Research

The inter-relationship of enzyme activity, stability, and dynamics

Much is known of enzyme structure and reaction mechanism, but we remain relatively ignorant of the timescales and dimensions of the molecular dynamics upon which enzyme catalysis depends. The long term aim of this work is to define the molecular motions required for enzyme activity. This work is an international collaboration, involving, in particular, collaboration with the groups of  Prof Jeremy Smith (Department of  Biocomputing, University of Heidelberg), Prof John Finney (Department of Physics and Astronomy, UCL, London). Much of the research utilises the neutron beam facilities at the Institute Laue-Langevin, Grenoble (see http://www.ill.fr/)

A recent extension of the work is the investigation of the effect of hydration on enzyme activity and dynamics, and the possible implications for life in dry environments (See "The molecular basis of life: is life possible without water?", a discussion meeting organised by Professor Ray Daniel FRSNZ, Professor John Finney and Professor Marshall Stoneham FRS. Details at: http://www.royalsoc.ac.uk/events/ )

For a general account of the background to this work, see "Enzyme dynamics and its relationship to stability and catalytic activity", R M.Daniel, NZ BioSci. 8 (2000) 21-23  [To download PDF click here]

Recent publications on this research:

        Torsten Becker, Jennifer Hayward, Roy M Daniel, John Finney, Jeremy C Smith. Neutron frequency windows and the protein dynamical transition. Biophysical Journal. [In Press].
 

        Dunn, R V, and Daniel, R M. The use of gas phase substrates to study enzyme catalysis at low hydration. Philosophical Transactions of the Royal Society of London Series B. [In Press].
 

        Erika Balog, Torsten Becker, Martin Oettl, Ruep Lechner, Roy Daniel, John Finney and Jeremy C Smith. Direct Determination of Vibrational Density of States Change on Ligand Binding to a Protein. Rhys Rev Lett. [In Press].
 

        Jennifer Hayward, John Finney, Roy Daniel, Jeremy Smith. Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophys J . 85, 679-685, 2003.
 

        Jennifer Hayward, Roy M Daniel, John L Finney, Jeremy C Smith. Use of computer simulation in the interpretation of dynamic elastic neutron scatting in complex molecular systems: a small protein in various environments. Chemical Physics. 292 (2003) 389-396.
 

        The Role of Dynamics in Enzyme Activity; R. M. Daniel, R. V. Dunn, J. L. Finney, J. C. Smith, Ann Rev Biophys Biomol Struct, 32: (2003) 69-92.

        The dynamic transition in proteins may have a simple explanation; Roy M. Daniel, John L. Finney, and Jeremy C. Smith  Faraday Discuss. 122 (2002) 163-169

        Protein folding and dynamics - New insights from computer simulation and scattering experiments, Bondar, N., Daniel, R.M., Finney, J.L., Fischer, S., Kataoka, M., Petrescu, A., and Smith, J.C. Proc. Int. Symposium on Advances in Neutron Scattering Research, Tokai, 2000. J. Phys. Soc. Jpn. 70 (2001) Suppl. A pp. 392-395.

        Solvent dependance of dynamical transitions in protein solutions. Reat, V., Dunn, R., Ferrand, M., Finney, J. L., Daniel, R.M. and Smith, J.C. Proc Natl. Acad. Sci. 97 (2000) 9961-9966

        Enzyme dynamics and its relationship to stability and catalytic activity. Daniel, R M. NZ BioSci. 8 (2000) 21-23

        Enzyme activity and dynamics:  Xylanase activity in the absence of fast anharmonic dynamics.  Dunn, R. V., Reat, V., Finney, J.L., Ferrand, M., Smith, J. C. and Daniel, R.M. Biochem. J., 346 (2000) 355-358

        Enzyme dynamics and activity:  Timescale dependance of dynamical transition in glutamate dehydrogenase solution, Daniel, R.M., Finney, J.L., Reat, V., Dunn, R., Ferrand, M. and Smith, J.C. Biophysical Journal, 77 (1999) 2184-2190

       Nanosecond protein dynamics:  First detection of a Neutron incoherent spin-echo signal.  Bellisent-Funel, M.C., Daniel, R. M., Durand, D., Ferrand, M., Finney, J. L., Pouget, S., Reat, V., and Smith, J.C.  Journal of the American Chemical Society  120 (1998) 7347-7348.

