Kinetics and Energetics of Ligand Binding Determined by Microcalorimetry: Insights into Active Site Mobility in a Psychrophilic α-Amylase

Journal of Molecular Biology

Volumn 358, Issue 5, 2006, Pages 1296-1304

  D'Amico, S ^a   Sohier, J S ^a   Feller, G ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

extremophiles; isothermal titration calorimetry; microcalorimetry; psychrophiles

Indexed keywords

AMYLASE; CHLORIDE; MALTOSE; OLIGOSACCHARIDE; POLYSACCHARIDE; STARCH;

ALLOSTERISM; ANTARCTICA; ARTICLE; BACTERIAL STRAIN; CATALYSIS; COLD; ENTHALPY; ENTROPY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ASSAY; ENZYME BINDING; ENZYME INHIBITION; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HYDROLYSIS; LIGAND BINDING; MICROCALORIMETRY; NONHUMAN; PANCREAS; PRIORITY JOURNAL; SWINE; THERMODYNAMICS;

BACTERIA (MICROORGANISMS); SUS SCROFA;

EID: 33646087677     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.03.004     Document Type: Article

References (45)

1. Deming J.W. Psychrophiles and polar regions. Curr. Opin. Microbiol. 5 (2002) 301-309
2. Junge K., Eicken H., and Deming J.W. Bacterial activity at -2 to -20 degrees C in Arctic wintertime sea ice. Appl. Environ. Microbiol. 70 (2004) 550-557
3. Feller G., and Gerday C. Psychrophilic enzymes: hot topics in cold adaptation. Nature Rev. Microbiol. 1 (2003) 200-208
4. Margesin R., Feller G., Gerday C., and Russell N.J. Cold-adapted microorganisms: adaptation strategies and biotechnological potential. In: Bitton G. (Ed). Encyclopedia of Environmental Microbiology vol. 2 (2002), Wiley, New York 871-885
5. Cavicchioli R., Thomas T., and Curmi P.M.G. Cold stress response in archaea. Extremophiles 4 (2000) 321-331
6. Lim J., Thomas T., and Cavicchioli R. Low temperature regulated DEAD-box RNA helicase from the Antarctic archaeon, Methanococcoides burtonii. J. Mol. Biol. 297 (2000) 553-567
7. Medigue C., Krin E., Pascal G., Barbe V., Bernsel A., Bertin P.N., et al. Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res. 15 (2005) 1325-1335
8. Saunders N.F., Thomas T., Curmi P.M., Mattick J.S., Kuczek E., Slade R., et al. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13 (2003) 1580-1588
9. Rabus R., Ruepp A., Frickey T., Rattei T., Fartmann B., Stark M., et al. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ. Microbiol. 6 (2004) 887-902
10. Methe B.A., Nelson K.E., Deming J.W., Momen B., Melamud E., Zhang X., et al. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc. Natl Acad. Sci. USA 102 (2005) 10913-10918
11. D'Amico S., Claverie P., Collins T., Georlette D., Gratia E., Hoyoux A., et al. Molecular basis of cold adaptation. Phil. Trans. Roy. Soc. ser. B 357 (2002) 917-925
12. Feller G. Molecular adaptations to cold in psychrophilic enzymes. Cell. Mol. Life Sci. 60 (2003) 648-662
13. Georlette D., Blaise V., Collins T., D'Amico S., Gratia E., Hoyoux A., et al. Some like it cold: biocatalysis at low temperatures. FEMS Microbiol. Rev. 28 (2004) 25-42
14. Wintrode P.L., and Arnold F.H. Temperature adaptation of enzymes: lessons from laboratory evolution. Advan. Protein Chem. 55 (2000) 161-225
15. Tehei M., Franzetti B., Madern D., Ginzburg M., Ginzburg B.Z., Giudici-Orticoni M.T., et al. Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering. EMBO Rep. 5 (2004) 66-70
16. D'Amico S., Gerday C., and Feller G. Structural similarities and evolutionary relationships in chloride-dependent alpha-amylases. Gene 253 (2000) 95-105
17. Da Lage J.L., Feller G., and Janecek S. Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the alpha-amylase model. Cell. Mol. Life Sci. 61 (2004) 97-109
18. Qian M., Haser R., and Payan F. Structure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 Å resolution. J. Mol. Biol. 231 (1993) 785-799
19. Aghajari N., Feller G., Gerday C., and Haser R. Crystal structures of the psychrophilic α-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Sci. 7 (1998) 564-572
20. Aghajari N., Feller G., Gerday C., and Haser R. Structures of the psychrophilic Alteromonas haloplanctis α-amylase give insights into cold adaptation at a molecular level. Structure 6 (1998) 1503-1516
21. Qian M., Haser R., Buisson G., Duee E., and Payan F. The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-Å resolution. Biochemistry 33 (1994) 6284-6294
22. Aghajari N., Roth M., and Haser R. Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase. Biochemistry 41 (2002) 4273-4280
