Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates

Enhanced degradation of phenolic pollutants by a novel cold-adapted laccase from Peribacillus simplex

Laccase (EC 1.10.3.2), as eco-friendly biocatalysts, holds immense potential for sustainable applications across various environmental and industrial sectors. Despite the growing interest, the exploration of cold-adapted laccases, especially their unique properties and applicability, remains limited. In this study, we have isolated, cloned, expressed, and purified a novel laccase from Peribacillus simplex (GenBank: PP430751), which was derived from permafrost layer. The recombinant laccase (PsLac) exhibited optimal activity at 30 °C and a pH optimum of 3.5. Remarkably, PsLac exhibited remarkable stability in the presence of organic solvents, with its enzyme activity increasing by 20 % after being incubated in a 30 % trichloromethane solution for 12 h, compared to its initial activity. Furthermore, the enzyme preserved 100 % of its activity after undergoing eight freeze-thaw cycles. Notably, the catalytic center of PsLac contains Zn2+ instead of the typically observed Cu2+ found in other laccases, and metal-ion substitution experiments raised the catalytic efficiency to 3-fold when Zn2+ was replaced with Fe2+. Additionally, PsLac has demonstrated a proficient ability to degrade phenolic pollutants, such as hydroquinone, even at a low temperature of 16 °C, positioning it as a promising candidate for environmental bioremediation and contributing to cleaner production processes.

Multi-objectives optimization on microwave-assisted-biological-based biogas upgrading and bio-succinic acid production

This study represents the first investigation of bio-succinic acid (bio-SA) production with methane enrichment using carbon-dioxide-fixating bacteria in the co-culture of ragi tapai and macroalgae, Chaetomorpha. Microwave irradiation has also been introduced to enhance the biochemical processes as it could provide rapid and selective heating of substrates. In this research, microwave irradiation was applied on ragi tapai as a pre-treatment process. Factors such as microwave irradiation dose on ragi tapai, Chaetomorpha ratio in the co-culture, and pH value were studied. Optimal conditions were identified using Design-Expert software, resulting in optimal experimental biomethane and bio-SA production of 85.7 % and 0.65 g/L, respectively, at a microwave dose of 1.45 W/g, Chaetomorpha ratio of 0.9 and pH value of 7.8. The study provides valuable insights into microwave control for promoting simultaneous methane enrichment and bio-SA production, potentially reducing costs associated with CO2 capture and storage and biogas upgrading.

Short-term steaming during processing impacts the quality of Citri Reticulatae 'Chachi' peel

Citrus peel is a commonly used food-medicine material in the production of fast-moving consumer goods (FMCGs). For instance, Ganpu tea is manufactured by combining the peel of Citri Reticulatae 'Chachi' (PCRC) with Pu-erh tea. The alleviated irritation of PCRC through years of aging makes Citri reticulatae Pericarpium a traditional Chinese medicine. Herein, we introduced short-term steaming into the processing of PCRC to favor the quick removal of its irritation while retaining its food-medicine properties. Sensory evaluation and volatile component analysis showed that 60-s steaming reduced irritation of freshly prepared PCRC. Biological evaluations indicated no effects of steaming on the neuroprotective activity of PCRC. The process increased the contents of several bioactive ingredients, including hesperidin, nobiletin, tangeretin, and synephrine. In addition, physical indications of accelerating PCRC aging were observed. Taken together, our findings suggest that short-term steaming may offer a promising new possibility for enhancing the quality of citrus peel.

Metagenomics-based gene exploration and biochemical characterization of novel glucoamylases and α-amylases in Daqu and Pu-erh tea microorganisms

α-Amylases and glucoamylases play a crucial role in starch degradation for various industrial applications. Further exploration of novel α-amylases and glucoamylases with diverse enzymatic characteristics is necessary. In this study, metagenomics analysis revealed a high abundance of these enzymes in the microorganisms of Daqu and Pu-erh tea, identifying 271 glucoamylases and 232 α-amylases with significant sequence identity to known enzymes. Functional studies indicated that these enzymes have broad optimal temperatures (30 °C to 70 °C) and acidic or neutral pH optima. Additionally, two novel low-temperature glucoamylases and one novel low-temperature α-amylases were characterized, demonstrating potential for use in industries operating under low temperature conditions. Further analysis suggested that fewer molecular interactions and more flexible coli regions may contribute to their high activity at low temperatures. In summary, this study not only highlights the feasibility of exploring enzymes through metagenomic approaches, but also presents a library of novel and diverse α-amylases and glucoamylases for potential industrial applications.

