Driving of a Small Solvated Peptide in the IR and THz Range—A Comparative Study of Energy Flow

Intramolecular Proton Transfer in the Hydrogen Oxalate Anion and the Cooperativity Effects of the Low-Frequency Vibrations: A Driven Molecular Dynamics Study

We report first-principles molecular dynamics (MD) and dipole-driven molecular dynamics (μ-DMD) simulations of the hydrogen oxalate anion at the MP2/aug-cc-pVDZ level of theory. We examine the role of vibrational coupling between the OH stretching bands, that is, the fundamental and a few combination bands spanning the 2900-3100 cm^-1 range, and several of the low-frequency bending and stretching fundamental modes. The low-frequency modes between 300 and 825 cm^-1 play a crucial role in the proton-transfer motion. Strong involvement of CO₂ and CCO bending and the CC stretching vibrations indicate that these large amplitude motions cause the shortening of the O···O distance and thus promote H⁺ transfer to the other oxygen by bringing it over the 3.4 kcal/mol barrier. Analysis of resonant μ-DMD trajectories shows that the complex spectral feature near 825 cm^-1, closely corresponding to both an overtone of two quanta of 425 cm^-1 and a combination band of low-frequency CO₂ rocking (300 cm^-1) and CCO bending (575 cm^-1) modes, is involved in the proton transfer. μ-DMD shows that exciting the system at these mode combinations leads to faster barrier activation than exciting at the OH fundamental mode.

Understanding the connection between conformational changes of peptides and equilibrium thermal fluctuations

Despite the increasing evidence that conformational transitions in peptides and proteins are driven by specific vibrational energy pathways along the molecule, the current experimental techniques of analysis do as yet not allow to study these biophysical processes in terms of anisotropic energy flows. Computational methods offer a complementary approach to obtain a more detailed understanding of the vibrational and conformational dynamics of these systems. Accordingly, in this work we investigate jointly the vibrational energy distribution and the conformational dynamics of trialanine peptide in water solution at room temperature by applying the Instantaneous Normal Mode analysis to the results derived from equilibrium molecular dynamics simulations. It is shown that conformational changes in trialanine are triggered by the vibrational energy accumulated in the low-frequency modes of the molecule, and that excitation is caused exclusively by thermal fluctuations of the solute-solvent system, thus excluding the possibility of an intramolecular vibrational energy redistribution process.

THz frequency spectrum of protein-solvent interaction energy using a recurrence plot-based Wiener-Khinchin method

The dynamics of a protein and the water surrounding it are coupled via nonbonded energy interactions. This coupling can exhibit a complex, nonlinear, and nonstationary nature. The THz frequency spectrum for this interaction energy characterizes both the vibration spectrum of the water hydrogen bond network, and the frequency range of large amplitude modes of proteins. We use a Recurrence Plot based Wiener-Khinchin method RPWK to calculate this spectrum, and the results are compared to those determined using the classical auto-covariance-based Wiener-Khinchin method WK. The frequency spectra for the total nonbonded interaction energy extracted from molecular dynamics simulations between the β-Lactamase Inhibitory Protein BLIP, and water molecules within a 10 Å distance from the protein surface, are calculated at 150, 200, 250, and 310 K, respectively. Similar calculations are also performed for the nonbonded interaction energy between the residues 49ASP, 53TYR, and 142PHE in BLIP, with water molecules within 10 Å from each residue respectively at 150, 200, 250, and 310 K. A comparison of the results shows that RPWK performs better than WK, and is able to detect some frequency data points that WK fails to detect. This points to the importance of using methods capable of taking the complex nature of the protein-solvent energy landscape into consideration, and not to rely on standard linear methods. In general, RPWK can be a valuable addition to the analysis tools for protein molecular dynamics simulations. Proteins 2016; 84:1549-1557. © 2016 Wiley Periodicals, Inc.

Far infrared spectra of solid state L-serine, L-threonine, L-cysteine, and L-methionine in different protonation states

In this study, experimental far infrared measurements of L-serine, L-threonine, L-cysteine, and L-methionine are presented showing the spectra for the 1.0-13.0 pH range. In parallel, solid state DFT calculations were performed on the amino acid zwitterions in the crystalline form. We focused on the lowest frequency far infrared normal modes, which required the most precision and convergence of the calculations. Analysis of the computational results, which included the potential energy distribution of the vibrational modes, permitted a detailed and almost complete assignment of the experimental spectrum. In addition to characteristic signals of the two main acid-base couples, CO2H/CO2(-) and NH3(+)/NH2, specific side chain contributions for these amino acids, including CCO and CCS vibrational modes were analyzed. This study is in line with the growing application of FIR measurements to biomolecules.

New insights into the role of water in biological function: studying solvated biomolecules using terahertz absorption spectroscopy in conjunction with molecular dynamics simulations

In life science, water is the ubiquitous solvent, sometimes even called the "matrix of life". There is increasing experimental and theoretical evidence that solvation water is not a passive spectator in biomolecular processes. New experimental techniques can quantify how water interacts with biomolecules and, in doing so, differs from "bulk" water. Terahertz (THz) absorption spectroscopy has turned out to be a powerful tool to study (bio)molecular hydration. The main concepts that have been developed in the recent years to describe the underlying solute-induced sub-picosecond dynamics of the hydration shell are discussed herein. Moreover, we highlight recent findings that show the significance of hydrogen bond dynamics for the function of antifreeze proteins and for molecular recognition. In all of these examples, a gradient of water motion toward functional sites of proteins is observed, the so-called "hydration funnel". By means of molecular dynamics simulations, we provide new evidence for a specific water-protein coupling as the cause of the observed dynamical heterogeneity. The efficiency of the coupling at THz frequencies is explained in terms of a two-tier (short- and long-range) solute-solvent interaction.