State-resolved terahertz spectroscopy of biomolecules
Terahertz (THz) spectroscopy provides fundamentally new information about biomolecular structure and functional dynamics. In the crystalline phase, the THz phonon modes reflect motions over extended length scales and include lattice translations, intermolecular librations, and intramolecular vibrations. The THz vibrational frequencies associated with these modes are largely determined by the forces (e.g. hydrogen bonding, electrostatic, van der Waals) responsible for binding including those associated with co-crystallized solvents. In the liquid phase, the unstructured THz absorption of aqueous samples can give information about the surrounding water layer including its effective thickness and impact on the folding dynamics. An intermediate domain of special interest also exists in co-solvated crystalline biomaterials where the THz absorption features remain discrete and well-resolved but where water is both labile and highly structured and consequently non-absorbing as it is in ice. Polypeptides co-crystallized with water fall into this intermediate class and are the focus of the studies presented here. A common property of these systems is the extensive multi-center hydrogen-bonding network that exists throughout the lattice. As shown here, subtle modifications to these networks by water can impact the phonon frequencies in surprising ways depending on the hydrophobic or hydrophilic nature of the peptide-water interaction.
Crystalline Trialanine: Extreme sensitivity to β-sheet structure and co-crystallized water
The three crystalline forms of trialanine (parallel, p-Ala3, and anti-parallel, ap-Ala3 β-sheet forms and hydrated anti-parallel β-sheet, ap-Ala3-H2O) exist as highly networked peptide crystals and serve as a benchmark system to investigate the sensitivity of THz features to β-sheet structure and the impact of water on hydrophilic sites in the crystal. Additionally, these systems are simple enough to treat computationally at the full quantum level of theory using density functional theory (DFT).
**Terahertz spectroscopy provides a sensitive probe of the different hydrogen bonding networks associated with β-sheet structures and to the hydration state near hydrophilic sites in the crystal as exemplified by the three different forms of trialanine.
**Based on these comparisons and others, the computational results suggest the force field parameters will require further refinement to reliable model the interactions with water and the large scale functional motions important in biomolecular systems. Particularly for the weak inter-sheet hydrogen bonding present in the anti-parallel β-sheet forms, the quantum chemical theory applied here (Density Functional Theory) is not inadequately predicting the THz absorption features suggesting the need for new functionals optimized for multiple hydrogen bonding centers and/or for advanced methods that explicitly treat electron correlation for periodic systems.
Crystalline Dipeptide Nanotubes: Water Permeability Dynamics Controlled by THz Mode Coupling
A series of crystalline dipeptides are known from x-ray studies to form nanotube structures having the central core region decorated with hydrophobic groups While the sidechain groups of this series can range from alanine to valine to isoleucine, the backbone structures and hydrogen bonding networks are very similar and present an opportunity to examine the sensitivity of THz features to the simplest of change in protein structure.
In some cases, the hydrophobic pore can accommodate small solvent molecules including water thus enabling THz studies of the impact of water confined within the hydrophobic pore regions of peptides which represents a model system for the water permeability through trans-membrane channels.
**In contrast to the drastic spectral changes found upon hydration at hydrophilic sites in the anti-parallel β-sheet of trialanine, the terahertz spectrum of the AI nanotube structure (and other nanotube spectra not shown) change very little when the hydrophobic pores are filled with water.
**THz modes may play an important role in the water permeability dynamics of peptide systems where a subtle balance exists between the attractive hydrophilic interactions within the water network and the repelling nature of hydrophobic regions of peptides. On-going THz studies are exploring model systems of β-amyloid peptides with water and the aggregation pathways for plaque formation that are associated with the protein misfolding diseases, Alzheimer’s, Parkinson’s, Huntington’s and islet amyloidosis in type 2 diabetes.
State-resolved THz and UV spectroscopy and dynamics of biomolecules:
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