5 good questions and answers about "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
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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
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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?
The free energy difference between two states can be calculated from the ratio of their probabilities.
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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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