Imaging conformations of holo- and apo-transferrin on the single-molecule level by low-energy electron holography

Conformational changes play a key role in the biological function of many proteins, thereby sustaining a multitude of processes essential to life. Thus, the imaging of the conformational space of proteins exhibiting such conformational changes is of great interest. Low-energy electron holography (LEEH) in combination with native electrospray ion beam deposition (ES-IBD) has recently been demonstrated to be capable of exploring the conformational space of conformationally highly variable proteins on the single-molecule level. While the previously studied conformations were induced by changes in environment, it is of relevance to assess the performance of this imaging method when applied to protein conformations inherently tied to a function-related conformational change. We show that LEEH imaging can distinguish different conformations of transferrin, the major iron transport protein in many organisms, by resolving a nanometer-scale cleft in the structure of the iron-free molecule (apo-transferrin) resulting from the conformational change associated with the iron binding/release process. This, along with a statistical analysis of the data, which evidences a degree of flexibility of the molecules, indicates that LEEH is a viable technique for imaging function-related conformational changes in individual proteins.

Landing Proteins on Graphene Trampoline Preserves Their Gas-Phase Folding on the Surface

Molecule-surface collisions are known to initiate dynamics that lead to products inaccessible by thermal chemistry. These collision dynamics, however, have mostly been examined on bulk surfaces, leaving vast opportunities unexplored for molecular collisions on nanostructures, especially on those that exhibit mechanical properties radically different from those of their bulk counterparts. Probing energy-dependent dynamics on nanostructures, particularly for large molecules, has been challenging due to their fast time scales and high structural complexity. Here, by examining the dynamics of a protein impinging on a freestanding, single-atom-thick membrane, we discover molecule-on-trampoline dynamics that disperse the collision impact away from the incident protein within a few picoseconds. As a result, our experiments and ab initio calculations show that cytochrome c retains its gas-phase folded structure when it collides onto freestanding single-layer graphene at low energies (∼20 meV/atom). The molecule-on-trampoline dynamics, expected to be operative on many freestanding atomic membranes, enable reliable means to transfer gas-phase macromolecular structures onto freestanding surfaces for their single-molecule imaging, complementing many bioanalytical techniques.

Phase Reconstruction of Low-Energy Electron Holograms of Individual Proteins

Low-energy electron holography (LEEH) is one of the few techniques capable of imaging large and complex three-dimensional molecules, such as proteins, on the single-molecule level at subnanometer resolution. During the imaging process, the structural information about the object is recorded both in the amplitude and in the phase of the hologram. In low-energy electron holography imaging of proteins, the object's amplitude distribution, which directly reveals molecular size and shape on the single-molecule level, can be retrieved via a one-step reconstruction process. However, such a one-step reconstruction routine cannot directly recover the phase information encoded in the hologram. In order to extract the full information about the imaged molecules, we thus implemented an iterative phase retrieval algorithm and applied it to experimentally acquired low-energy electron holograms, reconstructing the phase shift induced by the protein along with the amplitude data. We show that phase imaging can map the projected atomic density of the molecule given by the number of atoms in the electron path. This directly implies a correlation between reconstructed phase shift and projected mean inner potential of the molecule, and thus a sensitivity to local changes in potential, an interpretation that is further substantiated by the strong phase signatures induced by localized charges.

Catalyzing Bond-Dissociation in Graphene via Alkali-Iodide Molecules

Atomic design of a 2D-material such as graphene can be substantially influenced by etching, deliberately induced in a transmission electron microscope. It is achieved primarily by overcoming the threshold energy for defect formation by controlling the kinetic energy and current density of the fast electrons. Recent studies have demonstrated that the presence of certain species of atoms can catalyze atomic bond dissociation processes under the electron beam by reducing their threshold energy. Most of the reported catalytic atom species are single atoms, which have strong interaction with single-layer graphene (SLG). Yet, no such behavior has been reported for molecular species. This work shows by experimentally comparing the interaction of alkali and halide species separately and conjointly with SLG, that in the presence of electron irradiation, etching of SLG is drastically enhanced by the simultaneous presence of alkali and iodine atoms. Density functional theory and first principles molecular dynamics calculations reveal that due to charge-transfer phenomena the CC bonds weaken close to the alkali-iodide species, which increases the carbon displacement cross-section. This study ascribes pronounced etching activity observed in SLG to the catalytic behavior of the alkali-iodide species in the presence of electron irradiation.

Substrate-Selective Morphology of Cesium Iodide Clusters on Graphene

Formation and characterization of low-dimensional nanostructures is crucial for controlling the properties of two-dimensional (2D) materials such as graphene. Here, we study the structure of low-dimensional adsorbates of cesium iodide (CsI) on free-standing graphene using aberration-corrected transmission electron microscopy at atomic resolution. CsI is deposited onto graphene as charged clusters by electrospray ion-beam deposition. The interaction with the electron beam forms two-dimensional CsI crystals only on bilayer graphene, while CsI clusters consisting of 4, 6, 7, and 8 ions are exclusively observed on single-layer graphene. Chemical characterization by electron energy-loss spectroscopy imaging and precise structural measurements evidence the possible influence of charge transfer on the structure formation of the CsI clusters and layers, leading to different distances of the Cs and I to the graphene.

