Cold adaptation of enzyme reaction rates

Biochemistry

Volumn 47, Issue 38, 2008, Pages 10049-10057

  Bjelic, Sinisa ^a   Brandsdal, Bjørn O ^b   Åqvist, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF TROMSØ   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; ARRHENIUS PLOTS; CANNING; CATALYSTS; COMPUTATIONAL METHODS; COMPUTER SIMULATION; DYNAMICS; ELECTROSTATICS; ENTHALPY; ENTROPY; ENZYMES; FOOD ADDITIVES; IMAGE CODING; MOLECULAR DYNAMICS; PROTEINS; QUANTUM CHEMISTRY; REACTION KINETICS; REACTION RATES; STABILIZATION; STANDARDS; STRUCTURAL OPTIMIZATION; THERMODYNAMICS;

ACTIVATION ENTHALPIES; ACTIVATION ENTROPIES; ACTIVATION PARAMETERS; ACTIVE SITES; ARRHENIUS; CATALYTIC EFFECTS; CATALYTIC RATES; COLD ADAPTATION; COMPUTER SIMULATIONS; ELECTROSTATIC STABILIZATION; ENOLATE; ENZYME REACTIONS; EXTREME TEMPERATURES; HIGH-PRECISION; HYPERTHERMOPHILIC; MESOPHILIC; MOLECULAR DYNAMICS CALCULATIONS; NEGATIVE ENTROPIES; PROTEIN INTERACTIONS; PROTEIN STRUCTURES; REACTION-RATE; REVERSE ORDER; SIMULATION RESULTS; STRUCTURAL BASIS; STRUCTURE-FUNCTION RELATIONSHIPS; SYNTHASES; THERMAL STABILITY; TRANSITION STATE; WORKING TEMPERATURES;

RATE CONSTANTS;

CITRATE SYNTHASE;

ARTICLE; CATALYSIS; COLD ACCLIMATIZATION; COMPUTER SIMULATION; ELECTRICITY; ENTHALPY; ENTROPY; ENZYME ACTIVATION; ENZYME KINETICS; ENZYME STABILITY; ENZYME STRUCTURE; HYPERTHERMOPHILE; ISOMERIZATION; MESOPHILE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PSYCHROPHILE; STRUCTURE ACTIVITY RELATION; TEMPERATURE ACCLIMATIZATION;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; ARCHAEAL PROTEINS; ARTHROBACTER; BINDING SITES; CATALYSIS; CITRATE (SI)-SYNTHASE; COLD; COMPUTER SIMULATION; PROTEIN STRUCTURE, SECONDARY; PYROCOCCUS FURIOSUS; QUANTUM THEORY; STEREOISOMERISM; SWINE; THERMODYNAMICS;

EID: 52249116531     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801177k     Document Type: Article

References (47)

