Neutron frequency windows and the protein dynamical transition

Biophysical Journal

Volumn 87, Issue 3, 2004, Pages 1436-1444

  Becker, Torsten ^a   Hayward, Jennifer A ^a   Finney, John L ^b   Daniel, Roy M ^c   Smith, Jeremy C ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF WAIKATO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMATE DEHYDROGENASE; SOLVENT;

ARTICLE; CALCULATION; COMPUTER SIMULATION; DYNAMICS; ENERGY; FOURIER TRANSFORMATION; MATHEMATICAL ANALYSIS; MODEL; MOTION; NEUTRON FREQUENCY WINDOW; NEUTRON SCATTERING; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FUNCTION; SPECTROMETER; TEMPERATURE DEPENDENCE; TEMPERATURE SENSITIVITY; TIME; VIBRATION;

EID: 4444342895     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.042226     Document Type: Article

References (41)

1. Becker, T., and J. C. Smith. 2003. Energy resolution and dynamical heterogeneity effects on elastic neutron scattering from molecular systems. Phys. Rev. E. 67:021904.
2. Bee, M. 1988. Quasielastic Neutron Scattering: Principles and Applications in Solid-State Chemistry, Biology and Materials Science. Hilger, Bristol, UK.
3. Bellissent-Funel, M.-C., R. Daniel, D. Durand, M. Ferrand, J. Finney, S. Pouget, V. Real, and J. C. Smith. 1998. Nanosecond protein dynamics: first detection of a neutron incoherent spin-echo signal. J. Am. Chem. Soc. 120:7347-7348.
4. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM. J. Comput. Chem. 4:187-217.
5. Chong, S.-H., Y. Joti, A. Kidera, N. Go, A. Ostermann, A. Gassmann, and F. Parak. 2001. Dynamical transition of myoglobin in a crystal: comparative studies of x-ray crystallography and Mössbauer spectroscopy. Eur. Biophys. J. 30:319-329.
6. Cohen, S., E. Bauminger, I. Nowik, S. Ofer, and J. Yariv. 1981. Dynamics of the iron-containing core in crystals of the iron-storage protein, ferritin, through Mössbauer spectroscopy. Phys. Rev. Lett. 46:1244-1248.
7. Daniel, R., J. Finney, V. Réat, R. Dunn, M. Ferrand, and J. C. Smith. 1999. Enzyme dynamics and activity: timescale dependence of dynamical transitions in glutamate dehydrogenase solution. Biophys. J. 77:2184-2190.
8. Daniel, R., J. Finney, and J. C. Smith. 2003. The dynamical transition in proteins may have a simple explanation. Faraday Discuss. 122:163-169.
9. Daniel, R., J. C. Smith, M. Ferrand, S. Hery, R. Dunn, and J. Finney. 1998. Enzyme activity below the dynamical transition at 220 K. Biophys. J. 75:2504-2507.
10. Dellerue, S., A. Petrescu, J. C. Smith, S. Longeville, and M.-C. Bellisent-Funel. 2000. Collective dynamics of a photosynthetic protein probed by neutron spin-echo spectroscopy and molecular dynamics simulation. Phys. B. 276-278:514-515.
11. Ding, X., B. Rasmussen, G. A. Petesko, and D. Ringe. 1994. Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase. Biochemistty. 33:9285-9293.
12. Doster, W., S. Cusack, and W. Petty. 1989. Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature. 337:754-756.
13. Doster, W., M. Diehl, W. Petry, and M. Ferrand. 2001. Elastic resolution spectroscopy: a method to study molecular motions in small biological samples. Phys. B. 301:65-68.
14. Doster, W., and M. Settles. 1999. The dynamical transition in proteins: the role of hydrogen bonds. In Hydration Processes in Biology, NATO Science Series: Life Sciences, Vol. 305. M. C. Bellisent-Funel and J. Teixera, editors. IOS Press, Amsterdam, The Netherlands.
15. Dunn, R. V., V. Réat, J. Finney, M. Ferrand, J. C. Smith, and R. Daniel. 2000. Enzyme activity and dynamics: xylanase activity in the absence of fast anharmonic dynamics. Biochem. J. 346:355-358.
16. Elber, R., and M. Karplus. 1987. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science. 235:318-321.
17. Fenimore, P. W., H. Frauenfelder, B. H. McMahon, and F. Parak. 2002. Slaving: solvent fluctuations dominate protein dynamics and functions. Proc. Natl. Acad. Sci. USA. 99:16047-16051.