Trees have overlapping potential niches that extend beyond their realized niches

Tree species appear to prefer distinct climatic conditions, but the true nature of these preferences is obscured by species interactions and dispersal, which limit species' ranges. We quantified realized and potential thermal niches of 188 North American tree species to conduct a continental-scale test of the architecture of niches. We found strong and consistent evidence that species occurring at thermal extremes occupy less than three-quarters of their potential niches, and species' potential niches overlap at a mean annual temperature of ~12°C. These results clarify the breadth of thermal tolerances of temperate tree species and support the centrifugal organization of thermal niches. Accounting for the nonrealized components of ecological niches will advance theory and prediction in global change ecology.

The covalent immobilization of β-galactosidase from Aspergillus oryzae and alkaline protease from Bacillus licheniformis on amino-functionalized multi-walled carbon nanotubes in milk

This study aimed was to covalently immobilize β-galactosidase from Aspergillus oryzae and protease from Bacillus licheniformis on amino-functionalized multi-walled carbon nanotubes. In this study, a two-level factorial design was employed to investigate the impact of seven continuous variables (activation pH, glutaraldehyde molarity, activation time (0-8 h), buffer solution pH (8-0), buffer solution molarity, MWCNT-NH 2 -glutaraldehyde quantity, and stabilization time (0-180 h)) on the immobilization efficiency and enzymatic activity of protease and β-galactosidase. Furthermore, the effect of time on the percentage of enzymatic activity was examined during specific intervals (24, 48, 72, 96, and 120 h) of the immobilization process. The analysis of variance results for protease enzymatic activity revealed a notable influence of the seven variables on immobilization efficiency and enzymatic activity. Additionally, the findings indicate that activation time, buffer pH, MWCNT-NH 2 -glutaraldehyde quantity, and stabilization time significantly affect the activity of the protease enzyme. The interplay between buffer pH and stabilization time is also significant. Indeed, both activation time and the quantity of MWCNT-NH 2 -glutaraldehyde exert a reducing effect on enzyme activity. Notably, the influence of MWCNT-NH 2 -glutaraldehyde quantity is more significant (p < 0.05). In terms of beta-galactosidase enzymatic activity, the study results highlight that among the seven variables considered, only the glutaraldehyde molarity, activation time, and the interplay of activation time and the quantity of MWCNT-NH 2 -glutaraldehyde can exert a statistically significant positive impact on the enzyme's activity (p < 0.05). The combination of activation time and buffer solution molarity, as well as the interactive effect of buffer pH and MWCNT-NH2-glutaraldehyde, can lead to a significant improvement in the stabilization efficiency of the protease of carbon nanotubes. The analysis of variance results demonstrated that the efficiency of covalently immobilizing β-galactosidase from Aspergillus oryzae on amino-functionalized multi-walled carbon nanotubes is influenced by the molarity of glutaraldehyde, buffer pH, stabilization time, and the interplay of activation time + buffer pH, buffer pH + activation time, activation time + buffer molarity, and glutaraldehyde molarity + MWCNT-NH 2 -glutaraldehyde (p < 0.05). Through the optimization and selection of optimal formulations, the obtained results indicate enzyme activities and stabilization efficiencies of 64.09 % ± 72.63 % and 65.96 % ± 71.77 % for protease and beta-galactosidase, respectively. Moreover, increasing the enzyme stabilization time resulted in a reduction of enzyme activity. Furthermore, an increase in pH, temperature, and the duration of milk storage passing through the enzyme-immobilized carbon nanotubes led to a decrease in enzyme stabilization efficiency, and lactose hydrolysis declined progressively over 8-h. Hence, the covalent immobilization of β-galactosidase from Aspergillus oryzae and protease from Bacillus licheniformis onto amino-functionalized multi-walled carbon nanotubes is anticipated to be achievable for milk applications.

