Systematic investigation of the link between enzyme catalysis and cold adaptation

Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a dominant adaptive trait of enzymes to reduced temperature, and this expectation has informed physical models for enzyme catalysis and influenced bioprospecting strategies. To systematically test rate enhancement as an adaptive trait to cold, we paired kinetic constants of 2223 enzyme reactions with their organism’s optimal growth temperature (TGrowth) and analyzed trends of rate constants as a function of TGrowth. These data do not support a general increase in rate enhancement in cold adaptation. In the model enzyme ketosteroid isomerase (KSI), there is prior evidence for temperature adaptation from a change in an active site residue that results in a tradeoff between activity and stability. Nevertheless, we found that little of the rate constant variation for 20 KSI variants was accounted for by TGrowth. In contrast, and consistent with prior expectations, we observed a correlation between stability and TGrowth across 433 proteins. These results suggest that temperature exerts a weaker selection pressure on enzyme rate constants than stability and that evolutionary forces other than temperature are responsible for the majority of enzymatic rate constant variation.

Dynamics of small molecules within the F127 PEO-PPO-PEO triblock copolymer gel and sol phases studied at the molecular scale

The dynamics of naphthalene derivatives with different hydrophobicities bound to F127 polyethyleneoxide-polypropyleneoxide-polyethyleneoxide (PEO-PPO-PEO) micelles in the gel and sol phases were studied using a quenching methodology for the triplet excited states of the naphthalenes. Studies with triplet excited states probe a larger reaction volume than the volumes accessible when using fluorescent singlet excited states. The use of triplet excited states enables the determination of the dynamics between different compartments of a supramolecular system, which in the case of F127 micelles are the micellar core, the micellar corona and the aqueous phase. This report includes laser flash photolysis studies for the four naphthalene derivatives in the F127 gel and sol phases. The triplet excited states were quenched using the nitrite anion as the quenchers. The association and dissociation rate constants of the naphthalenes from the micelles and the quenching rate constants for the naphthalenes bound to the micelles were determines from the curved quenching plot (observed decay rate constant vs. nitrite concentration).

Simulation of Biochemical Reactions with ANN-Dependent Kinetic Parameter Extraction Method

The measurement of thermodynamic properties of chemical or biological reactions were often confined to experimental means, which produced overall measurements of properties being investigated, but were usually susceptible to pitfalls of being too general. Among the thermodynamic properties that are of interest, reaction rates hold the greatest significance, as they play a critical role in reaction processes where speed is of essence, especially when fast association may enhance binding affinity of reaction molecules. Association reactions with high affinities often involve the formation of a intermediate state, which can be demonstrated by a hyperbolic reaction curve, but whose low abundance in reaction mixture often preclude the possibility of experimental measurement. Therefore, we resorted to computational methods using predefined reaction models that model the intermediate state as the reaction progresses. Here, we present a novel method called AKPE (ANN-Dependent Kinetic Parameter Extraction), our goal is to investigate the association/dissociation rate constants and the concentration dynamics of lowly-populated states (intermediate states) in the reaction landscape. To reach our goal, we simulated the chemical or biological reactions as system of differential equations, employed artificial neural networks (ANN) to model experimentally measured data, and utilized Particle Swarm Optimization (PSO) algorithm to obtain the globally optimum parameters in both the simulation and data fitting. In the Results section, we have successfully modeled a protein association reaction using AKPE, obtained the kinetic rate constants of the reaction, and constructed a full concentration versus reaction time curve of the intermediate state during the reaction. Furthermore, judging from the various validation methods that the method proposed in this paper has strong robustness and accuracy.

Photochemical Degradation of Short-Chain Chlorinated Paraffins in Aqueous Solution by Hydrated Electrons and Hydroxyl Radicals

Short-chain chlorinated paraffins (SCCPs) are a complex mixture of polychlorinated alkanes (C10-C13, chlorine content 40-70%), and have been categorized as persistent organic pollutants. However, there are knowledge gaps about their environmental degradation, particularly the effectiveness and mechanism of photochemical degradation in surface waters. Photochemically-produced hydrated electrons (e-(aq)) have been shown to degrade highly chlorinated compounds in environmentally-relevant conditions more effectively than hydroxyl radicals (·OH), which can degrade a wide range of organic pollutants. This study aimed to evaluate the potential for e-(aq) and ·OH to degrade SCCPs. To this end, the degradation of SCCP model compounds was investigated under laboratory conditions that photochemically produced e-(aq) or ·OH. Resulting SCCP degradation rate constants for e-(aq) were on the same order of magnitude as well-known chlorinated pesticides. Experiments in the presence of ·OH yielded similar or higher second-order rate constants. Trends in e-(aq) and ·OH SCCP model compounds degradation rate constants of the investigated SCCPs were consistent with that of other chlorinated compounds, with higher chlorine content producing in higher rate constants for e-(aq) and lower for ·OH. Above a chlorine:carbon ratio of approximately 0.6, the e-(aq) second-order rate constants were higher than rate constants for ·OH reactions. Results of this study furthermore suggest that SCCPs are likely susceptible to photochemical degradation in sunlit surface waters, facilitated by dissolved organic matter that can produce e-(aq) and ·OH when irradiated.

