Study of the γD-crystallin protein using two-dimensional infrared (2DIR) spectroscopy: experiment and simulation

Area of Science:

• Biophysics
• Structural Biology
• Computational Chemistry

Background:

• Cataracts are protein misfolding diseases, with γD-crystallin being a key component.
• The aggregation mechanisms and conformational structures of aggregated γD-crystallin remain poorly understood.
• Previous experiments indicated distinct structural propensities for the N-terminal (disordered) and C-terminal (β-sheet rich) domains of γD-crystallin in the fiber state.

Purpose of the Study:

• To computationally investigate the local dynamics of the N-terminal and C-terminal domains of γD-crystallin.
• To correlate computational findings with experimental two-dimensional infrared (2DIR) spectroscopy data.
• To elucidate the factors contributing to differential stability and aggregation propensity between the two domains.

Main Methods:

• Combined molecular dynamics (MD) simulations and infrared spectroscopy.
• Calculation of 2DIR signals to compare with experimental results.
• Analysis of electrostatic environments and vibrational couplings within the protein domains.

Main Results:

• Computed 2DIR signals showed excellent agreement with experimental data.
• The N-terminal and C-terminal domains, despite sharing a Greek key fold, exhibit different electrostatic environments.
• The C-terminal domain demonstrates greater structural stability compared to the N-terminal domain.

Conclusions:

• The differing electrostatic environments likely contribute to the distinct structural stabilities of the γD-crystallin domains.
• Vibrational couplings are linked to specific energy dissipation mechanisms, providing insights into protein aggregation.
• This study offers a detailed molecular-level understanding of γD-crystallin dynamics relevant to cataract formation.