Thermodynamic Analysis by Denaturation
Chemical and thermal denaturation can be used to analyze the kinetic and thermodynamic stability of a protein. Thermal denaturation is considered irreversible and gives kinetic parameters. Chemical denaturation, in contrast, is reversible, and gives thermodynamic parameters.
We will use two different techniques to monitor the two different denaturation experiments. Thermal denaturation will be monitored by NMR spectroscopy. Because NMR requires significant amounts of material, we will perform this experiment as a class, using commercial lysozyme.
Chemical denaturation will be monitored by intrinsic fluorescence. This is a much more sensitive technique, and can be performed on small amounts of material. Depending on the yield from your purifications, you may analyze your own lysozyme, pool material with other students, or use commercial lysozyme, if necessary.
Chemical Denaturation of Lysozyme by Fluorescence
- Prepare GuHCl or Urea solution and enzyme in matching buffers
- Measure Refractive Index of stock GuHCl or Urea to determine concentration
- Use the scanning spectrometer to determine wavelengths of maximum emission for the native protein and the fully denatured protein
- Prepare blanks and samples in duplicate on a 96-well plate
- Read samples and blanks on Thermo Fluorescence plate reader
- Perfrom nonlinear curvefit to determin ymin (y0) and ymax (how to video)
- Plot data to determine free energy of folding
Preparation of Solutions
A. Prepare 50-100 mL of 0.10 M Tris and adjust the pH to 7.0 (if using GuHCl)
B. Prepare 50-100 mL of 0.10 M sodium phosphate and adjust the pH to 3.0 (if using Urea)
A. Prepare 50-100 mL of a fresh stock solution of ~7-8 M guanidine hydrochloride in 0.10 M Tris buffer and adjust to pH 7.0. (Note: You cannot simply prepare buffer and then add GuHCl to it. Why?)
A. Prepare 50-100 mL of a fresh stock solution of ~10 M urea in 0.10 M sodium phosphate buffer and adjust to pH 3.0. (Note: You cannot simply prepare buffer and then add Urea to it. Why?)
Determine the final concentrations of denaturant stock solutions by measurement of the refractive index. Measure the refractive index (RI) of the buffer solution without GdHCl. Next, measure the RI of the stock GdHCl solution. The concentration of GdHCl can be calculated according to the equation:
Molarity (M) = 57.147(ΔN) + 38.68(ΔN)2 – 91.60(ΔN)3 (ref )
ΔN is the difference in refractive index between the GdHCl or Urea solution and buffer (or water). There are also several online calculators based on the above equation.
Prepare ~100μM protein stock in buffer A or B.
A series of solutions containing a fixed amount of lysozyme (3 μM) and varying concentrations of guanidine hydrochloride or (0 –7.0 M) Urea (0-10M) should be prepared from the stock solution.
The final volume of each sample was should be 200 μL in the wells. Make sure the samples are well mixed by gently pipetting up and down using and 200μL pipet set to 100μL and without introducing air. Allow the solution to incubate for at least 1 h at RT or overnight. The advantage of the plate reader is that it allows for fast sample processing under many conditions. This allows you to record several excitation wavelengths and emission wavelengths. Measure the fluorescence spectrum of each blank and sample at an excitation wavelength of 280 nm (if your protein contains Tyr and Phe you can remove contributions from those residues by using an excitation of 295nm), and the emission wavelengths of 320nm, 340nm, and 360nm. All experiments should be done at a controlled temperature (~25 °C).
Analysis of Data
The denaturation of lysozyme will be analyzed using a two-state model.
Protein denaturation curves often to exhibit a sigmoid dependence of measured parameter on the denaturant concentration. Your collected fluorescence data will likely fit to the sigmoidal equation:
Equation 1 is commonly called the Hill equation in which y is the measured parameter (Em intensity at 340nm, ratio of 360nm/330nm, peak area, peak maximum, etc.), y0 is the baseline value of the measured parameter at low denaturant concentration, a is the difference between the maximum value of the parameter when the protein is completely unfolded and the baseline value (ymax - y0), x is the denaturant concentration, b is the Hill coefficient necessary to fit the data, and c is an interaction constant, equal to the denaturant concentration where ΔG = 0.
Fit your data to equation 1 using KaleidaGraph. The important parameters to draw out are the baseline and maximum values of the measured parameter estimated from the fit. They will be used in the next step.
Using Excel estimate the fraction of protein in the unfolded state (fU) at every denaturant concentration, as shown in Equation 2. It may be necessary to leave off data collected at the very low and very high concentrations of denaturant.
Next create a column to calculate the apparent equilibrium constant for unfolding (KU) at each value of fu for the denaturation process using Equation 3. and the free energy
From the values of KU you can estimate the free energy for unfolding at each concentration of denaturant using the expression:
What is the trend in free energy of unfolding as the denaturant concentration increases? Is this expected?
Finally, you can estimate the free energy of unfolding at zero concentration denaturant by extrapolation using equation 5.
