Standardized evaluation of protein stability.

Area of Science:

• Biophysics
• Computational Biology
• Protein Science

Background:

• Proteins exhibit diverse sequences and 3D folds, influencing their stability and function.
• Mean Force Potential (MFP) values offer a quantitative measure of protein stability.
• Understanding protein stability is key to predicting protein behavior and designing new proteins.

Purpose of the Study:

• To establish a standard Mean Force Potential (MFP) value for stable proteins.
• To investigate the relationship between amino acid sequence, 3D structure, and protein stability.
• To develop a method for evaluating protein models and identifying functional residues.

Main Methods:

• Comparison of MFP values for a large dataset of protein and peptide models from the Protein Data Bank (PDB).
• Calculation of median MFP values for individual amino acids within stably folded proteins.
• Scoring of protein primary sequences and 3D folds using calculated median amino acid MFP values.

Main Results:

• Proteins exceeding 200-250 residues exhibit a consistent MFP stability value of -65±3 kcal/aa, irrespective of sequence or fold.
• Median MFP values for amino acids range from -25 kcal/aa (Gly) to -115 kcal/aa (Trp), varying with sequence context.
• Scored protein sequences converge to a mean MFP value close to the standard stability value, while unfolded proteins show lower values.
• 3D protein folds represent a balance between regions of high and low residue stability scores, with functional residues often located at score extremes.

Conclusions:

• Protein sequences contain critical information for stability, with amino acid diversity being mandatory.
• The established standard MFP value provides a benchmark for protein stability.
• The developed scoring approach enables evaluation of 3D protein models, detection of functional residues, and guidance for mutation assays.