Study of the γD-Crystallin Protein Using Two-Dimensional Infrared (2DIR) Spectroscopy: Experiment and Simulation

Abstract

Cataracts is a misfolding protein disease in which one of its major components is the γD-crystallin protein. The conformational structure of the aggregated γD-crystallin and the interactions that cause aggregation are largely unknown. A recent experimental two-dimensional infrared (2DIR) spectroscopy study determined that the C-terminal domain has a high propensity to form β-sheets whereas the N-terminal domain forms a disordered structure in the fiber state. We present a combined computational molecular dynamics (MD) and infrared spectroscopy study of the local dynamics of these domains. The computed 2DIR signals agree remarkably well with experiment. We show that both domains having a Greek key structural fold experience different electrostatic environments, which may be related to the fact that the C-terminal domain is more structurally stable than the N-terminal domain. We correlate the vibrational couplings to known energy dissipation mechanisms and reveal their origin.

Amyloid β-Sheet Secondary Structure Identified in UV-Induced Cataracts of Porcine Lenses using 2D IR Spectroscopy

“…2). 33 The 2D peaks have elongated shapes that extend up to about 1660 cm −1 because of loops and disordered segments, as well as weaker modes of the β-sheets. 26; 34 Shown in Fig.…”

“…2D IR spectra of γD-crystallin have been previously reported 11; 31; 32 and computational modeling has helped to interpret these spectra. 33 Spectra of γD-crystallin are reported here to serve as comparisons to the spectra of αB-crystallin and ex vivo tissues.…”

“…46 These images and spectra are shown to illustrate the diversity in length that crystallin amyloids can adopt, as measured by TEM, and that 2D IR spectra exhibit characteristic amyloid β-sheet secondary structure even for lengths that are difficult to resolve with TEM. 2D IR spectroscopy is more sensitive to amyloid formation than TEM because only 4 or 5 strands are needed to create the spectroscopic signatures for amyloid β-sheets, 33 as explained below.…”

“…In contrast, 2D IR spectroscopy is sensitive to amyloid β-sheets made from only 4 or 5 strands of β-sheets, which is enough to form the delocalized vibrational modes that create the 2D IR spectroscopic signatures of amyloid, and become insensitive to the number of β-strands for sheets longer than the delocalization length of 12 strands (see Discussion above). 33 4 or 5 strands corresponds to a fiber length of <2 nm. 62 Assemblies this small might be considered oligomers that contain some fraction of amyloid β-sheet secondary structure.…”

Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method

“…Nevertheless, both classes of empirical models were shown to be quite useful in determining frequency shift fluctuations from molecular dynamics (MD) and reproducing experimental spectra. 7,13,20,21,[23][24][25][26][27] Despite that such semi-empirical approaches have shown to be highly useful, they are all based on various approximations and numerical fitting analyses. Therefore, a first-principle theory has been desired since it would provide significantly detailed description of vibrational solvatochromism.…”