How conformational changes are occurring in protein denaturation related to the Gibbs free energy changes of that particular protein? For example I have one protein having two domain in its native structure . I have denatured using GuHCl and fitted into three state model and got
delta G1= -0.57 Kcal/mol; m1= -0.06261Kcal/mol.M and
delta G2= 1.24 Kcal/mole; m2= 0.7206 Kcal/mol.M;
Delta G1&m1 is negative and delta G2&m2 is positive. What are the causes of this particular observations and why I am getting this much low values of delta G (1&2) and how to explain this?
If I fit in two state model fitting
ΔG [kcal/mol] = 1.84
m( Kcal/mol.M) = 0.86
When a question is raised about experimental data, it is always advisable to show an image of the experimental data and the data analysis. Otherwise, it is difficult to figure out what could be the problem or what suggestions to be made.
If a model with a single unfolding transition works fine, you should not go for a model with two transitions, unless you do a statistical test (parametric or non-parametric) to assess whether or not the more complex model is a statistically significantly better option. Judging estimated parameter values is part of the story.
The estimated values obtained through the data analysis together with the statistical test will be an indication for the appropriateness of either model. In your case, getting a negative ΔG1 and an almost zero m1 would already suggest the two-transition model is not appropriate.
If the model with a single transition is the one to be applied, a ΔG of 1.84 is low, but not too low. In general, protein stabilization energies are not larger than 10 kcal/mol, and very often they are below 5 kcal/mol. With a ΔG of 1.84 at 298.15 K, almost 96% of the protein is folded at that temperature. Whether or not the remaining 4% being unfolded is relevant (technically or physiologically) is another story.
The negative delta G value indicate in protein denaturation study tat there is restriction for the motion of the molecules . T.S. is less polar, Charge is spread and created in the substrate molecules.
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