Criteria that discriminate between native proteins and incorrectly folded models

Area of Science:

• Protein structure and folding
• Computational biology
• Biophysics

Background:

• Distinguishing native protein structures from misfolded models is essential for understanding proteinopathies.
• Previous methods for modeling misfolded proteins had limitations in side-chain conformation generation.

Purpose of the Study:

• To evaluate various theoretical concepts for their ability to discriminate between native proteins and misfolded protein models.
• To assess the capability of the CONGEN program in reproducing native protein conformations and constructing misfolded models.

Main Methods:

• Misfolded protein models were created by swapping side chains between alpha-helical hemerythrin and beta-sheeted immunoglobulin VL domain backbones.
• CONGEN, a conformational space sampling program, was used to construct side chains, allowing for non-trans conformations.
• Native and misfolded constructs were analyzed using theoretical concepts including free energy potentials, electrostatic interactions, atomic packing, and solvent-exposed surface.

Main Results:

• CONGEN successfully reproduced native side-chain conformations with low root-mean-square differences (2.2-2.4 Å).
• Misfolded and native protein models exhibited similar molecular surfaces, potential energies, surface charge densities, atomic packing, and electrostatic interactions.
• Solvent-exposed side-chain nonpolar surface, number of buried ionizable groups, and empirical free energy functions incorporating solvent effects clearly favored native structures.

Conclusions:

• Standard measures like surface charge and atomic packing are insufficient for differentiating native from misfolded proteins.
• Solvent-exposed nonpolar surface area, buried ionizable groups, and solvent-effect-inclusive free energy functions are key discriminators of protein folding states.