Protein folding
8 important questions on Protein folding
What is the RMSD to native?
- lower RMSD to native state is the folded state
Give the equation for the free energy and an interpretation of it.
As temperature increases, the entropy component becomes more dominant for stability (explains protein unfolding at higher temperatures)
Increasing the temperature increases the stability of the unfolded state.
What are the 4 major effects that contribute to a stably folded protein?
- Hydrophobicity (oil in water)
- note this is an effective force that contains enthalpic and entropic components
- 2.Hydrogen bonds form secondary structure
- Van der Waals
- Electrostatics (salt bridges)
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Why should you think of protein folding as a two-state process?
- From the folded state, some protein molecules can (and will) unfold
- From the unfolded state, some protein molecules (re-)fold (continually)
- --> Dynamic equilibrium: A (folded) ⇔ B (unfolded)
Why are the reversible folding experiment of Anfinsen the molecular basis for the central dogma?
- Anfinsen performed un-folding/re-folding experiments!
- Molecular basis for the central dogma of molecular biology: DNA makes RNA makes Protein–
- and –Sequence → Structure → Function
- Without reversible folding, ‘something’ could interfere in the step from sequence to structure (from DNA&RNA to Protein)
Name 4 examples of when for protein folding there is non-equilibrium in the cell.
- Protein aggregation
- Co-translational folding
- Activated process (driven by ATP)
- Chaperones
In the crowded environment of the cell, special precautions must be taken to allow proteins to fold properly, and to avoid problems due to accumulation of misfolded proteins.
What is meant by "the native state is heterogeneous"?
- Also a correctly folded protein is dynamic
- Crystal structureyields average position of the atoms
- ‘Breathing’ overall motion possible
- So proteins are flexible!
Also often conformational changes play an important role for the function of the protein
What is allosteric control?
- Often two conformations possible
- active T(ense) and inactive R(elaxed)
- Modulators change theconformation in the active form(or the inactive form)
- Not bound to active site:allosteric control
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