18. Ferrand, M., A. J. Dianoux, W. Petry, and G. Zaccai. 1993. Thermal motions and function of bacteriorhodopsin in purple membranes: effects of temperature and hydration studied by neutron scattering. Proc. Natl. Acad. Sci. USA. 90:9668-9672.
19. Fitter, J., R. E. Lechner, and N. A. Dencher. 1997. Picosecond molecular motions in bacteriorhodopsin from neutron scattering. Biophys. J. 73: 2126-2137.
20. Frauenfelder, H., G. Petsko, and D. Tsernoglou. 1979. Temperature-dependent x-ray diffraction as a probe of protein structural dynamics. Nature. 280:558-563.
21. Frauenfelder, H., S. Sligar, and P. Wolynes. 1991. The energy landscapes and motions of proteins. Science. 254:1598-1603.
22. Halle, B. 2004. Biomolecular cryocrystallography: structural changes during flash-cooling. Proc. Natl. Acad. Sci. USA. 101:4793-4798.
23. Hayward, J. A., J. L. Finney, R. M. Daniel, and J. C. Smith. 2003. Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophys. J. 85:679-685.
24. Joti, Y., M. Nakasako, A. Kidera, and N. Go. 2002. Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors. Acta Crystallogr. D. 58:1421-1432.
25. Keller, H., and P. Debrunner. 1980. Evidence for conformational and diffusional mean-square displacements in frozen aqueous solution of oxymyoglobin. Phys. Rev. Lett. 45:68-71.
26. Knapp, E., S. Fischer, and F. Parak. 1982. Protein dynamics from Mössbauer spectra: the temperature dependence. J. Phys. Chem. 86: 5042-5047.
27. Kneller, G., and J. C. Smith. 1994. Liquid-like side-chain dynamics in myoglobin. J. Mol. Biol. 242:181-185.
28. Kneller, G. R., V. Keiner, M. Kneller, and M. Schiller. 1995. nMOLDYN: a program package for a neutron scattering oriented analysis of molecular dynamics simulations. Comp. Phys. Com. 91:191-214.
29. Lamy, A. V., M. Souaille, and J. C. Smith. 1996. Simulation evidence for experimentally detectable low-temperature vibrational inhomogeneity in a globular protein. Biopolymers. 39:471-478.
30. Lehnert, U., V. Réat, M. Weik, G. Zaccai, and C. Pfister. 1998. Thermal motions in bacteriorhodopsin at different hydration levels studied by neutron scattering: correlation with kinetics and light-induced conformational changes. Biophys. J. 75:1945-1952.
31. Lovesey, S. 1987. Theory of Neutron Scattering from Condensed Matter, Vol. 1. Oxford University Press, Oxford, UK.
32. Mackerell, A. D., D. Bashford, M. Bellot, J. R. Dunbrack, R. L. Evenseck, M. J. Field, S. Fischer, J. Gao, H. Quo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, I. W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Store, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, J. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modelling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
33. Parak, F. 2003. Physical aspects of protein dynamics. Rep. Prog. Phys. 66:103-129.
34. Rahman, A. 1963. Intermediate scattering function in slow neutron scattering. Phys. Rev. 130:1334-1336.
35. Rasmussen, B., A. Stock, D. Ringe, and G. A. Petsko. 1992. Crystalline ribonuclease-a loses function below the dynamical transition at 22OK. Nature. 357:423-424.
36. Réat, V., R. Dunn, M. Ferrand, J. Finney, R. Daniel, and J. C. Smith. 2000. Solvent dependence of dynamic transitions in protein solutions. Proc. Natl. Acad. Sci. USA. 97:9961-9966.
37. Réat, V., G. Zaccai, M. Ferrand, and C. Pfister. 1997. Functional dynamics in purple membrane. In Biological Macromolecular Dynamics. Adenine Press, Schenectady, NY. 117-122.
38. Tarek, M., and D. J. Tobias. 2002. Role of protein-water hydrogen bond dynamics in the protein dynamical transition. Phys. Rev. Lett. 88:138101.
39. Teeter, M., A. Yamano, B. Stec, and U. Mohanty. 2001. On the nature of a glassy state of matter in a hydrated protein: relation to protein function. Proc. Natl. Acad. Sci. USA. 98:11242-11247.
40. Tournier, A., J. Xu, and J. C. Smith. 2003. Translational hydration water dynamics drives the protein glass transition. Biophys. J. 85:1871-1875.
41. Tournier, A. L., and J. C. Smith. 2003. Principal components of the protein dynamical transition. Phys. Rev. Lett. 91:208106.