The Multi-Factor Coupled Protein Folding: Insights from Molecular Dynamics Simulations

Deciphering the folding mechanism of proteins is significant to comprehend their physiological functions. In this chapter, several significant and yet common factors of protein folding have been discussed: 1) Space limitation (confinement and macromolecular crowding). Proteins are confined and crowded in cellular circumstances, which facilitates the folding and enhances the stability through the entropic reduction of the unfolded states. 2) Solvent effects. The various solvation models have been described. Water is more than the environment, and can also participate in the folding by mediating the collapse of protein chains and searching for the native topologies along the free energy landscapes. 3) Pressure, temperature and pH. The high hydrostatic pressure induces the volume decrease, destroys the non-covalent interactions and increases the roughness of free energy landscape, which generally drives the equilibrium toward the unfolded states. pH modulates protein structure and dynamics through protonation/deprotonation of sidechains and sometimes causes the misfolding. Temperature changes alter the conformational dynamics but not the folding pathway. 4) Structural modifications (mutation, truncation/insertion and protonation/deprotonation). The mutations of key residues significantly alter the folding by distorting the cooperative interactions, which can result in the misfolding or aggregation; nonetheless, the rational design by mutations can be beneficial to protein folding. The proper truncations do not show obvious influences on protein structure and dynamics, and the loop insertions may reduce the unfolding free energy barrier and facilitate the unfolding kinetics. Protonation of key residues affects significantly the folding/unfolding equilibrium by altering the non-covalent interactions.

Keywords: Confinement, conformational dynamics, cooperative interactions, denaturation and aggregation, folding/unfolding kinetics, free energy landscape, h-bonding, hydrophobic core, macromolecular crowding, misfolding, molecular dynamics, mutation, non-covalent interactions, ph, pressure, protein folding, solvation models, solvent effects, structural modification, temperature.