       Enzyme activity below the dynamical transition at 220K. Daniel R.M., Smith J.C.,Ferrand M, . Hery S, Dunn R. and Finney  J.L.  Biophysical Journal  75 (1998) 2504-2507

The effect of temperature on enzymes:

       As well as dealing generally with the effect of temperature extremes on enzyme activity and

       stability, this research extends to cover the implications for life under extremes of

       temperature, including the temperature effects on metabolites. Much of our recent efforts

       have centred on the discovery by us, in collaboration with Prof Michael Danson and Dr

       Robert Eisenthal (Deparment of Biology and Biochemistry, University of Bath, UK), of a

       new intrinsic thermal parameter of enzymes (See "The temperature optima of enzymes; a

       new perspective on an old phenomenon", Daniel, R.M., Danson, M.J. and Eisenthal, R.

       Trends Biochem. Sci., 26 (2001) 223-225.) [To download PDF click here]

       For a general outline of the limits of enzyme activity see "Astroenzymology – the

       environmental limits of enzyme activity", Roy M  Daniel; in Astronomical Telescopes and

       Instrumentation 2002: Topics in Astronomy: Information Technologies, MMW and

       Sub-MMW Detectors, Solar Astrophysics, Non-EM Astronomy, Exo-Planet

       Detection, and Astrobiology. The International Society for Optical Engineering, March

       2003; ISBN 0-8194-4674-2. [To download PDF click here]

                  Recent publications on this research:

   Michelle E Peterson, Robert Eisenthal, Michael J Danson, Alastair Spence and Roy M Daniel.   A new, intrinsic, thermal parameter for enzymes reveals true temperature optima. J Biol Chem, 279 (2004) 20717-10722.

       The Upper Temperature Limit for Life Based on Hyperthermophile Culture Experiments and Field Observations; James F. Holden and Roy M. Daniel In Subsurface Biosphere at Mid-Ocean Ridges (Wilcock, W.S.D., C.  Cary, E. DeLong, D.S. Kelley, and J.A. Baross, eds. American Geophysical  Union Monograph, Washington, D.C. (in press)

       Daniel, R.M., J.F. Holden, R. van Eckert, J. Truter and  D.A. Cowan The stability of  biomolecules and the implications for life at high temperatures. In Subsurface Biosphere at Mid-Ocean Ridges (Wilcock, W.S.D., C.  Cary, E. DeLong, D.S. Kelley, and J.A. Baross, eds. American Geophysical  Union Monograph, Washington, D.C.

       Astroenzymology – the environmental limits of enzyme activity, Roy M  Daniel; in Astronomical Telescopes and Instrumentation 2002: Topics in Astronomy: Information Technologies, MMW and Sub-MMW Detectors, Solar Astrophysics, Non-EM Astronomy, Exo-Planet Detection, and Astrobiology. The International Society for Optical Engineering, March 2003; ISBN 0-8194-4674-2

        The temperature optima of enzymes; a new perspective on an old phenomenon, Daniel, R.M., Danson, M.J. and Eisenthal, R. Trends Biochem. Sci., 26 (2001) 223-225.

       Assaying  activity  and assessing  thermostability of hyperthermophilic enzymes, Daniel, R.M. and Danson, M.J. Methods in Enzymology, 334 (2001) 283-293.

       Enzyme activity down to –100^oC.  Bragger, J. M., Dunn, R. V., and Daniel, R. M. Biochim. Biophys. Acta 1480 (2000) 278-282.

       Biomolecular stability and life at high temperatures. Daniel, R.M. and Cowan, D.A.C. Cell. Mol. Life Sci.  57 (2000) 250-264.

        Degradation and denaturation of stable enzymes.  D. Thompson, R Fernandez, C. Mateo, D. Cowan, J. Guisan, and R. Daniel. In Progress in Biotechnology  Vol 15 pp 349-352 (ed. A, Ballesteros et al. )  Elsevier,1998.

       Primitive coenzymes in archaeal/thermophilic metabolic pathways, Daniel R.M. Chapter 21 in, “Thermophiles – the keys to molecular evolution and the origin of life? (Eds. J.Wiegel  and  M.W.W.Adams)  Taylor and Francis, London. (1998) pp 299-310.

