Homochiral or Heterochiral: A Systematic Study of Threonine Clusters Using a FT ICR Mass Spectrometer

The strong chiral preferences of some magic clusters of amino acids have attracted continually increasing interests due to their unique structures, properties and possible roles in homochirogenesis. However, how chirality can influence the generation and stability of cluster ions in a wild range of cluster sizes is still unknown for most amino acids. In this study, the preference for threonine clusters to form homochiral and heterochiral complex ions has been investigated by electrospray ionization (ESI) mass spectrometry. Abundant cluster [Thrn+mH]m+ ions (7 ≤ n ≤ 78, 1 ≤ m ≤ 5) have been observed for both samples of enantiopure (100% L) and racemic (50:50 L:D) threonine solutions. Further analyses of the spectra show that the [Thr14+2H]2+ ion is characterized by its most outstanding homochiral preference, and [Thr7+H]+ and [Thr8+H]+ ions also clearly exhibit their homochiral preferences. Although most of the triply charged clusters (20 ≤ n ≤ 36) are characterized by heterochiral preferences, the quadruply charged [Thrn+4H]4+ ions (40 ≤ n ≤ 59) have no obvious chiral preference in general. On the other hand, a weak homochiral preference exists for most of the quintuply charged ions observed in the experiment.

A study on the fragmentation of sulfuric acid and dimethylamine clusters inside an atmospheric pressure interface time-of-flight mass spectrometer

Sulfuric acid and dimethylamine vapours in the atmosphere can form molecular clusters, which participate in new particle formation events. In this work, we have produced, measured, and identified clusters of sulfuric acid and dimethylamine using an electrospray ionizer coupled with a planar-differential mobility analyser, connected to an atmospheric pressure interface time-of-flight mass spectrometer (ESI–DMA–APi-TOF MS). This set-up is suitable for evaluating the extent of fragmentation of the charged clusters inside the instrument. We evaluated the fragmentation of 11 negatively charged clusters both experimentally and using a statistical model based on quantum chemical data. The results allowed us to quantify the fragmentation of the studied clusters and to reconstruct the mass spectrum by removing the artifacts due to the fragmentation.

Electrostatic Forces Mediate the Specificity of RHO GTPase-GDI Interactions

Three decades of research have documented the spatiotemporal dynamics of RHO family GTPase membrane extraction regulated by guanine nucleotide dissociation inhibitors (GDIs), but the interplay of the kinetic mechanism and structural specificity of these interactions is as yet unresolved. To address this, we reconstituted the GDI-controlled spatial segregation of geranylgeranylated RHO protein RAC1 in vitro. Various biochemical and biophysical measurements provided unprecedented mechanistic details for GDI function with respect to RHO protein dynamics. We determined that membrane extraction of RHO GTPases by GDI occurs via a 3-step mechanism: (1) GDI non-specifically associates with the switch regions of the RHO GTPases; (2) an electrostatic switch determines the interaction specificity between the C-terminal polybasic region of RHO GTPases and two distinct negatively-charged clusters of GDI1; (3) a non-specific displacement of geranylgeranyl moiety from the membrane sequesters it into a hydrophobic cleft, effectively shielding it from the aqueous milieu. This study substantially extends the model for the mechanism of GDI-regulated RHO GTPase extraction from the membrane, and could have implications for clinical studies and drug development.

Tracks on films and multi-charged clusters

When conducting experiments on the electric explosion of titanium foil in water, a “strange” radiation was detected, leaving dotted traces on the film. The velocity of the carriers of this radiation was estimated as 20–40 m/s, and their energy, estimated by the Coulomb drag mechanism, turned out to be equal to 700 MeV. Subsequently, it was found that similar traces are formed at various types of high-current arc discharges, both of artificial and natural origin. Many solutions have been proposed to explain the nature of “strange” radiation, but none of them describes the details of the process of formation of dotted traces. We believe that these traces on the film could appear due to the action of charged micron-sized clusters. The possibility of the existence of clusters in the form of a nucleus from a certain number of similarly charged ions enclosed in a spherical shell of water molecules is shown. The force of the Coulomb repulsion of ions is compensated by the compression force of the shell polarized by the inhomogeneous electric field created by the nuclear charge. As the cluster approaches the surface of the film, a cluster with a small charge separates from it. It is accelerated in the electric field of a “large” cluster to energy of about 1 GeV. Having received a recoil momentum, a large cluster moves away from the film, braking in an inhomogeneous electric field, and then “falls” onto it again, and the process is repeated.

