Calculate Fraction Unfolded Protein

This is a question from a homework pset of previous year.

Calculate fraction unfolded protein. Both the enthalpy δh and entropy δs can be calculated using a curve of a fraction of protein in folded and unfolded state. Made by faculty at the university of colorado boulder department of chemical and biological. Circular dichroism can be used to follow the folding or unfolding of proteins and peptides utilizing the fact that the spectra of folded and unfolded proteins and peptides usually have very different spectra figures 1a 1b. The rate equation is where p n is the fraction of protein in its native state n and p u is the fraction of protein in the unfolded state u.

In the simplest case a molecule undergoes a folding transition between two states. In biochemistry equilibrium unfolding is the process of unfolding a protein or rna molecule by gradually changing its environment such as by changing the temperature or pressure adding chemical denaturants or applying force as with an atomic force microscope tip. They suggest titrating the protein solution in the absence of osmolytes with urea to determine the parameter corresponding to the completely unfolded protein in this case θ f which can then be used to determine the fraction folded using equation 2. While doing this we record a protein property that changes as a result of unfolding.

Since equilibrium is maintained at all steps the process is reversible equilibrium folding. Calculating fraction of protein unfolded from spectroscopy data. We are then asked to calculate various thermodynamic quantities from these data. Where fn is the fraction native and yn is the contribution to the dependent variable y from the native state and fd is the fraction denatured and yd is the contribution to the dependent variable y from the denatured state.

The easiest way to get the entropy and enthalpy of protein folding is by recording protein melting renaturation curves like this one. Determine the fraction of protein folded or unfolded at different temps a protein melting curve see graph can be produced. The s and h values can be calculated using the van t hoff equation and plot. How to calculate dgo for n rightleftharpoons d.

Uses the gibbs free energy change to determine the fraction of protein unfolded at equilibrium. Note that the area under the cp vs t curve as the protein. The folding of some proteins appears to be a two state kinetic process 1. The folding rate is k f and the unfolding rate is k u.

For a very steep unfolding curve one can then show that the fraction of protein unfolded b depends on the square of the urea concentration u and is given by a 1 2 is the binding constant as b 0 and λ is a parameter that reflects the augmentation in affinities of protein for urea as the moles bound increases to the saturation.