      Properties and stabilisation of an extracellular a-glucosidase from the extremely thermophilic archaebacteria Thermococcus  strain AN1:  enzyme activity at 130oC.  K. Piller, R.M. Daniel and H. Petach.  Biochimica et Biophysica Acta, 1292 (1996) 197-205.

      The upper limits of enzyme thermal stability.  Daniel, R.M.  Enzyme and Microbial Technology, 19 (1996) 74-79.

      The denaturation and degradation of stable enzymes at high temperatures.  Daniel, R.M., Dines, M. and Petach, H.H.  Biochemical Journal,  317 (1996) 1-11.

       The effect of low temperature on enzyme activity.  N. More, R.M. Daniel and H. Petach.  Biochemical Journal 305 (1995) 17-20.

Properties and applications of stable enzymes, especially proteases:

This research area, arising out of our long-standing interest in very stable enzymes from extreme thermophiles, deals with a variety of properties and applications, but much of the work has centred on proteases, cellulases, and hemicellulases. Most of the source organisms have been isolated by us from New Zealand geothermal sources, and our culture collection of extreme thermophiles exceeds 500 isolates.

       For a general background, see "Thermophilic enzymes as industrial catalysts"  K Peek, L

       D Ruttersmith, R M Daniel, H W Morgan and P L Berquist.  Biotechnology Forum

       Europe. 9 (1992) 466-470.   [To download PDF click here]

Recent references on this research:

       Lin Chen, Tim Coolbear and Roy M. Daniel.  Characteristics of Proteinases and Lipases Produced by Seven Bacillus sp.  Isolated from a Milk Powder Production Line.  Int Dairy J 13 (2003) 255-275.

       L. Chen, R. M. Daniel and T. Coolbear.  Detection and impact of rotease and lipase activities in milk and milk powders:  A review.  International Dairy Journal 13 (2003) 255-275.

       Bacillus strain AK.1 protease, Toogood, H.S., Bunn, R and Daniel R.M.  Chapter S268 in Handbook of Proteolytic enzymes (Eds A.J. Barrett et al..), 2nd Edn, Academic press.  In Press.

       R. M.  Daniel and M.J.  Danson.  Assaying activity and assessing thermostability of hyperthermophilic enzymes.  Methods in Enzymology,  334 (2001) 283-293.

       Hyperthermophilic xylanases, Bergquist, P.L., Gibbs, M.D., Morris, D.D., Uhl, A.M., Thompson, D.R. and Daniel, R.M. Methods in Enzymology, 330 (2001) 301-308.

     Calcium-mediated thermostability in the subtilisin superfamily: the crystal structure of Bacillus AK.1 protease at 1.8A resolution. Smith, C.A., Toogood, H., Baker, H.M., Daniel, R.M. and Baker, E.N. J Mol. Biol., 294 (1999) 1027-1040.

     Purification and characterisation of AK.1 protease, a thermostable subtilisin with a disulphide bond in the substrate-binding cleft. Toogood, H.S., Smith, C.A., Baker, E.N. and Daniel, R.M.  Biochem. J., 350 (2000) 321-328.

       The first description of an archaeal hemicellulase: The xylanase from Thermococcus Zilligii strain AN1, Uhl, A.M. and. Daniel, R.M. Extremophiles, 3 (1999) 263-267.

       Hemicellulolytic and cellulytic functions of the domains of a beta-mannanase cloned from Caldocellosiruptor saccharolyticus, Frangos, T., Bullen, D., Berquist, P. and Daniel, R.M.  International Journal of Biochemistry and Cell Biology, 31(1999) 853-859.

     Properties of a thermostable ß-glucosidase immobilized using tris (hydroxymethyl) phosphine as a highly effective coupling agent, Oswald, P., Evans, R.A., Henderson, W., Fee, C., and Daniel, R.  Enzyme & Microbial Technology 23 (1998) 14-19.

       Compositions and methods for treating cellulose-containing fabrics using truncated cellulase enzyme compositions.  Farrington, G.K., Andson, P., Bergquist, P., Daniel, R., Gibbs, M., Morgan, H., and Williams D.P.  U.S Patent application 1997.

       Thermostable Proteases.  Daniel, R.M., Toogood, H.S. and Bergquist, P.L.  Biotechnology and Genetic Engineering Reviews  13 (1995) 51-100.