Probing protein stability: towards a computational atomistic, reliable, affordable, and improvable model

Area of Science:

• Computational biophysics
• Protein thermodynamics
• Molecular dynamics simulations

Background:

• Understanding protein stability is crucial for protein engineering and drug design.
• Predicting the impact of mutations on protein melting temperature remains a challenge.
• Accurate free energy calculations are essential for molecular simulations.

Purpose of the Study:

• To present an improved computational method for evaluating free energy changes related to protein collective variables.
• To assess the method's ability to predict changes in protein melting temperature upon single-point mutations.
• To validate the computational approach against experimental data for known protein systems.

Main Methods:

• Utilized altruistic well-tempered metadynamics, a variant of multiple-walkers metadynamics.
• Applied the maximal constrained entropy principle to enhance sampling of protein configurations.
• Performed all-atomistic simulations of proteins and their environments.

Main Results:

• Successfully computed melting temperature variations for wild-type and mutated bovine pancreatic trypsin inhibitor.
• Calculated free energy differences for wild-type and mutated frataxin variants.
• Demonstrated accurate prediction of the sign of melting temperature changes compared to in vitro experiments.

Conclusions:

• The refined computational method accurately predicts the impact of single-point mutations on protein melting temperature.
• The approach provides a reliable way to discriminate between stabilizing and destabilizing mutations.
• This method holds promise for guiding protein design and engineering efforts.