The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python

There are very few reactions the rate of which can be measured both in the gaseous state and in solution. Several bimolecular reactions have been investigated in solution, and since the rate of a bimolecular gas reaction can be calculated from the equation Ink = In Z — E/RT, where E is heat of activation and Z the collision number, the rate of reaction in solution can be compared with that of the hypothetical corresponding gas reaction. The observed velocity constants in solution have usually been found to be smaller by several powers of 10 than the calculated values. On the other hand, as shown in the previous paper, in the one example where direct comparison has been possible, namely, the decomposition of chlorine monoxide, the rate in solution in carbon tetrachloride is the same as that in the gas phase. Thus it is evident that the retardation of reactions by certain solvents is a specific action and need not occur in an “ideal” solvent. The rates of unimolecular gas reactions cannot be calculated, and direct comparison has hitherto been possible only in two examples. The equation Ink = 31•69 — 24,710/RT has been found to represent the rate of decomposition of nitrogen pentoxide in the gaseous state and in a series of eight similar, chemically rather inert, solvents. In nitric acid or in propylene dichloride, however, In Z increases by several units and E becomes 28,300 calories. Daniels regards as “normal” those solvents which do not produce an alteration in E, and as “abnormal” those which cause a deviation from the value characteristic of the gaseous state. The solvents in which the decomposition of nitrogen pentoxide could be studied were naturally not very varied in character, since most liquids would be attacked chemically. Thus the impression which the results tend to convey, namely, that “normal” or "ideal" behaviour is more common with unimolecular reactions than with bimolecular reactions, may be an illusory one. In the only other known example, the isomerisation of pinene, the rate of reaction in the gas, in the liquid, and in carbon tetrachloride is the same.

Extracellular, Membrane and Intracellular Proteins that Alter Integrin Cell Membrane Diffusion and Clustering

Extracellular, Membrane and Intracellular Proteins that Alter Integrin Cell Membrane Diffusion and Clustering

In general the rate of a chemical reaction is profoundly influenced by the solvent in which the reaction takes place. In Menschutkin’s experiments on the combination of tertiary amines and alkyl halides, for example, the reaction velocity in benzyl alcohol was several hundred times greater than that in hexane. While it is clear that the influence of the solvent, which cannot be correlated definitely with any physical properties, belongs to the category of specific chemical effects, it is not easy to see in exactly what it consists. Christiansen and Norrish and Smith have found that the rate of a bimolecular reaction in solution appears usually to be several powers of 10 smaller than that of a hypothetical reaction occurring in the gaseous phase with the same energy of activation. Norrish and Smith therefore suggest that, since each encounter between molecules of the reacting substances takes place with a solvent molecule in very close proximity, and is thus virtually a ternary collision, the influence of the solvent is primarily a deactivating one. On the other hand, the decomposition of nitrogen pentoxide—a unimolecular reaction—takes place at the same rate and possesses the same heat of activation in chloroform, in carbon tetrachloride and a number of similar solvents as it does in the gaseous phase. In certain other solvents, quite different rates and heats of activation are found. Daniels regards as “normal” those solvents in which the reaction occurs at the same rate as in the gaseous phase, and attributes the deviations found with other, “abnormal,” solvents to a definite formation of complex molecules whose stability differ from that of free nitrogen pentoxide. The isomerisation of pinene has also been found to take place at the same rate in the gaseous and in the liquid states. As far as this not very abundant evidence goes, then, it would suggest that bimolecular reactions are usually much slower in solution than in the gaseous phase, while unimolecular reactions tend usually to be uninfluenced by the presence of the solvent. This simple contrast, however, is by no means correct. In the first place, the variation in the rates of unimolecular reactions with change of solvent appears on closer inspection to be not less marked than that of bimolecular reactions. This aspect of the matter is dealt with more fully in the following paper. In the second place, there have hitherto been no data available for comparing the rate of a bimolecular reaction in the gas phase with its rate in solution in one of the relatively inert solvents which had been used for nitrogen pentoxide. It is shown in the present paper, however, that the decomposition of chlorine monoxide, which is essentially bimolecular, although somewhat complex in mechanism, occurs at almost exactly the same rate in carbon tetrachloride as in the gaseous state, and that the heat of activation is substantially the same. Thus it appears that, contrary to first impressions, the kinetic type of the reaction has little to do with the influence of solvents. The chemical nature of the solvent is the determining factor in all cases. Both for bimolecular and unimolecular reactions there appear to exist “ideal” solvents, of which carbon tetrachloride is a good example. This is being confirmed by Mr. Bowen and the writers by measurements on the rate of decomposition of ozone in carbon tetrachloride solution. For reactions that cannot be made to take place in the gas phase at all, and this includes the majority of measurable reactions, the rate in carbon tetrachloride or an analogous solvent would then appear to be a standard or ideal rate equal to that which the gas reaction would possess. Comparison of the rate and the energy of activation of a given reaction in any solvent with the corresponding values for the reaction in carbon tetrachloride thus provides a means of ascertaining whether the solvent has increased or decreased the normal heat of activation, and whether its effect is to be regarded as deactivating or positively catalytic. The similarity of behaviour of chlorine monoxide in the gaseous phase and in carbon tetrachloride solution suggests that, for bimolecular as well as for unimolecular reactions, solvents must be divided into two classes, and that the deactivating influences postulated by Norrish and Smith are as specific as the influence of “abnormal” solvents on unimolecular reactions.

