Biochemistry 35:8836–8845

    Article  CAS  PubMed  Google Scholar 

  • Pande VS, Rohksar DS (1999) Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G. Proc Natl Acad Sci USA 96:9062–9067

    Article  CAS  PubMed  Google Scholar 

  • Pastrana-Rios B (2001) Mechanism of unfolding of model helical peptide. Biochemistry 40:9074–9081

    Article  CAS  PubMed  Google Scholar 

  • Pittman IT, Tager HS (1995) A spectroscopic investigation of the conformational dynamics of insulin in solution. Biochemistry 34:10578–10590

    CAS  PubMed  Google Scholar 

  • Qiao ZS, Min CY, Hua QX, Weiss MA, Feng YM (2003) In vitro refolding of human proinsulin. Kinetic intermediates, putative disulfide-forming pathway folding initiation site, and potential role of C-peptide in folding process. J Biol Chem 278:17800–17809

    Article  CAS  PubMed  Google Scholar 

  • Schultz GE, Schirmer RH (1979) Principles of protein structure. Springer, New York

  • Snow CD, Nguyen H, Pande VS, Gruebele M (2002) Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420:102–106

    Article  PubMed  Google Scholar 

  • Stuerga DAC, Galliard P (1996) Microwave athermal effects in chemistry: a myth’s autopsy. J Microwave Power Electromagn Energy 31:87–100

    Google Scholar 

  • Wu C-S, Yang JT (1981) Conformation of insulin and its fragments in surfactant solutions. Biochim Biophys Acta 667:285–293

    Article  CAS  PubMed  Google Scholar 

  • Yao ZP, Zeng ZH, Li HM, Zhang Y, Feng YM, Wang DC (1999) Structure of an insulin dimer in an orthorhombic crystal: the structure analysis of a human insulin mutant (B9 Ser→Glu). Acta Crystallogr Sect D 55:1524–1532

    Article  Google Scholar 

  • Zhang Y, Whittingham JL, Turkenburg JP, Dodson EJ, Brange J, Dodson GG (2002) Crystallization and preliminary crystallographic investigation of a low-pH native insulin monomer with flexible behaviour. Acta Crystallogr Sect D 58:186–187

    Article  Google Scholar 

Download references

Acknowledgements

Useful discussions with A. Prof. John Carver (University of Wollongong, Australia), Yoke Berry (University of Wollongong, Australia), and Prof. David McKenzie (University of Sydney, Australia) are appreciated. The authors acknowledge the Australian Research Council (ARC) and Cytopia Pty. Ltd. for providing funding for this project, and the Australian Partnership for Advanced Computing (APAC) for the grant of computer time.

Author information

Authors and Affiliations

  1. Department of Applied Physics, RMIT University, GPO Box 2476V, 3001, Melbourne, Victoria , Australia

    A. Budi, S. Legge & I. Yarovsky

  2. Cytopia Pty. Ltd., Level 5, Baker Institute, Commercial Road, 3004, Melbourne, Victoria , Australia

    H. Treutlein

Authors
  1. A. Budi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. Legge
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. H. Treutlein
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. I. Yarovsky
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to I. Yarovsky.

Additional information

Submitted as a record of the 2002 Australian Biophysical Society meeting

Rights and permissions

Reprints and permissions

About this article

Cite this article

Budi, A., Legge, S., Treutlein, H. et al. Effect of external stresses on protein conformation: a computer modelling study. Eur Biophys J 33, 121–129 (2004). https://doi.org/10.1007/s00249-003-0359-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00249-003-0359-y

Keywords

Search

Navigation