Interaction of pH-responsive polyanions with phospholipid membranes

The behavior of two acrylate polymers, with carboxylic acid side groups, was investigated with regard to their pH-responsive interaction with phospholipid membranes.

Clinical and sensorimotor gating effects of ketamine in normals

The clinical similarities between PCP psychosis and schizophrenia have contributed importantly to the development of the glutamate hypothesis of schizophrenia. Sensory gating, as measured by prepulse inhibition of the acoustic startle reflex (PPI), is impaired in patients with schizophrenia. In animals, the noncompetitive NMDA antagonists PCP and ketamine disrupt PPI in a way that resembles the defect seen in schizophrenia. The purpose of this work is to investigate the modulation of sensory gating in humans by subanaesthetic doses of ketamine. 16 healthy male subjects received a 60-min infusion of ketamine (0.5 mg/kg) or normal saline on two separate days in a randomized double-blind crossover design. Clinical ratings and PPI were done during the infusion on both days. Ketamine produced robust clinical effects. Dissociative symptoms as measured by the CADSS increased from 0 +/- 0.0 to 29.3 +/- 14.3; negative symptoms (Affect Rating Scale) increased from 17.2 +/- 0.8 to 24.8 +/- 3.1; and total BPRS scores increased from 18.3 +/- 0.8 to 26.4 +/- 5.1. ANOVAs for these ratings were all significant at the p <.000 level, although BPRS increases were not in the range seen in decompensated schizophrenic patients. The amplitudes of the startle responses to pulse-alone stimuli were not significantly different on ketamine and placebo days. Ketamine did not cause disruption in PPI as expected. On the contrary, in the first block of the PPI session ketamine significantly enhanced PPI (ANOVA; F=6.15, p =.026). These results indicate that the clinical effects of ketamine are not coupled with schizophrenic-like disruption of PPI in normal controls.

Effects of smoking on acoustic startle and prepulse inhibition in humans

RATIONALE

Prepulse inhibition of the acoustic startle response (PPI) is a paradigm in which a startle response to an auditory stimulus is reduced when that stimulus is preceded by a lower intensity, non-startling stimulus (prepulse). PPI is used as an operational measure of sensorimotor gating in both humans and other mammals. Acute administration of nicotine enhances PPI in rats, an effect that has been recently demonstrated in humans.

OBJECTIVES

We compared PPI in 12 male smokers and 14 male non-smokers tested in four repeat startle sessions across 2 test days in order to examine further the effects of smoking and smoking withdrawal on acoustic startle and PPI.

METHODS

In a crossover design, the smokers smoked ad lib or abstained from smoking overnight prior to 9 a.m. testing. These 2 test days were in randomized order. On both days, smokers were immediately retested after smoking three cigarettes. Non-smokers were tested twice on each of 2 separate days.

RESULTS

Across sessions, the smokers had reduced startle to pulse alone stimuli in the first block of each session when compared to the non-smokers. The non-smokers had no change in gating across their four test sessions. For the smokers, the abstinence condition produced a non-significant reduction in PPI compared to that of the ad lib smoking day. During the smoking abstinence session, smokers had comparable gating to non-smokers. Smoking immediately after washout produced a significant improvement in PPI such that gating in the smokers exceeded that of the non-smokers.

CONCLUSION

Smoking after overnight washout from cigarettes enhanced sensorimotor gating compared to pre-smoking values and compared to gating in non-smokers.

Vinyl ether hydrolysis. XVII. Oxacyclonon-2,8-diene and the question of the unorthodox reaction mechanism for 9-methoxyoxacyclonon-2-ene

The acid-catalyzed hydrolysis of the nine-membered ring cyclic vinyl ether, oxacyclonon-2,8-diene, occurs with a normal isotope effect, [Formula: see text], which indicates that this reaction proceeds by the conventional vinyl ether hydrolysis mechanism involving rate-determining proton transfer to carbon. The specific rate of this reaction, [Formula: see text], may then be used to show that there is no significant ring-size effect on the rate of hydrolysis of a vinyl ether group in a nine-membered ring. The previously noted unusually great reactivity of the vinyl ether group in 9-methoxyoxacyclonon-2-ene, for which an unorthodox reaction mechanism has been claimed, must therefore be due to some other cause.

Vinyl ether hydrolysis. XIII. The failure of I-strain to produce a change in rate-determining step

Rates of hydrolysis of 1-ethoxy-3,3,5,5-tetramethylcyclopentene and 1-methoxy-2,3,3,5,5-pentamethylcyclopentene measured in mineral acid and formic and acetic acid buffer solutions show general acid catalysis and give large kinetic isotope effects in the normal direction (kH/kD > 1). This indicates that these reactions proceed by the conventional mechanism for vinyl ether hydrolysis in which proton transfer from the catalyzing acid to the substrate is rate-determining, and that the I-strain in these substrates is insufficiently great to shift the reaction mechanism to rapidly reversible substrate protonation followed by rate-determining hydration of the ensuing cationic intermediate.