Abstract
The function of the E. coli lactose operon requires the binding of the tetrameric repressor protein to the operator DNA. We have previously shown that γ-irradiation destabilises the repressor-operator complex because the repressor gradually loses its DNA-binding ability (Radiat Res 170:604–612, 2008). It was suggested that the observed oxidation of tyrosine residues and the concomitant structural changes of irradiated headpieces (DNA-binding domains of repressor monomers) could be responsible for the inactivation. To unravel the mechanisms that lead to repressor-operator complex destabilisation when tyrosine oxidation occurs, we have compared by molecular dynamic simulations two complexes: (1) the native complex formed by two headpieces and the operator DNA, and (2) the damaged complex, in which all tyrosines are replaced by their oxidation product 3,4-dihydroxyphenylalanine (DOPA). On a 20 ns time scale, MD results show effects consistent with complex destabilisation: increased flexibility, increased DNA bending, modification of the hydrogen bond network, and decrease of the positive electrostatic potential at the protein surface and of the global energy of DNA-protein interactions.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037–10041
Begusova M, Spotheim-Maurizot M, Sy D, Michalik V, Charlier M (2001) RADACK, a stochastic simulation of hydroxyl radical attack to DNA. J Biomol Struct Dyn 19:141–158
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
Case DA, Pearlman DA, Caldwell JW, Cheatham TE III, Wang J, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Gohlke H, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA (2002) AMBER 9. University of California, San Francisco
Chakravarti B, Chakravarti DN (2007) Oxidative modification of proteins: age-related changes. Gerontology 53:128–139
Darden TA, York D, Pederson L (1993) Particle Mesh Ewald: an n log(n) method for Ewald sums in large systems. J Chem Phys 98:10089–10092
Davies MJ, Dean RT (1997) Radical-mediated protein oxidation. From chemistry to medicine. Oxford University Press, Oxford
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32(Web server issue):W665–W667
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA (2007) PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35(Web Server issue):W522–W525
Eon S, Culard F, Sy D, Charlier M, Spotheim-Maurizot M (2001) Radiation disrupts protein-DNA complexes through damage to the protein. The lac repressor-operator system. Radiat Res 156:110–117
Gillard N, Goffinont S, Bure C, Davidkova M, Maurizot JC, Cadene M, Spotheim-Maurizot M (2007) Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor. Biochem J 403:463–472
Goffinont S, Davidkova M, Spotheim-Maurizot M (2009) Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor. Biochem Biophys Res Commun 386:300–304
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(33–8):27–28
Jain R, Freund HG, Budzinsky E, Sharma M (1997) Radiation-induced formation of 3,4-dihydroxyphenylalanine in tyrosine-containing peptides and proteins as a function of X-irradiation dose. Bioconjug Chem 8:173–178
Kalodimos CG, Boelens R, Kaptein R (2004) Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the lac repressor system. Chem Rev 104:3567–3586
Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE (2009) Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 19:120–127
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897
Lavery R, Sklenar H (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J Biomol Struct Dyn 6:63–91
Mazier S, Villette S, Goffinont S, Renouard S, Maurizot JC, Genest D, Spotheim-Maurizot M (2008) Radiation damage to a DNA-binding protein. Combined circular dichroism and molecular dynamics simulation analysis. Radiat Res 170:604–612
Petropoulos I, Friguet B (2006) Maintenance of proteins and aging: the role of oxidized protein repair. Free Radic Res 40:1269–1276
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimeria-ar visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612
Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–342
Spronk CA, Slijper M, van Boom JH, Kaptein R, Boelens R (1996) Formation of the hinge helix in the lac repressor is induced upon binding to the lac operator. Nat Struct Biol 3:916–919
Spronk CA, Bonvin AM, Radha PK, Melacini G, Boelens R, Kaptein R (1999) The solution structure of lac repressor headpiece 62 complexed to a symmetrical lac operator. Structure Fold Des 7:1483–1492
Srinivasan J, Cheatham TEI, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J Am Chem Soc 120:9401–9409
Strahs D, Schlick T (2000) A-Tract bending: insights into experimental structures by computational models. J Mol Biol 301:643–663
Wilson CJ, Zhan H, Swint-Kruse L, Matthews KS (2007) The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding. Cell Mol Life Sci 64:3–16
Acknowledgments
We gratefully acknowledge financial support from “La Ligue contre le cancer. Comité d’Eure-et-Loir (France)”. The technical assistance of Alain Boyer is greatly appreciated.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Aci-Sèche, S., Garnier, N., Goffinont, S. et al. Comparing native and irradiated E. coli lactose repressor-operator complex by molecular dynamics simulation. Eur Biophys J 39, 1375–1384 (2010). https://doi.org/10.1007/s00249-010-0591-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-010-0591-1