The Impact of Gene Expression Regulation on Evolution of Extracellular Signaling Pathways

Unimolecular and bimolecular reactions in the C 6H 6+· system. Experiment and theory

Theoretical studies of the decomposition mechanism of energetic materials quite often scrutinize only the primary thermolysis reactions. However, the secondary reactions are crucial, inter alia, for proper building of the combustion models and understanding the autocatalytic processes. In the present study, we applied predictive DLPNO-CCSD(T) calculations to elucidate the kinetics and decomposition mechanism of a novel promising energetic material, 1,3,4,6-tetranitrooctahydroimidazo [4,5-d] imidazole (BCHMX). We identified eight previously unknown BCHMX conformers, both cis and trans in accordance to the spatial position of the H atoms bonded to a carbon bridge. Among them, the relative enthalpies of cis isomers lie in the narrow range ∼10 kJ mol-1 rendering them thermally accessible in the course of decomposition. The radical N-NO2 bond cleavage via one of the novel conformers is the dominant primary decomposition channel of BCHMX with the kinetic parameters Ea = 168.4 kJ mol-1 and log(A, s-1) = 18.5. We also resolved several contradictory assumptions on the mechanism and key intermediates of BCHMX thermolysis. To get a deeper understanding of the decomposition mechanism, we examined a series of unimolecular and bimolecular secondary channels of BCHMX. Among the former reactions, the C-C bond unzipping followed by another radical elimination of a nitro group is the most energetically favorable pathway with an activation barrier ∼113 kJ mol-1. However, contrary to the literature assumptions, the bimolecular H atom abstraction from a pristine BCHMX molecule by a primary nitramine radical product, not the nitro one, followed by another NO2 radical elimination, is the most important bimolecular secondary thermolysis reaction of BCHMX at lower temperatures. The isokinetic temperature of the bimolecular and unimolecular secondary reactions is ∼620 K. Unimolecular reactions might be important in dilute solutions, where bimolecular reactions are suppressed. The secondary reactions considered in the present work might be pertinent in the case of related energetic nitramines (e.g., RDX, HMX, and CL-20).

Polyrate 2023: A computer program for the calculation of chemical reaction rates for polyatomics. New version announcement

The recent sequencing of entire eukaryotic genomes revealed a great number of open reading frames (ORFs), most of which potentially code for proteins of unknown function. Identifying interaction partners may facilitate the functional characterisation of unknown gene products. Moreover, large-scale approaches to identify protein interactions may be used to untangle the complete interaction network of all the gene products expressed in a given organism, the so-called interactome. Currently, the yeast two-hybrid system is the most widely used genetic assay for large-scale detection of protein – protein interactions and it has successfully been applied to map the interactome of several organisms. However, since interactions in this system are detected in the nuclear environment, it does not account for the particular biochemical requirements of extracellular and integral membrane proteins. In the first part of this thesis, I describe a novel genetic growth selection system to detect interactions between extracellular and transmembrane proteins in a topologically extracellular compartment of Saccharomyces cerevisiae. In this system the proteins of interest are expressed as fusions to mutually complementing mutant derivatives of the yeast ER resident transmembrane receptor Ire1p. Interaction between the proteins of interest causes dimerisation of the Ire1p moieties allowing for complementation and activation of Ire1p. Active Ire1p in turn triggers a signalling cascade, which induces expression of selectable reporter genes in the nucleus and promotes growth under selective conditions. The feasibility of this system to monitor interactions between extracellular proteins was demonstrated by specific pairings of epitope and single-chain Fv (scFv) antibody fragments. In part two, I describe the application of this system in a screening procedure to select scFv antibody fragments that specifically bind to human Interleukin-13 (hIL13). In a first round, hIL-13 binders were selected from a scFv-antibody library by yeast growth under selective conditions. In order to improve their binding affinity, parts of the scFv fragments obtained from the primary screening were randomised by homologous recombination in yeast and subjected to growth selection under increased selective conditions.

In order to map the extracellular or membrane proteome associated with the vasculature and the stroma in an embryonic organism in vivo, we developed a biotinylation technique for chicken embryo and combined it with mass spectrometry and bioinformatic analysis. We also applied this procedure to implanted tumors growing on the chorioallantoic membrane or after the induction of granulation tissue. Membrane and extracellular matrix proteins were the most abundant components identified. Relative quantitative analysis revealed differential protein expression patterns in several tissues. Through a bioinformatic approach, we determined endothelial cell protein expression signatures, which allowed us to identify several proteins not yet reported to be associated with endothelial cells or the vasculature. This is the first study reported so far that applies in vivo biotinylation, in combination with robust label-free quantitative proteomics approaches and bioinformatic analysis, to an embryonic organism. It also provides the first description of the vascular and matrix proteome of the embryo that might constitute the starting point for further developments.