A new β-galactosidase from Paenibacillus wynnii with potential for industrial applications

Commercial β-galactosidases exhibit undesirable kinetic properties regarding substrate affinity (Michaelis-Menten constant [KM] for lactose) and product inhibition (inhibitor constant [Ki] for galactose). An in silico screening of gene sequences was done and identified a putative β-galactosidase (Paenibacillus wynnii β-galactosidase, BgaPw) from the psychrophilic bacterium Paenibacillus wynnii. The cultivation of the wild-type P. wynnii strain resulted in very low β-galactosidase activities of a maximum of 150 nkat per liter of medium with o-nitrophenyl-β-d-galactopyranoside (oNPGal) as substrate. The recombinant production of BgaPw in Escherichia coli BL21(DE3) increased the yield ∼9,000-fold. Here, a volumetric activity of 1,350.18 ± 11.82 μkatoNPGal/Lculture was achieved in a bioreactor cultivation. The partly purified BgaPw showed a pH optimum at 7.0, a temperature maximum at 40°C, and an excellent stability at 8°C with a half-life of 77 d. Kinetic studies with BgaPw were done in milk or in milk-imitating synthetic buffer (Novo buffer), respectively. Remarkably, the KM value of BgaPw with lactose was as low as 0.63 ± 0.045 mM in milk. It was found that the resulting products of lactose hydrolysis, namely galactose and glucose, did not inhibit the β-galactosidase activity of BgaPw, but instead showed a striking activating effect in both cases (up to 144%). In a comparison study in milk, lactose was completely hydrolyzed by BgaPw in 72 h at 8°C, whereas 2 other known β-galactosidases were less powerful and converted only about 90% of lactose in the same time. Finally, the formation of galactooligosaccharides (GOS) was demonstrated with the new BgaPw, starting with pharma-lactose (400 g/L). A GOS production of about 144 g/L was achieved after 24 h (36.0% yield).

Cooperative Conformational Transitions Underpin the Activation Heat Capacity in the Temperature Dependence of Enzyme Catalysis

Many enzymes display non-Arrhenius behavior with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behavior and recently the role of the activation heat capacity (ΔCP⧧) has been widely discussed. If enzyme-catalyzed reactions occur with appreciable negative values of ΔCP⧧ (arising from narrowing of the conformational space along the reaction coordinate), then curved Arrhenius plots are a consequence. To investigate these phenomena in detail, we have collected high precision temperature-rate data over a wide temperature interval for a model glycosidase enzyme MalL, and a series of mutants that change the temperature-dependence of the enzyme-catalyzed rate. We use these data to test a range of models including macromolecular rate theory (MMRT) and an equilibrium model. In addition, we have performed extensive molecular dynamics (MD) simulations to characterize the conformational landscape traversed by MalL in the enzyme-substrate complex and an enzyme-transition state complex. We have crystallized the enzyme in a transition state-like conformation in the absence of a ligand and determined an X-ray crystal structure at very high resolution (1.10 Å). We show (using simulation) that this enzyme-transition state conformation has a more restricted conformational landscape than the wildtype enzyme. We coin the term "transition state-like conformation (TLC)" to apply to this state of the enzyme. Together, these results imply a cooperative conformational transition between an enzyme-substrate conformation (ES) and a transition-state-like conformation (TLC) that precedes the chemical step. We present a two-state model as an extension of MMRT (MMRT-2S) that describes the data along with a convenient approximation with linear temperature dependence of the activation heat capacity (MMRT-1L) that can be used where fewer data points are available. Our model rationalizes disparate behavior seen for MalL and previous results for a thermophilic alcohol dehydrogenase and is consistent with a raft of data for other enzymes. Our model can be used to characterize the conformational changes required for enzyme catalysis and provides insights into the role of cooperative conformational changes in transition state stabilization that are accompanied by changes in heat capacity for the system along the reaction coordinate. TLCs are likely to be of wide importance in understanding the temperature dependence of enzyme activity and other aspects of enzyme catalysis.