A study on the fragmentation of sulfuric acid and dimethylamine clusters inside an Atmospheric Pressure interface Time Of Flight Mass Spectrometer

Sulfuric acid and dimethylamine vapours in the atmosphere can form molecular clusters, which participate in new particle formation events. In this work, we have produced, measured and identified clusters of sulfuric acid and dimethylamine using an electrospray ionizer coupled with a planar differential mobility analyser, connected to an atmospheric pressure interface time-of-flight mass spectrometer (ESI–DMA–APi-TOF MS). This set-up is suitable for evaluating the extent of fragmentation of the charged clusters inside the instrument. We evaluated the fragmentation of 11 negatively charged clusters both experimentally and using a statistical model based on quantum chemical data. The results allowed us to quantify the fragmentation of the studied clusters and to reconstruct the mass spectrum removing the artifacts due to the fragmentation.

New Particle Formation Involving Charged Sulfuric Acid – Ammonia Clusters

<div> <p>The bulk of aerosol particles in the atmosphere are formed by gas-to-particle nucleation (Merikanto et al., 2009). However, the exact process of single molecules forming cluster, which subsequently can grow into particles, remains largely unknown. Recently, sulfuric acid has been identified to play a key role in this new particle formation enhanced by other compounds such as organic acids (Zhang, 2010) or ammonia (Anttila et al., 2005). To identify the characteristics of cluster formation and nucleation involving sulfuric acid and ammonia in neutral, positive and negative modes, we conducted a computational study. We used a layered approach for configurational sampling of the molecular clusters starting from utilizing a genetic algorithm in order to explore the whole potential energy surface (PES) with all plausible geometrical minima, however, with very unreliable energies. The structures were further optimized with a semi-empirical method and, then, at the ωB97X-D DFT level of theory. After each step, the optimized geometries were filtered to obtain the global minimum configuration. Further, a high level of theory (DLPNO-CCSD(T)) was used for obtaining the electronic energies, in addition to performing DFT frequency analysis, to calculate the Gibbs free energies of formation. These were passed to the Atmospheric Cluster Dynamics Code (ACDC) (McGrath et al., 2012) for studying the evolution of cluster populations. We determined the global minima for the following sulfuric acid - ammonia clusters: (H<sub>2</sub>SO<sub>4</sub>)<sub>m</sub>(NH<sub>3</sub>)<sub>n</sub> with m=n, m=n+1 and n=m+1 for neutral clusters, (H<sub>2</sub>SO<sub>4</sub>)<sub>m</sub>(HSO<sub>4</sub>)<sup>−</sup>(NH<sub>3</sub>)<sub>n</sub> with m=n and n=m+1 for positively charged clusters, and (H<sub>2</sub>SO<sub>4</sub>)<sub>m</sub>(NH<sub>4</sub>)<sup>+</sup>(NH<sub>3</sub>)<sub>n</sub> with m=n and m=n+1 for negatively charged clusters. Further, we present the formation rates, steady state concentrations and fluxes of these clusters calculated using ACDC and discuss how a new configurational sampling procedure, more precise quantum chemistry methods and parameters, such as symmetry and a quasiharmonic approach, impact these ACDC results in comparison to previous studies.</p> </div><div> <p><em>References:<br></em><em>J. Merikanto, D. V. Spracklen, G. W. Mann, S. J. Pickering, and K. S. Carslaw (2009). Atmos. Chem.  Phys., 9, 8601-8616. <br>R. Zhang (2010). Science, 328, 1366-1367. <br>T. Anttila, H. Vehkamäki, I. Napari, M. Kulmala (2005). Boreal Env. Res., 10, 523. <br>M.J. McGrath, T. Olenius, I.K. Ortega, V. Loukonen, P.  Paasonen, T. Kurten, M. Kulmala (2012). Atmos. Chem. Phys., 12, 2355. <br></em></p> </div>

