| Topic |
Reference |
Comment |
| Stopped-flow test reaction |
Tonomura, B., Nakatani, H., Ohnishi, M., Yamaguchi-Ito, J., and Hiromi, K. (1978) "Test Reactions for a Stopped-Flow Apparatus: Reduction of 2,6-Dichloroindolphenol and Potassium Ferricyanide by L-Ascorbic Acid" Analytical Biochemistry, 84, 370-383. |
DCIP Rxn |
| Dead Time Measurement |
Paul, C., Kirchner, K., and Haenisch (1980) "Calibration of Stoopped-Flow Spectrophotometers Using a Two-Step Disulfide Exchange Reaction" Analytical Biochemistry, 101, 442-448. |
DTNB Reaction (Abs) |
| Dead Time Measurement |
Peterman, B. F. (1979) "Measurement of the Dead Time of a Fluorescence Stopped-Flow Instrument" Analytical Biochemsitry, 93, 442-444. |
NATA Rxn (fluor) |
| Secondary Structure Analysis |
Compton, L.A. and Johnson, C.W. (1986) Anal. Biochem. 155, 155-167. |
Compton Fit |
| Dead Time Measurement |
Peintler, G., Nagy, A., Horvath, A. K., Kortvelyesi, T., and Nagypal, I. (2000) "Improved Calibration and Use of Stopped Flow Instruments" Physical Cheistry Chemical Physics 2, 2574. |
Dead time depends on reaction rate |
| Kinetic Analysis of SF |
Johnson, K. A. (1992) "Transient-State Kinetic Analysois of Enzyme Reaction Pathways" in The Enzymes, Academic Press, pp. 1-61. |
Good review of transient kinetics |
| SVD |
Wilson, M. T. and Torres, J. (2000) "Stopped-flow spectroscopy" in Spectrophotometry & Spectrofluorimetry (Ed. Gore, M. G.) Oxford Press, pp. 209-239. |
Good practical SVD summary |
| SVD-nitty gritty |
Henry, E. R. and Hofrichter, J. (1992) "Singular Value Decomposition: Application to Analaysis of Experimental Data" Meth. Enzymol. 210, 129-192. |
Very technical |
| Global Analysis |
Knutson, J. R., Beecham, J. M., and Brand, L. (1983) Chem. Phys. Lett. 102, 501 |
Rational for Global fitting |
| Factor Analysis |
Malinowski, E., R. (1991) "Factor Analysis in Chemistry" Second Edition, Wiley and Sons, New York. |
Good description of why to use factor analysis |
| PEM for stopped flow polarization |
Wampler, J. E. and DeSa, R. J. (1974) "Recording Polarization of Fluorescence Spectrometer-A Unique Application of Piezoelectric Birefringence Modulation" Analyical Chemistry, 46, 563-567. |
DeSa paper for SF using PEM |
| Matrix exponentiation |
Zamis, T. M., Parkhurst, L. J., and Gallup, G. A. (1989) Computers in Chemistry, 13, 165-171. |
|
| DCIP Exctinction |
Schilke, B., Voisine, C., Beinert, H., and Craig, E. (1999) Proc. Natl. Acad. Sci. 96, 10206-10211 |
21 mM-1 cm-1 @ 600 nm |
| MCD Cytochrome C |
Nantes, I. L., Zucchi, M. R., Nasimento, O. R., and Faljoni-Alario (2001) J. Biol. Chem., 276, 153-158 |
Also reference Selcon CD analysis |
| MCD Active site characterization |
Abraham, B. D., Sono, M., Boutaud, O., Shriner, A., Dawson, J. H., Brash, A. R., Gaffney, B. J. (2001) Biochemistry, 40, 2251-2259 |
Coral Allene Oxide Synthase; Nice MCD Quote about fingerprinting |
| NIR MCD of cyc cbb3 oxidase |
Pitcher, R. S., Cheesman, M. R., Watmough, N. J. (2002) J. Biol. Chem. 277, 31474-31483 |
Evidence for bishistidine coordination |
| Char. Of cytochromes w/ MCD, ESR, electrochemistry |
Field, S. J., Dobbin, P. S., Cheesman, M. R., Watmough, N. J., Thomson, A. J., and Richardson, D. J. (2000) J. Biol. Chem. 275, 8515-8522 |
|
| Selcon CD fits |
Sreenama, N., and Woody, R. W. (1993) Anal. Biochem. 209, 32-44 |
|
| Selcon CD Fits |
Sreenama, N., and Woody, R. W. (1994) J. Mol. Biol. 242, 497-507 |
|
| MCD Tryp determination |
Barth, G., Records, R., Bunnenberg, E., Djerassi, C., and Voelter, W. (1971) J. Amer. Chem. Soc. 93, 2545-2547 |
Detection limit (5T magnet) is 10 uM |
| MCD Tryp determination |
(1975) J. Amer. Chem. Soc. 97, 6653 |
|
| Tryptophan in membranes |
(1989) Biochemistry, 28, 3421 |
|
| MCD Measurement methods |
(1993) Inorg. Chem. 32, 1460. |
|
| NIR MCD of cyt C |
"Near Infrared Magnetic Circular Dichroism of Cytochrone c'," Rawlings, J., Stephens, P.J., Nafie, L.A., and Kamen, M.D. (1977) Biochemistry 16, 1725 1729. |
Jill Rawlings is at Auburn Montgomery |
| Original SVD |
Golub G., Reinsch C. Singular Value Decomposition andLeast Squares Solutions, in Wilkinson J.H. and Reinsch C.(editors) Handbook for Automatic Computation, vol II.Springer. 1971. |
|
| Extinction coefficient for dCSA |
Johnson, W. (2001) "Circular Dichroism Instrumentation" in Circular Dichroism and the Conformational Analysis of Biomolecules, ed. G. Fasman, Plenum Press, New York, pp. 635-652. |
e=34.5 @ 285 nm, 1mg/ml 5 cm cell A=0.743 (pp. 648) |
| CD Analysis of membrane proteins |
Sreerama, N., and Woody, R.W. (2004) Protein Science 13, 100-112 |
soluble reference proteins perform reasonably well in analyzing membrane proteins |
| CD Unfolding eqn. |
Santoro, M. M. and Bolen, D. W. (1988) Biochemistry, 27, 8063-8068 |
|
| Iain's Practical Guide to SVD |
DeSa, R. J. and Matheson, I. B. C. (2004) "A Practical Approach to Interpretation of Singular Value Decomposition Results" Meth. Enzymol. 384, 1-8. |
|
| Iain's Data Precompression |
Matheson, I. B. C. (2004) "Large Reduction in Singular Value Decomposition Calculation Time Using Savitsky-Golay Data Precompression" 384, 9-17 |
|
| Iain's Integration paper |
Matheson, I. B. C., Parkhurst, L. J., and DeSa, R. J. (2004) "Efficient Integration of Kinetic Differential Equation Sets Using Matrix Exponentiation" 384, 18-39. |
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