Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent...

Area of Science:

• Protein conformational dynamics
• Computational biophysics
• Biosensor design

Background:

• Proteins utilize allostery for functional regulation via conformational changes.
• Allosteric proteins are key components in designing fluorescent biosensors that signal environmental changes.
• Direct-response fluorescent biosensors translate ligand binding into enhanced fluorescence output.

Purpose of the Study:

• To identify critical "hot spot" residues driving protein conformational transitions using computational methods.
• To investigate the efficacy of a novel computational approach, Multiply Perturbed Response (MPR), in predicting allosteric sites.
• To compare computationally identified sites with experimentally validated insertion sites in biosensors.

Main Methods:

• Utilized a multiple force application approach termed Multiply Perturbed Response (MPR).
• Developed computational strategies to identify residues and forces maximizing conformational change overlap.
• Analyzed overlap maximizer residues across multiple force insertion locations.

Main Results:

• MPR successfully identified allosteric "hot spot" residues crucial for protein conformational transitions.
• Computationally identified residues closely matched experimentally determined insertion sites in fluorescent biosensors.
• The study validates the utility of linear response theory-based methods for uncovering functionally significant allosteric regions.

Conclusions:

• MPR enhances the design of protein-based biosensors by accurately predicting allosteric sites.
• The findings support the application of physics-based methods in understanding protein conformational dynamics.
• This approach may aid in developing new biosensors and mapping protein conformational pathways.