High temperature delays and low temperature accelerates evolution of a new protein phenotype

Since the origin of life, temperatures on earth have fluctuated both on short and long time scales. How such changes affect the rate at which Darwinian evolution can bring forth new phenotypes remains unclear. On the one hand, high temperature may accelerate phenotypic evolution because it accelerates most biological processes. On the other hand, it may slow phenotypic evolution, because proteins are usually less stable at high temperatures and therefore less evolvable. Here, to test these hypotheses experimentally, we evolved a green fluorescent protein in E. coli towards the new phenotype of yellow fluorescence at different temperatures. Yellow fluorescence evolved most slowly at high temperature and most rapidly at low temperature, in contradiction to the first hypothesis. Using high-throughput population sequencing, protein engineering, and biochemical assays, we determined that this is due to the protein-destabilizing effect of neofunctionalizing mutations. Destabilization is highly detrimental at high temperature, where neofunctionalizing mutations cannot be tolerated. Their detrimental effects can be mitigated through excess stability at low temperature, leading to accelerated adaptive evolution. By modifying protein folding stability, temperature alters the accessibility of mutational paths towards high-fitness genotypes. Our observations have broad implications for our understanding of how temperature changes affect evolutionary adaptations and innovations.

Protocol for building a user-friendly temperature control system to support microscopes, microfluidic chambers, and custom incubators

Biological experiments require precise temperature control, necessitating an integrated adjustable temperature system for instruments such as microscopes, microfluidic chambers, or custom incubators. We present a protocol for building a user-friendly temperature control system suitable for both in vitro and in vivo assays. We describe steps for preparing materials, assembling the printed circuit board and enclosure, and fine-tuning the heating algorithm for accuracy. This system can maintain a stable temperature of up to 60°C with stabilities under 0.06°C.

Effects of polyethylene, polylactic acid, and tire particles on the sediment microbiome and metabolome at high and low temperatures

Global warming has led to a high incidence of extreme heat events, and the frequent occurrence of extreme heat events has had extensive and far-reaching impacts on wetland ecosystems. The widespread distribution of plastics in the environment, including polyethylene (PE), polylactic acid (PLA), and tire particles (TPs), has caused various environmental problems. Here, high-throughput sequencing techniques and metabolomics were used for the first time to investigate the effects of three popular microplastic types: PE, PLA, and TP, on the sediment microbiome and the metabolome at both temperatures. The microplastics were incorporated into the sediment at a concentration of 3% by weight of the dry sediment (wt/wt), to reflect environmentally relevant conditions. Sediment enzymatic activity and physicochemical properties were co-regulated by both temperatures and microplastics producing significant differences compared to controls. PE and PLA particles inhibited bacterial diversity at low temperatures and promoted bacterial diversity at high temperatures, and TP particles promoted both at both temperatures. For bacterial richness, only PLA showed inhibition at low temperature; all other treatments showed promotion. PE, PLA, and TP microplastics changed the community structure of sediment bacteria, forming two clusters at low and high temperatures. Furthermore, PE, PLA, and TP changed the sediment metabolic profiles, producing differential metabolites such as lipids and molecules, organic heterocyclic compounds, and organic acids and their derivatives, especially TP had the most significant effect. These findings contribute to a more comprehensive understanding of the potential impact of microplastic contamination.IMPORTANCEIn this study, we added 3% (wt/wt) microplastic particles, including polyethylene, polylactic acid, and tire particles, to natural sediments under simulated laboratory conditions. Subsequently, we simulated the sediment microbial and ecosystem responses under different temperature conditions by incubating them for 60 days at 15°C and 35°C, respectively. After synthesizing these results, our study strongly suggests that the presence of microplastics in sediment ecosystems and exposure under different temperature conditions may have profound effects on soil microbial communities, enzyme activities, and metabolite profiles. This is important for understanding the potential hazards of microplastic contamination on terrestrial ecosystems and for developing relevant environmental management strategies.

Morphology Control of Self-Assembled Copper Coordination Polymers for Glucose Assays

Low-cost analytical assays enable accessible detection of clinically and environmentally important analytes; however, common enzyme-based assays suffer from high production and storage costs. Catalytically active synthetic materials serve as replacements for natural enzymes, but development of cost-effective, highly efficient synthetic strategies remains a challenge. Here, we utilized a facile synthesis for copper bipyridine coordination polymers (CuBpyCPs) and investigated structure-function relationships to achieve optimal catalytic properties for a glucose assay. We demonstrated the manipulation of CuBpyCP morphology, resulting in nanoscale petal-like structures and microscale high-index faceted structures, and identified three pure crystal morphologies exhibiting a comparable catalytic activity (Km = 0.3-0.5 mM) to horseradish peroxidase.

