Protein Folding Protein Structure and Function Lecture 3 Notes: Protein Folding - Proteins that are defined as having a common fold have different sequence and peripheral structures but may have the same major structures and topology. These proteins may not have a common evolutionary origin as structural similarities arise from the physics and chemistry of proteins favouring certain packaging arrangements and chain topologies. - Protein folding is the formation of a 1D linear structure into a complex 3D structure. Accurate predictions of protein structure are cannot be fully accurate but can be estimated using: (a) Anfinsen's thermodynamic hypothesis (b) Levinthal's paradox and kinetic mechanism (c) Multiple pathways and models of protein folding (d) Folding funnel (e) Spontaneous/assisted protein folding (macromolecular crowding inside the cell) (f) Protein misfolding diseases - Christian Anfinsen's thermodynamic hypothesis of protein folding (1961) suggests that the native (tertiary) structure of a protein could theoretically be determined from the amino acid sequence alone. This is correct (e.g. if the protein is folded in the cell after synthesis), although there are many other environmental factors involved in protein folding. - Many proteins are mis-folded and subsequently degraded in the cytoplasm despite having the same amino acid sequence. Therefore, this contradicts the thermodynamic hypothesis. - Bovine ribonuclease is a single polypeptide chain which is folded into a ring containing 4 disulphide bonds. It is possible to disrupt the structure with high concentrations of urea (CH4N2O) as it disrupts hydrogen bonds in the peptide backbone, reducing the hydrophobic effect. Additionally, excess B-mercaptoethanol reduces and breaks down the disulphide bonds (i.e. the S-H bond reacts with the disulphide bonds in the protein). Anfinsen's study used denaturing (unfolding) and renaturing (folding) of the protein bovine ribonuclease using urea and B-mercaptoethanol. This process is very slow as the formation of bonds and function changes over time. There is a lag phase before enzymatic activity appears, suggesting function is delayed compared to the bond formation and native molecules are not produced in a one-by-one fashion. - Therefore, Anfinsen concluded that the oxidation of SH groups in this system occurs initially through relatively random formation of SS bonds with subsequent rearrangement taking place under the influence of disulphide interchange driven by thermodynamic forces toward the most probable form, native ribonuclease. Thus, at least for a small globular protein in its standard physiological environment, the native structure is spontaneous (depends on the release of free energy) and determined by the protein's amino acid sequence. - The second law of thermodynamics is that a total entropy of an isolated system (closed system at constant temperature and pressure) can never decrease over time and such systems will spontaneously move towards the thermodynamic equilibrium (i.e. the state with maximum entropy). AG=AH system-T AS system<0 (AG is Gibbs free energy, AHsystem IS enthalpy, ASsystem is entropy and T is temperature).
Protein folding is spontaneous hence the free energy is released on folding (AG < 0, i.e. proteins have less free energy than reactants). This means protein folding is exergonic. The