Revisiting the tellurium clusters (Ten; n = 2–8) using ab initio methods

The optimized geometries and vibrational frequencies of Te clusters n = 2–8 are calculated using ab initio molecular orbital theory at B3LYP, MP2, BLYP, and BH–HLYP levels of approximation. We found that Te8 (D4d) cluster has the highest stability followed by Te7 and Te6 (D3d). The computed vibrational frequencies have small systematic deviations with IR spectra for crystalline Te5, Te6 (C2v). The stability of positively and negatively charged Te clusters is determined by the B3LYP method. This is because the B3LYP method demonstrated the best stability in every cluster geometry. In general, the results showed that the negatively charged clusters have the highest stability, followed by neutral clusters, and finally positively charged clusters. However, the predicted bond angle and bond distance for every cluster geometry displayed very close values with different levels of calculations. These calculations will provide predictions for future experimental studies.

Record-high stability and compactness of multiply-charged clusters aided by selected terminal groups

Multiply-charged clusters with compact sizes that are stable in the gas phase are important due to their potential applications as weakly-coordinating ions and building blocks of bulk materials.

ER reorganization and intracellular retention of CD58 are functionally independent properties of the human cytomegalovirus ER resident glycoprotein UL148

ABSTRACTThe human cytomegalovirus (HCMV) endoplasmic reticulum (ER)-resident glycoprotein UL148 is posited to play roles in immune evasion and regulation of viral cell tropism. UL148 prevents cell surface presentation of the immune cell costimulatory ligand CD58 while promoting maturation and virion incorporation of glycoprotein O, a receptor binding subunit for an envelope glycoprotein complex involved in entry. Meanwhile, UL148 activates the unfolded protein response (UPR) and causes large-scale reorganization of the ER. In an effort to determine whether the seemingly disparate effects of UL148 are related or discrete, we generated charged-cluster-to-alanine (CCTA) mutants of six charged clusters within the UL148 ectodomain, and compared them against wildtype UL148, in the context of recombinant viruses and in ectopic expression, assaying for effects on ER remodeling and CD58 surface presentation. Two mutants, targeting charged clusters spanning residues 79-83 (CC3) and 133-136 (CC4), respectively, retained the potential to impede CD58 presentation, and did so to an extent comparable to wildtype. Of the six mutants, only CC3 retained the capacity to reorganize the ER, showing a partial phenotype. Wildtype UL148 accumulates in a detergent-insoluble form during infection. However, all six CCTA mutants were fully soluble, which may imply a relationship between insolubility and organelle remodeling. Additionally, we found that the chimpanzee cytomegalovirus UL148 homolog suppresses CD58 presentation but fails to reorganize the ER, while the homolog from rhesus cytomegalovirus shows neither activity. Collectively, our findings illustrate varying degrees of functional divergence between homologous primate cytomegalovirus immunevasins and suggest that ER reorganization is unique to HCMV UL148.IMPORTANCEIn myriad examples, viral gene products cause striking effects on cells, such as activation of stress responses. It can be challenging to decipher how such effects contribute to the biological roles of the proteins. The HCMV glycoprotein UL148 retains CD58 within the ER, thereby preventing it from reaching the cell surface where it functions to stimulate cell-mediated antiviral responses. Intriguingly, UL148 also triggers the formation of large, ER-derived membranous structures, and activates the UPR, a set of signaling pathways involved in adaptation to ER stress. We demonstrate that the potential of UL148 to reorganize the ER and to retain CD58 are separable by mutagenesis and possibly, by evolution, since chimpanzee cytomegalovirus UL148 retains CD58 but does not remodel the ER. Our findings imply that ER reorganization contributes to other roles of UL148, such as modulation of alternative viral glycoprotein complexes that govern the virus’ ability to infect different cell types.