Elucidation of the Nucleophilic Potential of Diazocyclopentadiene

Diazocyclopentadiene reacts with benzhydrylium ions (Ar2CH+) to give 2,5-dibenzhydryl-substituted diazocyclopentadienes. The kinetics have been determined photometrically in dichloromethane under pseudo-first-order conditions using diazocyclopentadiene in excess. Plots of the second-order rate constants (log k 2) versus the electrophilicity parameters E of the benzhydrylium ions gave the nucleo­philicity parameter N = 4.84 and susceptibility s N = 1.06 for diazo­cyclopentadiene according to the correlation log k(20 °C) = s N(E + N). Diazocyclopentadiene thus has a similar nucleophilic reactivity as pyrrole. Previously reported electrophilic substitutions of diazocyclopentadiene are rationalized by these parameters and new reaction possibilities are predicted.

Nearly maximal information gain due to time integration in central dogma reactions

Living cells process information about their environment through the central dogma processes of transcription and translation, which drive the cellular response to stimuli. Here, we study the transfer of information from environmental input to the transcript and protein expression levels. Evaluation of both experimental and analogous simulation data reveals that transcription and translation are not two simple information channels connected in series. Instead, we show that the central dogma reactions often create a time-integrating information channel, where the translation channel receives and integrates multiple outputs from the transcription channel. This information channel model of the central dogma provides new information-theoretic selection criteria for the central dogma rate constants. Using the data for four well-studied species we show that their central dogma rate constants achieve information gain due to time integration while also keeping the loss due to stochasticity in translation relatively low (< 0.5 bits).

Modelling the adsorption of phospholipid vesicles to a silicon dioxide surface using Langmuir kinetics

The rate constants and equilibrium constant for the adsorption and desorption of lipid vesicles from a SiO2 surface have been determined.

Toward benchmarking theoretical computations of elementary rate constants on catalytic surfaces: formate decomposition on Au and Cu

With the emergence of methods for computing rate constants for elementary reaction steps of catalytic reactions, benchmarking their accuracy becomes important. The unimolecular dehydrogenation of adsorbed formate on metal surfaces...

Colorimetric Monitoring of a Chemical Reaction Using Cesium Lead Halide Assays

Cesium lead halide (CsPbX3, X = F, Cl, Br, I ) nanomaterials have a number of novel optoelectronic and physical properties, both of which are tailorable based on halide type and concentration, such as halide composition-dependent photoluminescence and rapid halide exchange while maintaining crystal structure. In this work we take advantage of these properties and use colloidal CsPbI3 nanoparticles as a proxy and colorimetric sensor of a chemical reaction in real-time. A solvolysis reaction between 2-bromo-2-methylbutane and butanol was used as a model system. A product of reaction, a bromide ion, could be detected via halide exchange with CsPbI3, by way of a quantitative blue shift (Δλ) in photoluminescence. The kinetics of this shift was calibrated against a known Br - source, which allowed for conversion to apparent values solvation kinetics. The observed rate constants (k) and corresponding activation energies (Ea) measured via the CsPbI3 probe were consistent with literature values for the reaction, confirming the validity of the approach.

Bioaccumulation of Pyraoxystrobin and Its Predictive Evaluation in Zebrafish

This paper aims to understand the bioaccumulation of pyraoxystrobin in fish. Using a flow-through bioconcentration method, the bioconcentration factor (BCF) and clearance rate of pyraoxystrobin in zebrafish were measured. The measured BCF values were then compared to those estimated from three commonly used predication models. At the exposure concentrations of 0.1 μg/L and 1.0 μg/L, the maximum BCF values for pyraoxystrobin in fish were 820.8 and 265.9, and the absorption rate constants (K1) were 391.0 d−1 and 153.2 d−1, respectively. The maximum enrichment occurred at 12 d of exposure. At the two test concentrations, the clearance rate constant (K2) in zebrafish was 0.5795 and 0.4721, and the half-life (t1/2) was 3.84 d and 3.33 d, respectively. The measured BCF values were close to those estimated from bioconcentration predication models.