Temperature-dependent effects of microplastics on sediment bacteriome and metabolome

The increasing prevalence of microplastics in the environment has become a concern for various ecosystems, including wetland ecosystems. Here, we investigated the effects of three popular microplastic types: polyethylene, polylactic acid, and tire particles at 5 °C and 25 °C on the sediment microbiome and metabolome at the 3% (w/w) level. Results indicated that temperature greatly influenced catalase and neutral phosphatase activities, whereas the type of microplastic had a more significant impact on urease and dehydrogenase activities. The addition of microplastic, especially tire particles, increased microbial diversity and significantly altered the microbial community structure and metabolic profile, leading to the formation of different clusters of microbial communities depending on the temperature. Nonetheless, the effect of temperature on the metabolite composition was less significant. Functional prediction showed that the abundance of functional genes related to metabolism and biogeochemical cycling increased with increasing temperature, especially the tire particles treatment group affected the nitrogen cycling by inhibiting ureolysis and nitrogen fixation. These observations emphasize the need to consider microplastic type and ambient temperature to fully understand the ecological impact of microplastics on microbial ecosystems.

Streamlined Chemo-Enzymatic Synthesis of Molnupiravir via Lipase Catalyst

An enzymatic approach for the synthesis of Molnupiravir has been developed using immobilized lipase as a biocatalyst. This method involves a concise process of the regioselective esterification of uridine with isobutyric anhydride using Lipase (Addzyme-011). This efficient route gets 97% conversion of uridine 3, with an overall 73% yield of molnupiravir 1 in two steps. The use of inexpensive and easily available lipase makes the synthesis cost-effective and accessible globally, promoting the principles of green chemistry.

Diketopyrrolopyrrole-based fluorescent probe for visualizing over-expressed carboxylesterase in fever via ratiometric imaging

Fever is the result of inflammation and the innate self-defense response of organisms, can cause abnormal changes in the activity of many enzymes in organisms, including the important carboxylesterase (CE). Monitoring the activity changes of CE in vivo during a fever will help to understand heat-related pathological mechanisms. In this paper, we designed diketopyrrolopyrrole-based ratiometric fluorescent probes DPP-FBC-P and DPP-FBO-P containing alkyl chain and diethylene glycol monomethyl ether chain respective for detection of CE. Both probes could realized fast response to CE and displayed good selectivity and high sensitivity. Compared with DPP-FBO-P, DPP-FBC-P had better biocompatibility, larger signal to noise ratio (225-fold vs 125-fold) and lower detection limit (1.6 × 10-5 U/mL vs 4.2 × 10-5 U/mL). Moreover, the probe DPP-FBC-P had been successfully applied to image the endogenous CE in HepG2 cells and solid tumors, and also visualized the over expressed CE in fever cells. Most importantly, the changes of CE level in the liver of fever mice model induced by LPS were monitored with the assistance of DPP-FBC-Pvia dual channel ratio imaging for the first time. In addition, fluorescence color signal in solution was captured by smart phone, and the linear relationship between RGB ratio (G/R) and CE concentration was established. This work will provide a potential approach for investigating the physiological and pathological processes of heat related diseases.

High-Performance Production of N-Acetyl-d-Neuraminic Acid with Whole Cells of Fast-Growing Vibrio natriegens via a Thermal Strategy

High performance is the core objective that biotechnologists pursue, of which low efficiency, low titer, and side products are the chief obstacles. Here, a thermal strategy is proposed for simultaneously addressing the obstacles of whole-cell catalysis that is widely applied in the food industry. The strategy, by combining fast-growing Vibrio natriegens, thermophilic enzymes, and high-temperature whole-cell catalysis, was successfully applied for the high-performance production of N-acetyl-d-neuraminic acid (Neu5Ac) that plays essential roles in the fields of food (infant formulas), healthcare, and medicine. By using this strategy, we realized the highest Neu5Ac titer and productivity of 126.1 g/L and up to 71.6 g/(L h), respectively, 7.2-fold higher than the productivity of Escherichia coli. The major byproduct acetic acid was also eliminated via quenching complex metabolic side reactions enabled by temperature elevation. This study offers a broadly applicable strategy for producing chemicals relevant to the food industry, providing insights for its future development.