1. Feller, G., and Gerday, C. (2003) Psychrophilic enzymes: Hot topics in cold adaptation. Nat. Rev. Microbiol 1, 200-208.
2. Siddiqui, K. S., and Cavicchioli, R. (2006) Cold-adapted enzymes. Annu. Rev. Biochem. 75, 403-433.
3. 4 orthologs of Antarctic notofhenioid fishes. Proc. Natl. Acad. Sci. U.S.A. 95, 11476-11481.
4. Lonhienne, T., Gerday, C., and Feller, G. (2000) Psychrophilic enzymes: revisiting the thermodynamic parameters of activation may explain local flexibility. Biochim. Biophys. Acta 1543, 1-10.
5. Roca, M., Liu, H., Messer, B., and Warshel, A. (2007) On the relationship between thermal stability and catalytic power of enzymes. Biochemistry 46, 15076-15088.
6. Olufsen, M., Smalås, A. O., Moe, E., and Brandsdal, B. O. (2005) Increased flexibility as a strategy for cold adaptation - A comparative molecular dynamics study of cold- and warm-active uracil DNA glycosylase. J. Biol. Chem. 280, 18042-18048.
7. Bell, G. S., Russell, R. J. M., Connaris, H., Hough, D. W., Danson, M. J., and Taylor, G. L. (2002) Stepwise adaptations of citrate synthase to survival at life's extremes-From psychrophile to hyperthermophile. Eur. J. Biochem. 269, 6250-6260.
8. Kumar, S., and Nussinov, R. (2004) Different roles of electrostatics in heat and in cold: Adaptation by citrate synthase. ChemBioChem 5, 280-290.
9. Russell, R. J. M., Gerike, U., Danson, M. J., Hough, D. W., and Taylor, G. L. (1998) Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium. Structure 6, 351-361.
10. Gerike, U., Danson, M. J., and Hough, D. W. (2001) Cold-active citrate synthase: mutagenesis of active-site residues. Protein Eng. 14, 655-661.
11. Warshel, A. (1991) Computer modeling of chemical reactions in enzymes and solutions, John Wiley & Sons, New York.
12. Åqvist, J., and Warshel, A. (1993) Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chem. Rev. 93, 2523-2544.
13. Remington, S., Wiegand, G., and Huber, R. (1982) Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 Åresolution. J. Mol. Biol. 158, 111-152.
14. Wiegand, G., and Remington, S. J. (1986) Citrate synthase: Structure, control, and mechanism. Annu. Rev. Biophys. Biophys. Chem. 15, 97-117.
15. Kurz, L. C., Drysdale, G., Riley, M., Tomar, M. A., Chen, J., Russell, R. J. M., and Danson, M. J. (2000) Kinetics and mechanism of the citrate synthase from the thermophilic Archaeon Thermoplasma acidophilum. Biochemistry 39, 2283-2296.
16. Gerike, U., Danson, M. J., Russell, N. J., and Hough, D. W. (1997) Sequencing and expression of the gene encoding a cold-active citrate synthase from an Antarctic bacterium, strain DS2-3R. Eur. J. Biochem. 248, 49-57.
17. Feierberg, I., and Åqvist, J. (2002) Computational modeling of enzymatic keto-enol isomerization reactions. Theor. Chem. Acc. 108, 71-84.
18. Gerlt, J. A., and Gassman, P. G. (1993) An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: Importance of late transition states in concerted mechanisms. J. Am. Chem. Soc. 115, 11552-11568.
19. Donini, O., Darden, T., and Kollman, P. A. (2000) QM-FE calculations of aliphatic hydrogen abstraction in citrate synthase and in solution: Reproduction of the effect of enzyme catalysis and demonstration that an enolate rather than an enol is formed. J. Am. Chem. Soc. 122, 12270-12280.
20. Mulholland, A. J., and Richards, W. G. (1997) Acetyl-CoA enolization in citrate synthase: A quantum mechanical molecular mechanical (QM/MM) study. Proteins: Struct., Funct., Genet. 27, 9-25.
21. Mulholland, A. J., Lyne, P. D., and Karplus, M. (2000) Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved. J. Am. Chem. Soc. 122, 534-535.
22. van der Kamp, M. W., Perruccio, F., and Mulholland, A. J. (2007) Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase. Proteins 69, 521-535.
23. van der Kamp, M. W., Perruccio, F., and Mulholland, A. J. (2007) Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase. J. Mol. Graphics Modell. 26, 676-690.
24. van der Kamp, M. W., Perruccio, F., and Mulholland, A. J. (2008) High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase. Chem. Commun. 16, 1874-1876.
25. Åqvist, J., and Fothergill, M. (1996) Computer simulation of the triosephosphate isomerase catalyzed reaction. J. Biol. Chem. 271, 10010-10016.
26. Hegarty, A. F., and Jencks, W. P. (1975) Bifunctional catalysis of the enolization of acetone. J. Am. Chem. Soc. 97, 7188-7189.
27. Amyes, T. L., and Richard, J. P. (1992) Generation and stability of a simple thiol ester enolate in aqueous solution. J. Am. Chem. Soc. 114, 10297-10302.
28. Lienhard, G. E., and Wang, T. C. (1968) Kinetics of proton transfer from the α carbon of ethyl thioacetate and its dimethyliminium derivative. J. Am. Chem. Soc. 90, 3781-3787.
29. Bjelic, S., and Åqvist, J. (2004) Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site. Biochemistry 43, 14521-14528.
30. Strajbl, M., Florian, J., and Warshel, A. (2000) Ab initio evaluation of the potential surface for general base-catalyzed methanolysis of formamide: A reference solution reaction for studies of serine proteases. J. Am. Chem. Soc. 122, 5354-5366.
31. Russell, R. J. M., Ferguson, J. M. C., Hough, D. W., Danson, M. J., and Taylor, G. L. (1997) The crystal structure of citrate synthase from the hyperthermophilic Archaeon Pyrococcus furiosus at 1.9 Å resolution. Biochemistry 36, 9983-9994.
32. Marelius, J., Kolmodin, K., Feierberg, I., and Åqvist, J. (1998) Q: A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J. Mol. Graphics Modell. 16, 213-225.
33. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force-field for the simulation of proteins, nucleic-acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
34. Jorgensen, W., Chandrasekhar, J., Madura, J., Rw, I., and Klein, M. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
35. Lee, F. S., and Warshel, A. (1992) A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J. Chem. Phys. 97, 3100-3107.
36. King, G., and Warshel, A. (1989) A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91, 3647-3661.
37. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Debolt, S., Ferguson, D., Seibel, G., and Kollman, P. (1995) AMBERr, a package of computer-programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91, 1-41.
38. Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N•log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092.
39. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341.
40. Arnott, M. A., Michael, R. A., Thompson, C. R., Hough, D. W., and Danson, M. J. (2000) Thermostability and thermoactivity of citrate synthases from the thermophilic and hyperthermophilic archaea, Thermoplasma acidophilum and Pyrococcus furiosus. J. Mol. Biol. 304, 657-668.
41. Almlöf, M., Brandsdal, B. O., and Åqvist, J. (2004) Binding affinity prediction with different force fields: Examination of the linear interaction energy method. J. Comput. Chem. 25, 1242-1254.
42. Trobro, S., and Åqvist, J. (2005) Mechanism of peptide bond synthesis on the ribosome. Proc. Natl. Acad. Sci. U.S.A. 102, 12395-12400.
43. Warshel, A. (1978) Energetics of enzyme catalysis. Proc. Natl. Acad. Sci. U.S.A. 75, 5250-5254.
44. Warshel, A. (1998) Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. J. Biol Chem. 273, 27035-27038.
45. Cannon, W. R., and Benkovic, S. J. (1998) Solvation, reorganization energy, and biological catalysis. J. Biol. Chem. 273, 26257-26260.
46. Warshel, A., Sharma, P. K., Chu, Z. T., and Åqvist, J. (2007) Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: Phenolates binding to the oxyanion hole of ketosteroid isomerase. Biochemistry 46, 1466-1476.
47. Shoichet, B. K., Baase, W. A., Kuroki, R., and Matthews, B. W. (1995) A relationship between protein stability and protein function. Proc. Natl. Acad. Sci. U.S.A. 92, 452-456.