Plot ΔGoU[d] versus denaturant concentration [d] and fit the data to the linear relationship above. The y-intercept is an estimate of the free energy of unfolding in buffer. For additional ideas for discussion consult the Proteins Textbook by Whitford.
Additional reading suggested
 Protein Structure: A Practical Approach, 2nd Ed., Creighton, p306.
 Nozaki, Y. (1972) In Methods in enzymology, Vol 26, p 43, Academic Press, NY
 C. Pace in G. D. Fasman, Ed. (1975) CRC Critical Reviews in Biochemistry, Vol. 3, pp. 1–43, CRC Press, Cleveland, OH.
We will come back to this NMR experiment later in the semester.
Denaturation by NMR
Review reading on NMR from week 8 and denaturation reading on previous page
Hydrogen bonding significantly affects the electronic environment of amide and alpha protons in a protein backbone. This change in electron density can be monitored as a change in chemical shift by 1D or 2D NMR.
We will be using 1D 1H NMR to monitor the thermal denaturation of lysozyme. We will first record the NMR spectra of the sample at a variety of temperatures. We will identify peaks that change in intensity as the sample is heated, then integrate those peaks in each spectra. In week 12, we will fit those values to a melting curve in order to determine the denaturation parameters.
NMR determines the chemical shift of each proton relative to a standard (trimethyl silane, TMS, is common in organic solvents). In biomolecular NMR, a water-soluble standard is needed, and DSS (sodium 2,2-dimethyl-2-silapentane-5-sulfonate) is used instead. This standard will be defined as ‘0.000’ ppm. The incorporation of a standard will allow us to compare the chemical shifts of peaks across different NMR runs.
The NMR program will initially reference the spectra to D2O, but the chemical shifts of H2O and D2O vary significantly with temperature. Therefore, when you first process data collected at high temperature, it will appear as if the entire spectrum has shifted. Referencing all the spectra to DSS will fix this problem.
Kurutz, J. “Chemical Shift Referencing for Biomolecular NMR.”
As a class, prepare three lysozyme samples for NMR. Determine the amount of lysozyme necessary to prepare 750 uL of ~5 mM lysozyme. Weigh this out and dissolve in 675 uL distilled H2O.
Make up 0.5 mL of 20 mM DSS dissolved in D2O (MW of DSS is 218.3 g/mol). You might need to make a more concentrated stock solution initially in order to weigh accurately.
Add 75 uL of the DSS/D2O to the lysozyme sample, so the final solution is 10% D2O + 10 uM DSS.
Spin the tube for 1 minute at full speed in the microcentrifuge to precipitate any fibers or undissolved lysozyme.
Transfer the supernatant to a clean NMR tube with a P200. (The P1000 tends to give bubbles.)
Small groups of students will take turns acquiring 1D 1H NMRs of the lysozyme at rising temperatures. Determine a reasonable number of temperatures for a first pass, bearing in mind that the instrument and sample take ~fifteen minutes to equilibrate between each sample.
After the first pass determines the approximate melting temperature, the second and third samples will be used to monitor the denaturation a second time with finer temperature steps.
Each spectrum will be phased and the chemical shift adjusted to the DSS standard. Once the spectra have been calibrated, they can be overlaid to determine several peaks that appear or disappear as the denaturation occurs.
As a class, integrate these peaks in each spectrum and plot them versus the temperature to determine the melting profile of lysozyme.
Analysis of Thermal Denaturation
Yu, C, et al. Folding of the SARS Coronavirus Spike Glycoprotein Immunological Fragment (SARS•S1B).” Biochemistry 2005, 44, 1453-1463. (Focus on the results sections as an example of the kind of analysis we are doing.)
Reread: Lehninger, pages 143-144
Hammes. Physical Chemistry for the Biological Sciences. Section 3.6, pages 57-60.
Analysis of NMR Data
The NMR data will likely fit to the sigmoidal equation:
Hill equation, Eq. 1
where y is the measured parameter (integration in this case), y0 is the minimum value of the measured parameter, a is the difference between the maximum value of the parameter and the baseline value (ymax - y0), x is the temperature, b is the Hill coefficient necessary to fit the data, and T is an interaction constant, equal to the temperature where ΔG = 0.
Fit your data to equation 1 using KaleidaGraph. Determine the denaturation temperature (Tm) and the max and min values.
For each data point, determine:
- Then plot
- for each data point and fit to a linear curve.
- The slope should be –E/R, where E is the desired parameter (energy of denaturation), and R is the gas constant.
- Did you have sufficient data points to accurately estimate y0 and ymax? Comment on the quality of the sigmoidal fit.
- How did you decide which data series to fit?
- What could you do differently to improve data collection or analysis?
- What was the TM of the sigmoidal fit? Does that fit reasonably well with your estimates for the TMs of the other data series that weren’t fit to the Hill equation?
- How does the Efolding for lysozyme compare to that of an average protein? to the literature value for lysozyme? (Include citations.)
- How does the folding for lysozyme (measured by thermal denaturation) compare to its Gfolding (measured by chemical denaturation)? Is this expected?
- Provide a final summary inegrated the results of both experiments