Thermal Sensitivity of the Enzymatic Activity of β-Glucosidase: Simulations Lend Mechanistic Insights into Experimental Observations

A crucial prerequisite for industrial applications of enzymes is the maintenance of specific activity across wide thermal ranges. β-Glucosidase (EC 3.2.1.21) is an essential enzyme for converting cellulose in biomass to glucose. While the reaction mechanisms of β-glucosidases from various thermal ranges (hyperthermophilic, thermophilic, and mesophilic) are similar, the factors underlying their thermal sensitivity remain obscure. The work presented here aims to unravel the molecular mechanisms underlying the thermal sensitivity of the enzymatic activity of the β-glucosidase BglB from the bacterium Paenibacillus polymyxa. Experiments reveal a maximum enzymatic activity at 315 K, with a marked decrease in the activity below and above this temperature. Employing in silico simulations, we identified the crucial role of the active site tunnel residues in the thermal sensitivity. Specific tunnel residues were identified via energetic decomposition and protein-substrate hydrogen bond analyses. The experimentally observed trends in specific activity with temperature coincide with variations in overall binding free energy changes, showcasing a predominantly electrostatic effect that is consistent with enhanced catalytic pocket-substrate hydrogen bonding (HB) at Topt. The entropic advantage owing to the HB substate reorganization was found to facilitate better substrate binding at 315 K. This study elicits molecular-level insights into the associative mechanisms between thermally enabled fluctuations and enzymatic activity. Crucial differences emerge between molecular mechanisms involving the actual substrate (cellobiose) and a commonly employed chemical analogue. We posit that leveraging the role of fluctuations may reveal unexpected insights into enzyme behavior and offer novel paradigms for enzyme engineering.

Organic Catalytic Activity as a Method for Agnostic Life Detection

An ideal life detection instrument would have high sensitivity but be insensitive to abiotic processes and would be capable of detecting life with alternate molecular structures. In this study, we propose that catalytic activity can be the basis of a nearly ideal life detection instrument. There are several advantages to catalysis as an agnostic life detection method. Demonstrating catalysis does not necessarily require culturing/growing the alien life and in fact may persist even in dead biomass for some time, and the amplification by catalysis is large even by minute amounts of catalysts and, hence, can be readily detected against abiotic background rates. In specific, we propose a hydrolytic catalysis detection instrument that could detect activity in samples of extraterrestrial organic material from unknown life. The instrument uses chromogenic assay-based detection of various hydrolytic catalytic activities, which are matched to corresponding artificial substrates having the same, chromogenic (preferably fluorescent) upon release, group; D- and L-enantiomers of these substrates can be used to also answer the question whether unknown life is chiral. Since catalysis is a time-proportional product-concentration amplification process, hydrolytic catalytic activity can be measured on a sample of even a minute size, and with instruments based on, for example, optofluidic chip technology.

A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies

Cold environments are more frequent than people think. They include deep oceans, cold lakes, snow, permafrost, sea ice, glaciers, cold soils, cold deserts, caves, areas at elevations greater than 3000 m, and also artificial refrigeration systems. These environments are inhabited by a diversity of eukaryotic and prokaryotic organisms that must adapt to the hard conditions imposed by cold. This adaptation is multifactorial and includes (i) sensing the cold, mainly through the modification of the liquid-crystalline membrane state, leading to the activation of a two-component system that transduce the signal; (ii) adapting the composition of membranes for proper functions mainly due to the production of double bonds in lipids, changes in hopanoid composition, and the inclusion of pigments; (iii) producing cold-adapted proteins, some of which show modifications in the composition of amino acids involved in stabilizing interactions and structural adaptations, e.g., enzymes with high catalytic efficiency; and (iv) producing ice-binding proteins and anti-freeze proteins, extracellular polysaccharides and compatible solutes that protect cells from intracellular and extracellular ice. However, organisms also respond by reprogramming their metabolism and specifically inducing cold-shock and cold-adaptation genes through strategies such as DNA supercoiling, distinctive signatures in promoter regions and/or the action of CSPs on mRNAs, among others. In this review, we describe the main findings about how organisms adapt to cold, with a focus in prokaryotes and linking the information with findings in eukaryotes.

