Protein folding
Cards (18)
- Hydrophobic collapse protein folding pathway:
- Unfolded
- Secondary structure forms (Hydrophobic bonds)
- Hydrophobic collapse and molten globule formation (dynamic)
- Native - most thermodynamically stable / at lowest free energy
- The molten globule is an intermediate polypeptide with backbone of a native like topology
- Protein folding is determined by non covalent interactions between different parts of a polypeptide
- Non covalent interactions during protien folding:
- Hydrogen bonding
- Electrostatic bonds
- Van der Waals forces
- Hydrophobic clustering
- Folded state of a protein has the lowest free energy
- The most stable combination of non covalent interactions determines protein structure and function
- The folding of the alpha helix and tertiary structure takes place in the exit tunnel (vestibule) of the ribosome - exit tunnel may change shape to influence folding
- Ligands and co factors like ATP and Zinc can induce folding
- Protein folding occurs from n terminal to c terminal
- Method for studying protein folding:
- X ray crystallography
- Isotope labelling and mass spectrometry
- Fluorescence measurements
- Site directed mutagenesis
- NMR
- Hydrogen exchange
- Bioinformatics
- Fluorescence measurements (FRET) involves aromatic side chains (tyrosine and tryptophan)
- Site directed mutagenesis - analysis of effects of mutations on folding kinetics
- NMR changes in magnetic resonance around 13C and 15N during folding and refolding
- Hydrogen exchange - amide hydrogen exchange with solvent (water) , depends on the environment pH
- Computational methods for structure prediction:
- Template based modelling
- Template free modelling
- Fragment based assembly
- Template based modelling - predictions based on previously determined structure
- Template free modelling - sequences used to predict secondary structure features
- Fragment based assembly involves 3 to 15 amino acid fragments modelled based on similarity with other proteins - model assemble from fragments