InSty: A ProDy Module for Evaluating Protein Interactions and Stability

Area of Science:

• Computational Biology
• Structural Biology
• Biophysics

Background:

• Protein dynamics and interactions are crucial for biological function.
• Existing tools may not fully capture the complexity of these interactions across ensembles.
• Bridging protein structure and function requires advanced analytical methods.

Purpose of the Study:

• Introduce InSty, a novel module for the ProDy application programming interface.
• Identify and quantify intra- and intermolecular interactions influencing protein stability and dynamics.
• Provide insights into the functional significance and evolutionary conservation of these interactions.

Main Methods:

• Analysis of non-covalent interactions using conformational ensemble data (experimental and predicted).
• Assessment of interaction time evolution and persistence during molecular dynamics simulations.
• Evaluation of interaction conservation across homologous proteins.

Main Results:

• InSty quantifies critical intra- and intermolecular interactions.
• The module analyzes interaction dynamics, persistence, and conservation.
• Outputs facilitate statistical evaluation, visualization, and automated ensemble analysis.

Conclusions:

• InSty integrates seamlessly with ProDy, offering a versatile tool for computational biology.
• The module aids in understanding protein stability, function, and allostery.
• InSty supports mutagenesis studies and identifies key sites for functional interactions.