Resolution of multiphasic reactions by the combination of fluorescence total-intensity and anisotropy stopped-flow kinetic experiments.
Multiphasic kinetics are often observed in stopped-flow investigations. To characterize further these kinetic phases, we have developed a methodology whereby fluorescence total intensity and anisotropy stopped-flow data can be combined in a single analysis. Fluorescence total intensity and anisotropy are highly interrelated and contain two very complementary forms of information. Total-intensity changes are useful in determining changes in populations with differing quantum yields, whereas anisotropy changes contain additional contributions caused by the rotational dynamics of the species. For cases in which the fluorescence quantum yield increases, the observed rate of anisotropy change will be more rapid than the total-intensity change, whereas in cases in which the total intensity decreases, the observed change in anisotropy will lag behind. In all cases, with quantum yield changes the stopped-flow anisotropy signals cannot be fit with models consisting of exponentials. Case studies examining these effects are described for the protein folding/refolding transitions of Staphylococcal nuclease and phosphoglycerate kinase. A multiphasic DNA exonuclease reaction using bacteriophage T4 DNA polymerase is also examined. In all of these cases, combined analysis of both data types revealed insights into reaction mechanism, which could not be obtained by either data type in isolation. Quantum yields and steady-state anisotropies associated with transiently populated intermediate species can be resolved. The data analysis methodologies described allow characterization of multiphasic reactions in terms of internally consistent kinetic rates, quantum yields, and steady-state anisotropies.
Otto
M R
MR
Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232.
Lillo
M P
MP
Beechem
J M
JM
D017122:Bacteriophage T4 / Q000201:enzymology; D055592:Biophysical Phenomena; D001703:Biophysics; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism; D005454:Fluorescence Polarization / Q000379:methods*; D007700:Kinetics; D008836:Micrococcal Nuclease / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D010735:Phosphoglycerate Kinase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017510:Protein Folding; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D013050:Spectrometry, Fluorescence / Q000379:methods*
D010735:Phosphoglycerate Kinase; D004259:DNA-Directed DNA Polymerase; D008836:Micrococcal Nuclease