Proteomic identification of protein interactions with membrane associated molecules in their native membrane environment pose a challenge because of technical problems of membrane handling. We investigate the possibility of employing membrane nanodiscs for harboring the membrane associated molecule to tackle the challenges. Nanodiscs are stable, homogenous pieces of membrane with a discoidal shape. They are stabilized by an encircling amphipatic protein with an engineered epitope tag. In the present study we employ the epitope tag of the nanodiscs for detection and co-immunoprecipitation of interaction partners of the glycolipid ganglioside GM1 harbored by nanodiscs. Highly specific binding activity for nanodisc-GM1 immobilized on sensorchips was observed by surface plasmon resonance in culture media from enterotoxigenic Escherischia coli. To isolate the interaction partner(s) from enterotoxigenic Escherischia coli, GM1-nanodiscs were employed for co-immunoprecipitation. The B subunit of heat labile enterotoxin was identified as a specific interaction partner by mass spectrometry, thus demonstrating that nanodisc technology is useful for highly specific detection and identification of interaction partners to specific lipids embedded in a membrane bilayer.

Extracellular and membrane-associated proteins play essential roles in nearly all our body's biochemical processes and are implicated in cancer, autoimmune disorders, and neurodegenerative diseases. Consequently, a selective and universally applicable technique for the degradation of these proteins in disease-relevant conditions could significantly improve human health prospects. Lysosome-targeting chimeras (LYTACs) are bifunctional degraders comprising of an antibody conjugated with a cell-surface receptor ligand that enables cargo lysosome shuttling and degradation. Herein, we demonstrate that conjugation of antibodies with a small ketoboronate-based, lysine-reactive, covalent-reversible uptake tag (KB) enables the internalization of plasma membrane and extracellular proteins, directing them to lysosomal degradation via receptor-mediated endocytosis. Chemoproteomic target deconvolution revealed that reversible modification of lysine residues on the transferrin receptor protein 1 (TFRC) and HLA class I histocompatibility antigen A, B and C (HLA-ABC) enabled efficient uptake and lysosomal targeting through both clathrin-dependent and -independent mechanisms. KB-antibody conjugates (KB-TACs) efficiently degrade the epidermal growth factor receptor (EGFR), vascular endothelial growth factor A (VEGFA) and epidermal growth factor receptor 2 (HER2) in cancer cells. Furthermore, we showed KB-TTZ degrades HER2 in vivo in BT-474 tumor xenografts, with a significant reduction in tumor volumes compared to TTZ and vehicle treatments. Altogether, the KB tag represents a versatile, minimal-size chemical unit to functionalize therapeutic antibodies for targeted protein degradation through dual receptor-mediated endocytosis and lysosomal delivery.

BackgroundIn bacterial pathogens, both cell surface-exposed outer membrane proteins and proteins secreted into the extracellular environment play crucial roles in host-pathogen interaction and pathogenesis. Considerable efforts have been made to identify outer membrane (OM) and extracellular (EX) proteins produced by Leptospira interrogans, which may be used as novel targets for the development of infection markers and leptospirosis vaccines.ResultIn this study we used a novel computational framework based on combined prediction methods with deduction concept to identify putative OM and EX proteins encoded by the Leptospira interrogans genome. The framework consists of the following steps: (1) identifying proteins homologous to known proteins in subcellular localization databases derived from the "consensus vote" of computational predictions, (2) incorporating homology based search and structural information to enhance gene annotation and functional identification to infer the specific structural characters and localizations, and (3) developing a specific classifier for cytoplasmic proteins (CP) and cytoplasmic membrane proteins (CM) using Linear discriminant analysis (LDA). We have identified 114 putative EX and 63 putative OM proteins, of which 41% are conserved or hypothetical proteins containing sequence and/or protein folding structures similar to those of known EX and OM proteins.ConclusionOverall results derived from the combined computational analysis correlate with the available experimental evidence. This is the most extensive in silico protein subcellular localization identification to date for Leptospira interrogans serovar Lai genome that may be useful in protein annotation, discovery of novel genes and understanding the biology of Leptospira.

Condensed-phase alkoxy (RO) radicals can undergo unimolecular (e.g., intramolecular H atom abstraction) reactions as well as bimolecular (intermolecular H atom abstraction) reactions, though the competition between these two channels is not well constrained. Here, we examine this branching by generating RO radicals from the photolysis of a large alkyl nitrite (C20H41ONO) in hexanes and nebulizing the mixture into an aerosol mass spectrometer for analysis. Product ions associated with unimolecular (isomerization) reactions were observed to increase upon photolysis. However, no formation of the C20 alcohol (C20H41OH, the expected product from RO + RH reactions) was observed, suggesting that bimolecular reactions are at most a minor channel for this condensed-phase system (involving saturated hydrocarbons). This result, combined with previous studies of liquid-phase RO radicals carried out at higher concentrations, suggests that when 1,5-H atom abstraction reactions are facile (i.e., in which a 1,5-H atom shift from a secondary or tertiary carbon can occur), this channel will dominate over bimolecular reactions.

Role of transalkylation reactions in the conversion of anisole over HZSM-5