Protein thermodynamics
5 important questions on Protein thermodynamics
In this context, what are macrostates?
- The entropy, enthalpy and energy we have discussed so far are properties of macrostates (e.g. the native state, unfolded state)
- Macrostates consist of an ensemble of microstates: the individual conformations
The free energy components of a microstate (A) can be expressed in terms of the probabilities of the microstates (i) in that macrostate
What is meant by ensemble average?
- A macrostate is not a single conformation, it consists of an collection of conformations
- To describe the properties of a macrostate (A), we typically calculate an ensemble average
What kind of experimental values can be measured that you expect to be different between the folded and the unfolded state?
- N-C distance
- Total hydrophobic surface area
- Enzymatic activity
- Hydrogen bonds
- Radius of gyration
- Fluorescence (e.g. FRET)
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How can the free energy difference between two states be calculated?
What would happen if visited all possible states were visited?
- Imagine a 100-residue protein where the φ-and ψ-angles can only have 3 values →3200≈ 1095possible structures
- Assume 10 ps(10-11 s) per structure
- To visit all states, this would take ~ 1076 years
- Number of relevant non-folded structures is much smaller than the number of possible non-folded structures
- If the number of relevant non-folded structures increases proportionally with the folding time, only 109 protein structures need to be simulated instead of 1095 structures
- So perhaps simpler after all...
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