Time-resolved backbone desolvation and mutational hot spots in folding proteins

Area of Science:

• Protein folding dynamics
• Computational biophysics
• Molecular evolution

Background:

• Understanding protein folding is crucial for deciphering biological functions and diseases.
• Identifying critical residues that drive protein folding is a key challenge in molecular biology.

Purpose of the Study:

• To present a novel method for identifying hot mutational spots in two-state folding proteins.
• To predict the surface burial extent of residues at the transition state of protein folding.
• To elucidate the nucleation mechanism of protein folding using ab initio simulations.

Main Methods:

• Ab initio simulations of protein folding histories.
• Analysis of conformational transitions and pairwise interactions influenced by solvent environments.
• Identification of three-body correlations and their role in stabilizing the folding nucleus.
• Validation using Phi-value analysis on chymotrypsin inhibitor 2.

Main Results:

• A nucleation process was identified in mammalian ubiquitin folding, marked by a sudden decrease in structural fluctuations.
• Three-body correlations, involving hydrophobic units and hydrogen-bonded residue pairs, were found to stabilize the folding nucleus.
• Residues involved in both protecting hydrogen bonds and being protected were predicted as hot mutational spots.
• The method's predictions were validated against experimental data from chymotrypsin inhibitor 2.

Conclusions:

• The study presents a kinetic model for protein folding nucleation, highlighting the importance of specific residue interactions and solvent structuring.
• Hot mutational spots are identified as residues critical for nucleus stabilization during folding.
• The findings offer insights into protein evolution and the design of proteins with altered stability or function.