Chapter 2: Folding Flashcards
Central dogma of Molecular Biology
DNA -> RNA -> Protein
Anfinsen dogma
Amino acid sequence contains all information needed for correct protein folding
Factors determining favourable folding conditions
1) Conformational entropy
2) Hydrophobic effect (very important!!!)
3) Van der Waals interactions
4) Charge-charge interactions
5) Internal H-bonds
Describe hydrphobic effect in protein folding
Unfolded state in entropically favoured until its concentration reached a certain point when folding becomes favourable as a result of enthalpic effect driven by hydrophobic forces
Interpreting heat denaturation curves
Signal versus temperature, 50% of protein is unfolded at melting temperature
Fluorescence method
Local environment around fluorescent groups affects the wavelength of maximal fluorescence, 350 nm for unfolded and 330 nm for folded
Chemical denaturation
Chaotropes such as urea and guanidine hydrochloride
Main concepts of protein stability
1) Free energy minimum for the folded state is achieved under physiological conditions and increases in either direction
2) Proteins are marginally stable
3) Two-state cooperative folding for most proteins, one contact site increases chances for the next binding site formation
Leventhal’s paradox
Protein must go through all possible folding states to reach its native conformation, which requires more time than biological systems have at their disposal, so how do proteins find their way to native state in the biologically relevant time frame
Two problems in protein folding
1) How to do it in a biologically relevant time (kinetics)
2) What is its native structure and how to determine it (Rosetta)
Nucleation-condensation model
Rate-limiting step is nucleus formation, which consists of weak secondary structures. It is coupled to tertiary structure, when other domains collapse around the nucleus to form native structure
