Ultrafast Molecular Transport on Carbon Surfaces: The Diffusion of Ammonia on Graphite

We present a combined experimental and theoretical study of the self-diffusion of ammonia on exfoliated graphite. Using neutron time-of-flight spectroscopy we are able to resolve the ultrafast diffusion process of adsorbed ammonia, NH$_3$, on graphite. Together with van der Waals corrected density functional theory calculations we show that the diffusion of NH$_3$ follows a hopping motion on a weakly corrugated potential energy surface with an activation energy of about 4 meV which is particularly low for this type of diffusive motion. The hopping motion includes further a significant number of long jumps and the diffusion constant of ammonia adsorbed on graphite is determined with D=3.9 \cdot 10^{-8}~\mbox{m}^2 /\mbox{s} at 94 K

Determination of Conformational Entropy of Fully and Partially Folded Conformations of Holo- and Apomyoglobin

Holo- and apomyoglobin can be stabilized in native folded, partially folded molten globules (MGs) and denatured states depending on the solvent composition. Although the protein has been studied as a model system in the field of protein folding, little is known about the internal dynamics of the different structural conformations on the picosecond time scale. In a comparative experimental study we investigated the correlation between protein folding and dynamics on the picosecond time scale using incoherent quasielastic neutron scattering (QENS). The measured mean square displacements (MSDs) of conformational motions depend significantly on the secondary structure content of the protein, whereas the correlation times of the observed internal dynamics were found to be similar irrespective of the degree of folding. The conformational entropy difference Δ<i>S</i>_<i>conf</i> between the folded conformations and the acid denatured state could be determined from the measured MSDs and was compared to the entropy difference Δ<i>S</i> obtained from thermodynamic parameters reported in the literature. The observed difference between Δ<i>S</i> and Δ<i>S</i>_<i>conf</i> was attributed to the entropy difference Δ<i>S</i>_<i>hydr</i> of dynamically disordered water molecules of the hydration shell. The entropy content of the hydration water is significantly larger in the native folded proteins than in the partially folded MGs. We demonstrate the potential of incoherent neutron scattering for the investigation of the role of conformational dynamics in protein folding

A quasielastic neutron scattering investigation on the molecular self-dynamics of human myelin protein P2

Abstract The human myelin protein P2 is a membrane binding protein believed to maintain correct lipid composition and organization in peripheral nerve myelin. Its function is related to its ability to stack membranes, and this function can be enhanced by the P38G mutation, whereby the overall protein structure does not change but the molecular dynamics increase. Mutations in P2 are linked to human peripheral neuropathy. Here, the dynamics of wild-type P2 and the P38G variant were studied using quasielastic neutron scattering on time scales from 10 ps to 1 ns at 300 K. The results suggest that the mutant protein dynamics are increased on both the fastest and the slowest measured time scales, by increasing the dynamics amplitude and/or the portion of atoms participating in the movement

Time-of-flight neutron spectroscopy: a new application of aerodynamic sample levitation

A new version of a laser-heated aerodynamic levitation apparatus that enables the study of high temperature liquids by neutron spectroscopy is presented. This levitator was developed to be used on the IN6 neutron TimeOf-Flight (TOF) spectrometer at the European High Flux Neutron Source of the Institute Laue Langevin (ILL) in Grenoble, France. This device overcomes earlier restrictions to small sample sizes as routinely used for neutron diffraction studies on levitated liquids at high temperature, and makes other improvements in signal-to-noise ratio. A factor of more than three increase in sample volume in combination with the high flux and low background instrument IN6 makes quasielastic neutron scattering (QENS) studies on levitated molten oxides feasible. Here, we present results of a first QENS experiment towards the study of the relaxation dynamics of a molten CaO-Al2O3 sample. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

The “Protein Dynamical Transition” Does Not Require the Protein Polypeptide Chain

We give experimental evidence that the main features of protein dynamics revealed by neutron scattering, i.e., the “protein dynamical transition” and the “boson peak”, do not need the protein polypeptide chain. We show that a rapid increase of hydrogen atoms fluctuations at about 220 K, analogous to the one observed in hydrated myoglobin powders, is also observed in a hydrated amino acids mixture with the chemical composition of myoglobin but lacking the polypeptide chain; in agreement with the protein behavior, the transition is abolished in the dry mixture. Further, an excess of low-frequency vibrational modes around 3 meV, typically observed in protein powders, is also observed in our mixture. Our results confirm that the dynamical transition is a water-driven onset and indicate that it mainly involves the amino acid side chains. Taking together the present data and recent results on the dynamics of a protein in denatured conformation and on the activity of dehydrated proteins, it can be concluded that the “protein dynamical transition” is neither a necessary nor a sufficient condition for active protein conformation and function

Energy landscapes of human acetylcholinesterase and its huperzine A-inhibited counterpart

Enzymes are animated by a hierarchy of motions occurring on time scales that span more than 15 orders of magnitude from femtoseconds (10-15 s) to several minutes. As a consequence, an enzyme is characterized by a large number of conformations, so-called conformational substates that interconvert via molecular motions. The energy landscapes of these macromolecules are very complex, and many conformations are separated by only small energy barriers. Movements at this level are fast thermal atomic motions occurring on a time scale between 10-7 and 10-12 s, which are experimentally accessible by incoherent neutron scattering techniques. They correspond to local fluctuations within the molecule and are believed to act as coupling links for larger, conformational changes. Several questions related to this hierarchy of motions are a matter of very active research: which of the motions are involved in the biological functions of the macromolecule and are motions of different energy (and thus time) scale correlated? How does the distribution of motions change when an enzyme is inhibited? We report here on investigations of the enzyme human acetylcholinesterase, unliganded and in complex with the noncovalent inhibitor Huperzine A, by incoherent neutron scattering. Different time scales are explored to shed light on the interplay of enzyme activity, dynamics, and inhibition. Surprisingly the average molecular dynamics do not seem to be altered by the presence of the inhibitor used in this study within the considered time scales. The activation energy for the free and the inhibited form of the enzyme is moreover found to be almost identical despite changes of interactions inside the gorge, which leads to the active site of the enzyme

Raman and Infrared spectroscopies and X-ray diffraction data on bupivacaine and ropivacaine complexed with 2-hydroxypropyl−β−cyclodextrin

The data presented in this article are related to the research article entitled “Probing the dynamics of complexed local anesthetics via neutron scattering spectroscopy and DFT calculations (http://dx.doi.org/10.1016/j.ijpharm.2017.03.051)” (Martins et al., 2017) [1]. This work shows the molecular and structural behavior of the local anesthetics (LAs) bupivacaine (BVC, C18H28N2O) and ropivacaine (RVC, C17H26N2O) before and after complexation with the water-soluble oligosaccharide 2-hydroxypropyl−β−cyclodextrin (HP-β-CD)