Analysis of residuals from enzyme kinetic and protein folding experiments in the presence of correlated experimental noise

Analytical Biochemistry

Volumn 395, Issue 1, 2009, Pages 1-7

  Kuzmič, Petr ^a   Lorenz, Thorsten ^b   Reinstein, Jochen ^b  

^a BioKin Ltd   (United States)

^b MAX PLANCK INSTITUTE FOR MEDICAL RESEARCH   (Germany)

Author keywords

Autocorrelation function; Data filter; Enzyme kinetics; HIV protease; Mathematics; Michaelis Menten; Protein folding; Regression; Runs of signs test; Statistics

Indexed keywords

AUTOCORRELATION; ENZYME KINETICS; FUNCTIONS; MATHEMATICAL TECHNIQUES; PROTEIN FOLDING; REGRESSION ANALYSIS; STATISTICS;

AUTOCORRELATION FUNCTIONS; DATA FILTER; HIV-PROTEASE; MICHAELIS-MENTEN; REGRESSION;

KINETICS;

CYTIDINE PHOSPHATE; GLOBULAR PROTEIN; PHOSPHOTRANSFERASE; PROTEINASE; URIDINE PHOSPHATE;

ALGORITHM; ARTICLE; CORRELATIONAL STUDY; DICTYOSTELIUM DISCOIDEUM; ENZYME KINETICS; ENZYME SUBSTRATE; HUMAN IMMUNODEFICIENCY VIRUS; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN FOLDING; RESIDUE ANALYSIS;

DICTYOSTELIUM DISCOIDEUM;

ALGORITHMS; ANIMALS; BIOCATALYSIS; DATA INTERPRETATION, STATISTICAL; HIV PROTEASE; HUMANS; KINETICS; MODELS, THEORETICAL; NUCLEOSIDE-PHOSPHATE KINASE; PROTEIN FOLDING; REGRESSION ANALYSIS; SOFTWARE;

EID: 70349142179     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2009.05.051     Document Type: Article

References (23)

1. Johnson M.L. Why, when, and how biochemists should use least squares. Anal. Biochem. 206 (1992) 215-225
2. Johnson M.L., and Frasier S.G. Nonlinear least-squares analysis. Methods Enzymol. 117 (1985) 301-342
3. Johnson M.L. Use of least-squares techniques in biochemistry. Methods Enzymol. 240 (1994) 1-22
4. Peranteau A.G., Kuzmič P., Angell Y., García-Echeverría C., and Rich D.H. Increase in fluorescence upon the hydrolysis of tyrosine peptides: application to proteinase assays. Anal. Biochem. 227 (1995) 242-245
5. Lorenz T., and Reinstein J. The influence of proline isomerization and off-pathway intermediates on the folding mechanism of eukaryotic UMP/CMP kinase. J. Mol. Biol. 381 (2008) 443-455
6. Kuzmič P. Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal. Biochem. 237 (1996) 260-273
7. Fersht A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. third ed. (1998), Macmillan, New York
8. Chatfield C. The Analysis of Time Series: An Introduction. fourth ed. (1989), Chapman & Hall, New York
9. Reich J.G. Curve Fitting and Modelling for Scientists and Engineers (1992), McGraw-Hill, New York
10. Box G.E.P., and Jenkins G. Time Series Analysis: Forecasting and Control (1976), Holden-Day, San Francisco
11. Mannervik B. Design and analysis of kinetic experiments for discrimination between rival models. In: Endrényi L. (Ed). Kinetic Data Analysis: Design and Analysis of Enzyme and Pharmacokinetic Experiments (1981), Plenum, New York 235-270
12. Mannervik B., analysis R., and error e. Regression analysis, experimental error, and statistical criteria in the design and analysis of experiments for discrimination between rival kinetic models. Methods Enzymol. 87 (1982) 370-390
13. Rawlings J.O. Applied Regression Analysis: A Research Tool (1988), Wadsworth, Belmont, CA
14. Kuzmič P., Peranteau A.G., García-Echeverría C., and Rich D.H. Mechanical effects on the kinetics of the HIV proteinase deactivations. Biochem. Biophys. Res. Commun. 221 (1996) 313-317
15. Barshop B.A., Wrenn R.W., and Frieden C. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM-a flexible, portable system. Anal. Biochem. 130 (1983) 134-145
16. Zimmerle C.T., and Frieden C. Analysis of progress curves by simulations generated by numerical integration. Biochem J. 258 (1989) 381-387
17. Johnson K.A., Simpson Z.B., and Blom T. Global kinetic explorer: a new computer program for dynamic simulation and fitting of kinetic data. Anal. Biochem. 387 (2009) 20-29
18. Johnson K.A., Simpson Z.B., and Blom T. Fitspace explorer: an algorithm to evaluate multidimensional parameter space in fitting kinetic data. Anal. Biochem. 387 (2009) 30-41
19. Cornish-Bowden A. Fundamentals of Enzyme Kinetics (1979), Butterworth, London
20. Durbin J., and Watson G.S. Testing for serial correlation in least squares regression. I. Biometrika 37 (1950) 409-428
21. Durbin J., and Watson G.S. Testing for serial correlation in least squares regression. II. Biometrika 38 (1951) 159-179
22. R. D'Agostino, M. Stephens, Goodness-of-Fit Techniques, Marcel Dekker, New York, 1986.
23. Rayner J.C.W., and Best D.J. Smooth Tests of Goodness of Fit (1989), Oxford Univ. Press, Oxford