23. Feller G., d'Amico D., and Gerday C. Thermodynamic stability of a cold-active α-amylase from the Antarctic bacterium Alteromonas haloplanctis. Biochemistry 38 (1999) 4613-4619
24. Feller G., Payan F., Theys F., Qian M., Haser R., and Gerday C. Stability and structural analysis of α-amylase from the Antarctic psychrophile Alteromonas haloplanctis A23. Eur. J. Biochem. 222 (1994) 441-447
25. D'Amico S., Gerday C., and Feller G. Structural determinants of cold adaptation and stability in a large protein. J. Biol. Chem. 276 (2001) 25791-25796
26. D'Amico S., Gerday C., and Feller G. Temperature adaptation of proteins: engineering mesophilic-like activity and stability in a cold-adapted alpha-amylase. J. Mol. Biol. 332 (2003) 981-988
27. D'Amico S., Marx J.C., Gerday C., and Feller G. Activity-stability relationships in extremophilic enzymes. J. Biol. Chem. 278 (2003) 7891-7896
28. Feller G., Bussy O., Houssier C., and Gerday C. Structural and functional aspects of chloride binding to Alteromonas haloplanctis alpha-amylase. J. Biol. Chem. 271 (1996) 23836-23841
29. Aghajari N., Feller G., Gerday C., and Haser R. Structural basis of alpha-amylase activation by chloride. Protein Sci. 11 (2002) 1435-1441
30. Lonhienne T., Baise E., Feller G., Bouriotis V., and Gerday C. Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases. Biochim. Biophys. Acta 1545 (2001) 349-356
31. Todd M.J., and Gomez J. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity?. Anal. Biochem. 296 (2001) 179-187
32. Goldberg R.N. Thermodynamics of enzyme-catalyzed reactions: Part 6-1999 update. J. Phys. Chem. Ref. Data 28 (1999) 931-965
33. Goldberg R.N., Bell D., Tewari Y.B., and McLaughlin M.A. Thermodynamics of hydrolysis of oligosaccharides. Biophys. Chem. 40 (1991) 69-76
34. Rauscher E., Neumann U., Schaich E., von Bulow S., and Wahlefeld A.W. Optimized conditions for determining activity concentration of alpha-amylase in serum, with 1,4-alpha-d-4-nitrophenylmaltoheptaoside as substrate. Clin. Chem. 31 (1985) 14-19
35. Seigner C., Prodanov E., and Marchis-Mouren G. On porcine pancreatic alpha-amylase action: kinetic evidence for the binding of two maltooligosaccharide molecules (maltose, maltotriose and o-nitrophenylmaltoside) by inhibition studies. Correlation with the five-subsite energy profile. Eur. J. Biochem. 148 (1985) 161-168
36. Turnbull W.B., and Daranas A.H. On the value of c: can low affinity systems be studied by isothermal titration calorimetry?. J. Am. Chem. Soc. 125 (2003) 14859-14866
37. Fukada H., and Takahashi K. Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. Proteins: Struct. Funct. Genet. 33 (1998) 159-166
38. Feller G., D'Amico S., Benotmane A.M., Joly F., Van Beeumen J., and Gerday C. Characterization of the C-terminal propeptide involved in bacterial wall spanning of alpha-amylase from the psychrophile Alteromonas haloplanctis. J. Biol. Chem. 273 (1998) 12109-12115
39. Collins T., Meuwis M.A., Gerday C., and Feller G. Activity, stability and flexibility in glycosidases adapted to extreme thermal environments. J. Mol. Biol. 328 (2003) 419-428
40. Georlette D., Damien B., Blaise V., Depiereux E., Uversky V.N., Gerday C., and Feller G. Structural and functional adaptations to extreme temperatures in psychrophilic, mesophilic, and thermophilic DNA ligases. J. Biol. Chem. 278 (2003) 37015-37023
41. Siddiqui K.S., Feller G., D'Amico S., Gerday C., Giaquinto L., and Cavicchioli R. The active site is the least stable structure in the unfolding pathway of a multidomain cold-adapted alpha-amylase. J. Bacteriol. 187 (2005) 6197-6205
42. Fields P.A., and Somero G.N. Hot spots in cold adaptation: localized increases in conformational flexibility in lactate dehydrogenase A(4) orthologs of Antarctic notothenioid fishes. Proc. Natl Acad. Sci. USA 95 (1998) 11476-11481
43. Xu Y., Feller G., Gerday C., and Glansdorff N. Metabolic enzymes from psychrophilic bacteria: challenge of adaptation to low temperatures in ornithine carbamoyltransferase from Moritella abyssi. J. Bacteriol. 185 (2003) 2161-2168
44. Fersht A. Enzyme Structure and Mechanism (1985), Freeman and Co., New York
45. Wiegand G., Epp O., and Huber R. The crystal structure of porcine pancreatic alpha-amylase in complex with the microbial inhibitor Tendamistat. J. Mol. Biol. 247 (1995) 99-110