Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

A new interpretation of the meaning of the center of line slope from a two-dimensional infrared spectrum

This article presents a new approximation to understand the connection between the center of line slope from a single peak of a two-dimensional (2D) infrared spectrum and the frequency-frequency correlation function. This approximation which goes beyond the short-time approximation includes explicitly pure dephasing mechanisms by introducing a time parameter that separates the fast fluctuations and slow fluctuations. While in the short-time approximation, the center of line slope is given by the normalized frequency fluctuations auto-correlation function, I show using this new approximation that the center of line slope measures on long time scales a shifted and scaled correlation function. The results present a new interpretation of the meaning of the center of line slope that allows for a better understanding of what 2D experiments can measure. To illustrate these findings, I compare this approximation with the short-time approximation for several examples of frequency-frequency correlation functions. I also give an estimate of the value of the time separation parameter for a correlation function with a simple exponential decay.

Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of plaque deposits in the human brain. The main component of these plaques consists of highly ordered structures called amyloid fibrils, formed by the amyloid β-peptide (Aβ). The mechanism connecting Aβ and AD is yet undetermined. In a previous study, a coarse-grained united-residue model and molecular dynamics simulations were used to model the growth mechanism of Aβ amyloid fibrils. On the basis of these simulations, a dock/lock mechanism was proposed, in which Aβ fibrils grow by adding monomers at either end of an amyloid fibril template. To examine the structures in the early time-scale formation and growth of amyloid fibrils, simulated two-dimensional ultraviolet spectroscopy is used. These early structures are monitored in the far ultraviolet regime (λ = 190-250 nm) in which the computed signals originate from the backbone nπ* and ππ* transitions. These signals show distinct cross-peak patterns that can be used, in combination with molecular dynamics, to monitor local dynamics and conformational changes in the secondary structure of Aβ-peptides. The protein geometry-correlated chiral xxxy signal and the non-chiral combined signal xyxy-xyyx were found to be sensitive to, and in agreement with, a dock/lock pathway.

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.

An Efficient N(3)-Scaling Propagation Scheme for Simulating Two-Dimensional Infrared and Visible Spectra

In this paper, we develop and test a new approximate propagation scheme for calculating two-dimensional infrared and visible spectra. The new scheme scales one order more efficiently with the system size than the existing schemes. A Trotter type of approximation is used for the matrix exponent that describes the time evolution of the quantum system. This is needed for calculating the third-order response functions governing the two-dimensional infrared and visible spectra. The method is tested on a model dimer system, the amide I spectrum of the Gramicidin A antimicrobial peptide, the spectrum of the OH stretching vibration of bulk water, and a homogeneous J-aggregate. Errors due to the approximation are hardly observable in the calculated spectra. Scaling simulations with different system sizes are used to demonstrate that the new scheme is indeed scaling with the system size to the third power, one order faster than the existing methods.

Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations

The infrared optical response of amyloid fibrils Aβ(1-40) is investigated. Simulations of two models corresponding to different protonation states are compared with experiment. The simulations reveal that vibrational frequency distributions inside the fibrils are dominated by side chain fluctuations. We further confirm earlier suggestions based on 2D-IR measurements that water molecules can be trapped inside the fibrils.