Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1992 Jan;61(1):235–245. doi: 10.1016/S0006-3495(92)81830-1

Determination of rate distributions from kinetic experiments.

P J Steinbach 1, K Chu 1, H Frauenfelder 1, J B Johnson 1, D C Lamb 1, G U Nienhaus 1, T B Sauke 1, R D Young 1
PMCID: PMC1260237  PMID: 1540692

Abstract

Rate processes in proteins are often not adequately described by simple exponential kinetics. Instead of modeling the kinetics in the time domain, it can be advantageous to perform a numerical inversion leading to a rate distribution function f(lambda). The features observed in f(lambda) (number, positions, and shapes of peaks) can then be interpreted. We discuss different numerical techniques for obtaining rate distribution functions, with special emphasis on the maximum entropy method. Examples are given for the application of these techniques to flash photolysis data of heme proteins.

Full text

PDF
239

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alberding N., Austin R. H., Beeson K. W., Chan S. S., Eisenstein L., Frauenfelder H., Nordlund T. M. Tunneling in ligand binding to heme proteins. Science. 1976 Jun 4;192(4243):1002–1004. doi: 10.1126/science.1273579. [DOI] [PubMed] [Google Scholar]
  2. Ansari A., Berendzen J., Bowne S. F., Frauenfelder H., Iben I. E., Sauke T. B., Shyamsunder E., Young R. D. Protein states and proteinquakes. Proc Natl Acad Sci U S A. 1985 Aug;82(15):5000–5004. doi: 10.1073/pnas.82.15.5000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ansari A., Berendzen J., Braunstein D., Cowen B. R., Frauenfelder H., Hong M. K., Iben I. E., Johnson J. B., Ormos P., Sauke T. B. Rebinding and relaxation in the myoglobin pocket. Biophys Chem. 1987 May 9;26(2-3):337–355. doi: 10.1016/0301-4622(87)80034-0. [DOI] [PubMed] [Google Scholar]
  4. Austin R. H., Beeson K. W., Eisenstein L., Frauenfelder H., Gunsalus I. C. Dynamics of ligand binding to myoglobin. Biochemistry. 1975 Dec 2;14(24):5355–5373. doi: 10.1021/bi00695a021. [DOI] [PubMed] [Google Scholar]
  5. Berendzen J., Braunstein D. Temperature-derivative spectroscopy: a tool for protein dynamics. Proc Natl Acad Sci U S A. 1990 Jan;87(1):1–5. doi: 10.1073/pnas.87.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dlott D. D., Frauenfelder H., Langer P., Roder H., DiIorio E. E. Nanosecond flash photolysis study of carbon monoxide binding to the beta chain of hemoglobin Zürich [beta 63(E7)His leads to Arg]. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6239–6243. doi: 10.1073/pnas.80.20.6239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Elber R., Karplus M. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science. 1987 Jan 16;235(4786):318–321. doi: 10.1126/science.3798113. [DOI] [PubMed] [Google Scholar]
  8. Frauenfelder H., Parak F., Young R. D. Conformational substates in proteins. Annu Rev Biophys Biophys Chem. 1988;17:451–479. doi: 10.1146/annurev.bb.17.060188.002315. [DOI] [PubMed] [Google Scholar]
  9. Hong M. K., Braunstein D., Cowen B. R., Frauenfelder H., Iben I. E., Mourant J. R., Ormos P., Scholl R., Schulte A., Steinbach P. J. Conformational substates and motions in myoglobin. External influences on structure and dynamics. Biophys J. 1990 Aug;58(2):429–436. doi: 10.1016/S0006-3495(90)82388-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Iben IE, Braunstein D, Doster W, Frauenfelder H, Hong MK, Johnson JB, Luck S, Ormos P, Schulte A, Steinbach PJ. Glassy behavior of a protein. Phys Rev Lett. 1989 Apr 17;62(16):1916–1919. doi: 10.1103/PhysRevLett.62.1916. [DOI] [PubMed] [Google Scholar]
  11. Kuriyan J., Wilz S., Karplus M., Petsko G. A. X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution. J Mol Biol. 1986 Nov 5;192(1):133–154. doi: 10.1016/0022-2836(86)90470-5. [DOI] [PubMed] [Google Scholar]
  12. Lavalette D., Tetreau C., Brochon J. C., Livesey A. Conformational fluctuations and protein reactivity. Determination of the rate-constant spectrum and consequences in elementary biochemical processes. Eur J Biochem. 1991 Mar 28;196(3):591–598. doi: 10.1111/j.1432-1033.1991.tb15854.x. [DOI] [PubMed] [Google Scholar]
  13. Livesey A. K., Brochon J. C. Analyzing the distribution of decay constants in pulse-fluorimetry using the maximum entropy method. Biophys J. 1987 Nov;52(5):693–706. doi: 10.1016/S0006-3495(87)83264-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Noguti T., Go N. Structural basis of hierarchical multiple substates of a protein. I: Introduction. Proteins. 1989;5(2):97–103. doi: 10.1002/prot.340050203. [DOI] [PubMed] [Google Scholar]
  15. Ormos P., Braunstein D., Frauenfelder H., Hong M. K., Lin S. L., Sauke T. B., Young R. D. Orientation of carbon monoxide and structure-function relationship in carbonmonoxymyoglobin. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8492–8496. doi: 10.1073/pnas.85.22.8492. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Steinbach P. J., Ansari A., Berendzen J., Braunstein D., Chu K., Cowen B. R., Ehrenstein D., Frauenfelder H., Johnson J. B., Lamb D. C. Ligand binding to heme proteins: connection between dynamics and function. Biochemistry. 1991 Apr 23;30(16):3988–4001. doi: 10.1021/bi00230a026. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES