David M. Leitner

An extended dynamical hydration shell around proteins

The focus in protein folding has been very much on the protein backbone and sidechains. However, hydration waters make comparable contributions to the structure and energy of proteins. The coupling between fast hydration dynamics and protein dynamics is considered to play an important role in protein folding. Fundamental questions of protein hydration include, how far out into the solvent does the influence of the biomolecule reach, how is the water affected, and how are the properties of the hydration water influenced by the separation between protein molecules in solution? We show here that Terahertz spectroscopy directly probes such solvation dynamics around proteins, and determines the width of the dynamical hydration layer. We also investigate the dependence of solvation dynamics on protein concentration. We observe an unexpected nonmonotonic trend in the measured terahertz absorbance of the five helix bundle protein λ6–85* as a function of the protein: water molar ratio. The trend can be explained by overlapping solvation layers around the proteins. Molecular dynamics simulations indicate water dynamics in the solvation layer around one protein to be distinct from bulk water out to ≈10 Å. At higher protein concentrations such that solvation layers overlap, the calculated absorption spectrum varies nonmonotonically, qualitatively consistent with the experimental observations. The experimental data suggest an influence on the correlated water network motion beyond 20 Å, greater than the pure structural correlation length usually observed.

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

The dynamics of water surrounding a solute is of fundamental importance in chemistry and biology. The properties of water molecules near the surface of a bio-molecule have been the subject of numerous, sometimes controversial experimental and theoretical studies, with some suggesting the existence of rather rigid water structures around carbohydrates and proteins [Pal, S. K., Peon, J., Bagchi, B. & Zewail A. H. (2002) J. Phys. Chem. B 106, 12376–12395]. Hydrogen bond rearrangement in water occurs on the picosecond time scale, so relevant experiments must access these times. Here, we show that terahertz spectroscopy can directly investigate hydration layers. By a precise measurement of absorption coefficients between 2.3 THz and 2.9 THz we could determine the size and the characteristics of the hydration shell. The hydration layer around a carbohydrate (lactose) is determined to extend to 5.13 ± 0.24 Å from the surface corresponding to ≈123 water molecules beyond the first solvation shell. Accompanying molecular modeling calculations support this result and provide a microscopic visualization. Terahertz spectroscopy is shown to probe the collective modes in the water network. The observed increase of the terahertz absorption of the water in the hydration layer is explained in terms of coherent oscillations of the hydration water and solute. Simulations also reveal a slowing down of the hydrogen bond rearrangement dynamics for water molecules near lactose, which occur on the picosecond time scale. The present study demonstrates that terahertz spectroscopy is a sensitive tool to detect solute-induced changes in the water network.

Long-Range Influence of Carbohydrates on the Solvation Dynamics of Water-Answers from Terahertz Absorption Measurements and Molecular Modeling Simulations

We present new terahertz (THz) spectroscopic measurements of solvated sugars and compare the effect of two disaccharides (trehalose and lactose) and one monosaccharide (glucose) with respect to the solute-induced changes in the sub-picosecond network dynamics of the hydration water. We found that the solute affects the fast collective network motions of the solvent, even beyond the first solvation layer. For all three carbohydrates, we find an increase of 2-4% in the THz absorption coefficient of the hydration water in comparison to bulk water. Concentration-dependent changes in the THz absorption between 2.1 and 2.8 THz of the solute-water mixture were measured with a precision better than 1% and were used to deduce a dynamical hydration shell, which extends from the surface up to 5.7 +/- 0.4 and 6.5 +/- 0.9 A for the disaccharides lactose and trehalose, respectively, and 3.7 +/- 0.9 A for the glucose. This exceeds the values for the static hydration shell as determined, for example, by scattering, where the long-range structure was found to be not significantly affected by the solute beyond the first hydration shell. When comparing all three carbohydrates, we found that the solute-induced change in the THz absorption depends on the product of molar concentration of the solute and the number of hydrogen bonds between the carbohydrate and water molecules. We can conclude that the long-range influence on the sub-picosecond collective water network motions of the hydration water is directly correlated with the average number of hydrogen bonds between the molecule and adjacent water molecules for carbohydrates. This implies that monosaccharides have a smaller influence on the surrounding water molecules than disaccharides. This could explain the bioprotection mechanism of sugar-water mixtures, which has been found to be more effective for disaccharides than for monosaccharides.

Energy Flow in Proteins

Energy flows anisotropically through the residues and vibrational states of globular proteins. A variety of experimental and computational studies have identified energy transport channels traversing many residues, in some cases connecting functional regions, potentially important in allostery, and in other cases having no apparent function. This property and the diffusion of energy in proteins are mimicked by transport on a percolation cluster. I review work that addresses connections between globular proteins, percolation clusters, and the similarity of energy flow and thermal transport in these systems. I also review experimental and theoretical studies of the anisotropic flow of energy through the vibrational states of a protein, a property that also can be understood by comparison with simple model disordered systems.

Long-range protein-water dynamics in hyperactive insect antifreeze proteins.

Antifreeze proteins (AFPs) are specific proteins that are able to lower the freezing point of aqueous solutions relative to the melting point. Hyperactive AFPs, identified in insects, have an especially high ability to depress the freezing point by far exceeding the abilities of other AFPs. In previous studies, we postulated that the activity of AFPs can be attributed to two distinct molecular mechanisms: (i) short-range direct interaction of the protein surface with the growing ice face and (ii) long-range interaction by protein-induced water dynamics extending up to 20 Å from the protein surface. In the present paper, we combine terahertz spectroscopy and molecular simulations to prove that long-range protein–water interactions make essential contributions to the high antifreeze activity of insect AFPs from the beetle Dendroides canadensis. We also support our hypothesis by studying the effect of the addition of the osmolyte sodium citrate.

Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy

Solvation free energy changes induced by protein folding and function are comparable to the corresponding overall free energy changes. Yet the structure, dynamics, and energetics of the protein itself have received more attention because they are easier to probe. Here we use terahertz (far-infrared) spectroscopy to directly probe the effect of mutations and solvent pH on the solvent shell−protein interaction. We study absorption spectra of the 80 residue viral protein, a five helix bundle, in the 2.1−2.8 THz region. We find that the wild type at pH 7 has a much more pronounced effect on long-distance solvation water than mutants replacing a single polar glutamine side chain with aromatic residues (tyrosine, histidine). This is true both in the context of enhanced and decreased helix stability (via alanine and glycine substitutions). Bringing the wild type and mutants closer to the unfolding transition by lowering the pH likewise reduces the long distance solvation effect. Thus terahertz spectroscopy can b...

Rattling in the Cage: Ions as Probes of Sub-picosecond Water Network Dynamics

We present terahertz (THz) measurements of salt solutions that shed new light on the controversy over whether salts act as kosmotropes (structure makers) or chaotropes (structure breakers), which enhance or reduce the solvent order, respectively. We have carried out precise measurements of the concentration-dependent THz absorption coefficient of 15 solvated alkali halide salts around 85 cm(-1) (2.5 THz). In addition, we recorded overview spectra between 30 and 300 cm(-1) using a THz Fourier transform spectrometer for six alkali halides. For all solutions we found a linear increase of THz absorption compared to pure water (THz excess) with increasing solute concentration. These results suggest that the ions may be treated as simple defects in an H-bond network. They therefore cannot be characterized as either kosmotropes or chaotropes. Below 200 cm(-1), the observed THz excess of all salts can be described by a linear superposition of the water absorption and an additional absorption that is attributed to a rattling motion of the ions within the water network. By providing a comprehensive set of data for different salt solutions, we find that the solutions can all be very well described by a model that includes damped harmonic oscillations of the anions and cations within the water network. We find this model predicts the main features of THz spectra for a variety of salt solutions. The assumption of the existence of these ion rattling motions on sub-picosecond time scales is supported by THz Fourier transform spectroscopy of six alkali halides. Above 200 cm(-1) the excess is interpreted in terms of a change in the wing of the water network librational mode. Accompanying molecular dynamics simulations using the TIP3P water model support our conclusion and show that the fast sub-picosecond motions of the ions and their surroundings are almost decoupled. These findings provide a complete description of the solute-induced changes in the THz solvation dynamics for the investigated salts. Our results show that THz spectroscopy is a powerful experimental tool to establish a new view on the contributions of anions and cations to the structuring of water.

Solvation dynamics of biomolecules: modeling and terahertz experiments

The role of water in biomolecule dynamics has attracted much interest over the past decade, due in part to new probes of biomolecule‐water interactions and developments in molecular simulations. Terahertz (THz) spectroscopy, among the most recent experimental methods brought to bear on this problem, is able to detect even small solute induced changes of the collective water network dynamics at the biomolecule‐water interface. THz measurements reveal that proteins influence up to 1000 water molecules in their surroundings, and that even small saccharides influence the dynamics of hundreds of surrounding water molecules. The THz spectrum of a protein is sensitive to mutation and depends on the surface charge and flexibility of the protein. Influence on the salvation shell appears most pronounced for native wildtype proteins and decreases upon partial unfolding or mutation. THz spectra of solvated saccharides reveal that the number of water molecules coupled dynamically to a saccharide, forming a dynamical hydration shell around it, is related to the number of exposed oxygen atoms on the solute. The thickness of this layer appears correlated with the bioprotection efficiency of the saccharide. All findings support the thesis of a long‐range dynamic coupling between biomolecule and solvent.

Quantum mechanics of small Ne, Ar, Kr, and Xe clusters

We compute energy levels and wave functions of Ne, Ar, Kr, and Xe trimers, modeled by pairwise Lennard‐Jones potentials, using the discrete variable representation (DVR) and the successive diagonalization‐truncation method. For the Ne and Ar trimers, we find that almost all of the energy levels lie above the energy required classically to achieve a collinear configuration. For the Kr and Xe trimers, we are able to determine a number of energy levels both below the classical transition energy as well as above it. Energy level statistics for these heavier clusters reveal behavior that correlates well with classical chaotic behavior that has previously been observed above the transition energy. The eigenfunctions of these clusters show a wide variety of behavior ranging from very regular behavior for low lying eigenstates to a combination of regular and irregular behavior at energies above the transition energy. These results, along with quantum Monte Carlo calculations of the ground states for a variety of ...

Melting and phase space transitions in small clusters: Spectral characteristics, dimensions, and K entropy

The Grassberger–Procaccia method has been employed to study the transitions which occur as a classical Ar3 cluster, modeled by pairwise Lennard‐Jones potentials, passes from a rigid, solid‐like form to a nonrigid, liquid‐like form with increasing energy. Power spectra and lower bounds on the fractal dimensions and K entropies are presented at several energies along the caloric curve for the Ar3 cluster. In addition, the full spectrum of Liapunov exponents has been computed at these same energies to get an accurate value of the K entropy. Chaotic behavior, though relatively small, is observed even at low energies where the power spectrum displays largely normal‐mode structure. The degree of chaotic behavior increases with energy at energies where some degree of regularity is observed in the spectrum. However, at energies that just allow the system to pass into and across saddle regions separating local potential minima, the phase space appears to be separable into a region within the equilateral triangle p...