Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions
Abstract
:1. Introduction
−kBT (∂ln Keq/∂P)T = ΔV
2. Principle
3. Results and Discussion
3.1. Diffusion Changes
3.2. Enthalpy and Volume Change
3.3. Change in Heat Capacity
3.4. Thermal Expansion Coefficient Change
3.5. Change in Compressibility
4. Conclusions and Perspective
- This method can be used for irreversible reactions, and is also capable of measuring the thermodynamic properties and D in a time resolved manner. Using this method, the D values of various transient, short lived radicals were measured, and it was found that D was very different between stable molecules and transient radicals [15,16].
- 2.
- This TG technique has a high sensitivity because the homodyne detection of the TG method is background free. Proteins generally and easily form oligomers at high concentrations, and the reaction is altered by the formation of oligomers. High sensitivity is important for measurements at dilute concentrations. Furthermore, ΔV of a few cm3/mol was detected. For example, ΔV of −7 cm3/mol obtained for the reaction of PYP was only ~0.7% of the total protein volume [52]. Using a conventional ΔV measurement, that is, the pressure dependence of Keq, ΔκT should be calculated from the deviation of the linear relation of Keq vs. P. This deviation should be subtle, and it is almost impossible to measure ΔκT for any protein solution. Hence, the experimental measurement of this property of a protein in solution is quite difficult. The reported ΔκT measurements clearly demonstrate the high sensitivities of ΔV and ΔκT. Due to its high sensitivity, a variety of light intensities can be used, and, as a result, the light intensity dependence on the reaction can be studied. Using this merit, some nonlinear light intensity dependence of DSCC has been observed for various photosensor proteins. For example, in addition to BlrP1, shown above, a BLUF protein of decamer PixD (SyPixD) from Synechocystis sp. PCC6803 dissociates into five dimers when two protomers in the decamer are excited but not one [61]. Accompanying this dissociation of SyPixD, a cyanobacterial response regulator PixE was released from the PixD10-PixE5 complex. This suggests that the biological response of PixD is a nonlinear light intensity sensor for light intensity dependent biological functions.
- 3.
- The thermodynamic properties of this method should be exactly along the reaction coordinate. This advantage was demonstrated by the ΔH measurement of the intermediates of octopus rhodopsin, reported above. Furthermore, this advantage becomes apparent for a case in which the photochemical reaction is pressure dependent. In this case, the reaction scheme can be altered by pressure, and “the molecular volume” cannot be determined from the pressure dependence of Keq. However, ΔV from the volume grating intensity should be an intrinsic value for the reaction. Similarly, the temperature dependence measurement Keq for ΔH determination could not be correct because protein conformation and the reactivity are sensitive to the temperature. ΔH, which is measured without changing any external properties, should be intrinsic.
- 4.
- The TG method does not require any modifications or mutations of the target protein. Some spectroscopic methods require a probe molecule to be attached to the protein. Mutation or binding of a probe molecule may alter the reaction. Hence, the reaction monitored for native proteins using the TG method is appropriate.
- 5.
- Water molecules and other nonreactive species in the sample solution do not disturb the measurements. Hence, a variety of sample solutions have been used, such as various pH values, temperatures, solutions containing salts, or crowding macromolecules. The effect of crowding on protein reaction was also examined [62,63]. In some reactions, reactivity was found to be very sensitive to temperature. Based on these findings, it was proposed that this protein may function as a temperature sensor [64].
- 6.
- The TG signal originates only from the reacting species. Hence, the presence of nonreacting species does not disturb or interfere with the measurements. This merit is a big advantage compared with other methods that monitor the ensemble average of the reaction system, such as calorimetry, dynamic light scattering, SAXS, and IR spectroscopy. For example, the IR spectrum in the dark state must be subtracted from the light spectrum to obtain any changes in the reaction. If the reaction yield is small, the analysis of the SAXS signal becomes difficult, because of the superposition of the solvent and nonreactive species. Gel chromatography and other diffusion detection methods monitor the ensemble averages of the species in solution. Consequently, it may be difficult to detect oligomer formation in a sample using gel chromatography, unless the population of the dimer is dominant. Moreover, while covalently linked or stable protein aggregates may be detected by a size exclusion chromatography approach, a noncovalent protein aggregate that is formed by weak hydrophobic or hydrogen bond interactions may not be detected because the aggregate might dissociate during elution through the column. The TG technique can overcome these difficulties, because the measurement is performed in solution, so that even a weak binding complex is maintained in solution.
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Terazima, M. Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions. J 2022, 5, 186-197. https://doi.org/10.3390/j5010014
Terazima M. Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions. J. 2022; 5(1):186-197. https://doi.org/10.3390/j5010014
Chicago/Turabian StyleTerazima, Masahide. 2022. "Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions" J 5, no. 1: 186-197. https://doi.org/10.3390/j5010014
APA StyleTerazima, M. (2022). Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions. J, 5(1), 186-197. https://doi.org/10.3390/j5010014