[Paper Review] Electrostatics in the Stability and Misfolding of the Prion Protein: Salt Bridges, Self-Energy, and Solvation

Will Guest, Neil R. Cashman+1 more|PubMed|Apr 9, 2010

Prion Diseases and Protein Misfolding47 references3 citations

TL;DR

This study uses a mesoscopic dielectric theory to calculate electrostatic contributions—salt bridge energies, self-energy, and solvation effects—to prion protein stability and misfolding. It reveals that salt bridges and intrinsic electrostatic stabilization are critical for native structure, while desolvation penalties create regional constraints that favor specific sequence regions for amyloid recruitment, with disease-susceptible mutants showing reduced salt bridge stabilization.

ABSTRACT

Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self energies play key roles in stabilizing secondary and tertiary structural elements of the prion protein. The total electrostatic potential energy of each residue was found to be invariably stabilizing. Residues frequently found to be mutated in familial prion disease were among those with the largest electrostatic energies. The large barrier to charged group desolvation imposes regional constraints on involvement of the prion protein in an amyloid aggregate, resulting in an electrostatic amyloid recruitment profile that favours regions of sequence between alpha helix 1 and beta strand 2, the middles of helices 2 and 3, and the region N-terminal to alpha helix 1. We found that the stabilization due to salt bridges is minimal among the proteins studied for disease-susceptible human mutants of prion protein.

Motivation & Objective

• To understand the role of electrostatics in stabilizing the native prion protein (PrP C) and promoting misfolding to the pathogenic PrP Sc form.
• To quantify salt bridge, self-energy, and solvation contributions to the free energy landscape of PrP.
• To identify electrostatic barriers to amyloid formation by calculating transfer energies of charged residues into low-dielectric environments.
• To assess how familial prion disease mutations alter electrostatic stabilization and thus predispose to misfolding.
• To develop a dielectric model that accounts for heterogeneous protein interior responses, improving accuracy over fixed-dielectric continuum methods.

Proposed method

• Applied a mesoscopic theory of protein dielectrics that derives the effective dielectric constant from all-atom molecular dynamics simulations, avoiding arbitrary assumptions about internal dielectric values.
• Calculated salt bridge energies by summing solvation energy changes and Coulombic interactions between charged residues upon desolvation.
• Computed total residue electrostatic potential energy and transfer energy into a low-dielectric (ε ≈ 4) amyloid-like phase.
• Used NMR ensemble structures to average salt bridge energies, accounting for conformational variability.
• Applied the Born model approximation to estimate desolvation penalties, with key equation: ΔE_total ≈ q²/ε_prot (1/r_ion − 1/r_AB), showing always-positive energy cost.
• Validated results against known disease mutations and aggregation propensities, linking electrostatic profiles to experimental observations.

Experimental results

Research questions

• RQ1 How do salt bridge and self-energy contributions stabilize the native prion protein structure across wild-type and mutant forms?
• RQ2 What is the electrostatic barrier to desolvation of charged residues during PrP Sc formation, and how does it vary across the sequence?
• RQ3 Which regions of the prion protein are most likely to be recruited into the amyloid core based on electrostatic transfer energy profiles?
• RQ4 How do familial prion disease-causing mutations alter the electrostatic stabilization of the native state?
• RQ5 To what extent do electrostatic effects, particularly desolvation penalties, constrain the formation of PrP Sc and influence its regional recruitment?

Key findings

• Salt bridges and self-energy contributions were found to be universally stabilizing for each residue in the prion protein, with the total electrostatic potential energy always favorable in the native state.
• Residues frequently mutated in familial prion disease exhibited the largest electrostatic energies, indicating their critical role in structural stability.
• The desolvation penalty for charged groups creates a significant energetic barrier, resulting in an electrostatic recruitment profile that favors specific regions—between α1 and β2, the middle of α2 and α3, and the N-terminus of α1—for inclusion in the amyloid core.
• Disease-susceptible human mutants of the prion protein showed minimal salt bridge stabilization, suggesting reduced electrostatic resilience contributes to misfolding propensity.
• The heterogeneous dielectric model outperformed fixed-dielectric approaches by accurately capturing both buried and surface salt bridge strengths, improving prediction reliability.
• The study confirms that net charge and charge distribution significantly influence aggregation resistance, with higher net charge increasing the energetic cost of amyloid formation.