Abstract
Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of the same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.
Highlights
Characterization of molecular structures of transient species formed during chemical and biologically relevant reactions is necessary for understanding their reaction mechanisms and functions
The results of singular value decomposition-aided pseudo principal-component analysis (SAPPA) for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of the same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy
Determining the optimum kinetic model is an essential prerequisite for characterizing the dynamics of a reaction and molecular structures of transient species formed during the reaction
Summary
Characterization of molecular structures of transient species formed during chemical and biologically relevant reactions is necessary for understanding their reaction mechanisms and functions. As a result of this SVD-aided kinetic analysis, we obtained both time-dependent concentrations of transient intermediate species and timeindependent difference X-ray scattering curves, which are directly associated with the structure of the intermediate species These species-associated difference X-ray scattering curves (SACs) obeying the optimum kinetic model were further examined to reveal molecular structures of the intermediate species by performing structure refinement.. We introduce a new method of extracting model-dependent kinetic information directly from the experimental data without considering any candidate kinetic model In this method termed as the P method, from the SVD analysis in the entire time. The principal-component analysis of the pseudo SACs provides time-dependent relative population of each intermediate species In this way, we can determine the optimum kinetic model and accurately without considering any candidate kinetic model. We demonstrate the applicability of this SVD-aided pseudo principal-component analysis (SAPPA) by examining experimental TRXSS data for wild-type sperm whale MbCO63 and wild-type homodimeric hemoglobin liganded with CO molecules (HbI(CO)2). In addition, we show that the new method can be extended to transient absorption (TA) data on HbI(CO)
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