Comprehensive structural, infrared spectroscopic and kinetic investigations of the roles of the active-site arginine in bidirectional hydrogen activation by the [NiFe]-hydrogenase 'Hyd-2' from Escherichia coli

The active site of [NiFe]-hydrogenases contains a strictly-conserved pendant arginine, the guanidine head group of which is suspended immediately above the Ni and Fe atoms. Replacement of this arginine (R479) in hydrogenase-2 from E. coli results in an enzyme that is isolated with a very tightly-bound diatomic ligand attached end-on to the Ni and stabilised by hydrogen bonding to the Nζ atom of the pendant lysine and one of the three additional water molecules located in the active site of the variant. The diatomic ligand is bound under oxidising conditions and is removed only after a prolonged period of reduction with H2 and reduced methyl viologen. Once freed of the diatomic ligand, the R479K variant catalyses both H2 oxidation and evolution but with greatly decreased rates compared to the native enzyme. Key kinetic characteristics are revealed by protein film electrochemistry: most importantly, a very low activation energy for H2 oxidation that is not linked to an increased H/D isotope effect. Native electrocatalytic reversibility is retained. The results show that the sluggish kinetics observed for the lysine variant arise most obviously because the advantage of a more favourable low-energy pathway is massively offset by an extremely unfavourable activation entropy. Extensive efforts to establish the identity of the diatomic ligand, the tight binding of which is an unexpected further consequence of replacing the pendant arginine, prove inconclusive.

Psychrophilic enzymes: strategies for cold-adaptation

Psychrophilic organisms thriving at near-zero temperatures synthesize cold-adapted enzymes to sustain cell metabolism. These enzymes have overcome the reduced molecular kinetic energy and increased viscosity inherent to their environment and maintained high catalytic rates by development of a diverse range of structural solutions. Most commonly, they are characterized by a high flexibility coupled with an intrinsic structural instability and reduced substrate affinity. However, this paradigm for cold-adaptation is not universal as some cold-active enzymes with high stability and/or high substrate affinity and/or even an unaltered flexibility have been reported, pointing to alternative adaptation strategies. Indeed, cold-adaptation can involve any of a number of a diverse range of structural modifications, or combinations of modifications, depending on the enzyme involved, its function, structure, stability, and evolutionary history. This paper presents the challenges, properties, and adaptation strategies of these enzymes.

Glycosylation increases active site rigidity leading to improved enzyme stability and turnover

Glycosylation is the most prevalent protein post-translational modification, with a quarter of glycosylated proteins having enzymatic properties. Yet, the full impact of glycosylation on the protein structure-function relationship, especially in enzymes, is still limited. Here, we show that glycosylation rigidifies the important commercial enzyme horseradish peroxidase (HRP), which in turn increases its turnover and stability. Circular dichroism spectroscopy revealed that glycosylation increased holo-HRP's thermal stability and promoted significant helical structure in the absence of haem (apo-HRP). Glycosylation also resulted in a 10-fold increase in enzymatic turnover towards o-phenylenediamine dihydrochloride when compared to its nonglycosylated form. Utilising a naturally occurring site-specific probe of active site flexibility (Trp117) in combination with red-edge excitation shift fluorescence spectroscopy, we found that glycosylation significantly rigidified the enzyme. In silico simulations confirmed that glycosylation largely decreased protein backbone flexibility, especially in regions close to the active site and the substrate access channel. Thus, our data show that glycosylation does not just have a passive effect on HRP stability but can exert long-range effects that mediate the 'native' enzyme's activity and stability through changes in inherent dynamics.

Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA

Residues beyond the first coordination shell are often observed to make considerable cumulative contributions in enzymes. Due to typically indirect perturbations of multiple physicochemical properties of the active site, however, their individual and specific roles in enzyme catalysis and disease-causing mutations remain difficult to predict and understand at the molecular level. Here we analyze the contributions of several second-shell residues in phosphate-irrepressible alkaline phosphatase of flavobacterium (PafA), a representative system as one of the most efficient enzymes. By adopting a multifaceted approach that integrates quantum-mechanical/molecular-mechanical free energy computations, molecular-mechanical molecular dynamics simulations, and density functional theory cluster model calculations, we probe the rate-limiting phosphoryl transfer step and structural properties of all relevant enzyme states. In combination with available experimental data, our computational results show that mutations of the studied second-shell residues impact catalytic efficiency mainly by perturbation of the apo state and therefore substrate binding, while they do not affect the ground state or alter the nature of phosphoryl transfer transition state significantly. Several second-shell mutations also modulate the active site hydration level, which in turn influences the energetics of phosphoryl transfer. These mechanistic insights also help inform strategies that may improve the efficiency of enzyme design and engineering by going beyond the current focus on the first coordination shell.

A Cold-Active Flavin-Dependent Monooxygenase from Janthinobacterium svalbardensis Unlocks Applications of Baeyer–Villiger Monooxygenases at Low Temperature

Cold-active enzymes maintain a large part of their optimal activity at low temperatures. Therefore, they can be used to avoid side reactions and preserve heat-sensitive compounds. Baeyer-Villiger monooxygenases (BVMO) utilize molecular oxygen as a co-substrate to catalyze reactions widely employed for steroid, agrochemical, antibiotic, and pheromone production. Oxygen has been described as the rate-limiting factor for some BVMO applications, thereby hindering their efficient utilization. Considering that oxygen solubility in water increases by 40% when the temperature is decreased from 30 to 10 °C, we set out to identify and characterize a cold-active BVMO. Using genome mining in the Antarctic organism Janthinobacterium svalbardensis, a cold-active type II flavin-dependent monooxygenase (FMO) was discovered. The enzyme shows promiscuity toward NADH and NADPH and high activity between 5 and 25 °C. The enzyme catalyzes the monooxygenation and sulfoxidation of a wide range of ketones and thioesters. The high enantioselectivity in the oxidation of norcamphor (eeS = 56%, eeP > 99%, E > 200) demonstrates that the generally higher flexibility observed in the active sites of cold-active enzymes, which compensates for the lower motion at cold temperatures, does not necessarily reduce the selectivity of these enzymes. To gain a better understanding of the unique mechanistic features of type II FMOs, we determined the structure of the dimeric enzyme at 2.5 Å resolution. While the unusual N-terminal domain has been related to the catalytic properties of type II FMOs, the structure shows a SnoaL-like N-terminal domain that is not interacting directly with the active site. The active site of the enzyme is accessible only through a tunnel, with Tyr-458, Asp-217, and His-216 as catalytic residues, a combination not observed before in FMOs and BVMOs.

Discrimination of psychrophilic enzymes using machine learning algorithms with amino acid composition descriptor

Introduction

Psychrophilic enzymes are a class of macromolecules with high catalytic activity at low temperatures. Cold-active enzymes possessing eco-friendly and cost-effective properties, are of huge potential application in detergent, textiles, environmental remediation, pharmaceutical as well as food industry. Compared with the time-consuming and labor-intensive experiments, computational modeling especially the machine learning (ML) algorithm is a high-throughput screening tool to identify psychrophilic enzymes efficiently.

Methods

In this study, the influence of 4 ML methods (support vector machines, K-nearest neighbor, random forest, and naïve Bayes), and three descriptors, i.e., amino acid composition (AAC), dipeptide combinations (DPC), and AAC + DPC on the model performance were systematically analyzed.

Results and discussion

Among the 4 ML methods, the support vector machine model based on the AAC descriptor using 5-fold cross-validation achieved the best prediction accuracy with 80.6%. The AAC outperformed than the DPC and AAC + DPC descriptors regardless of the ML methods used. In addition, amino acid frequencies between psychrophilic and non-psychrophilic proteins revealed that higher frequencies of Ala, Gly, Ser, and Thr, and lower frequencies of Glu, Lys, Arg, Ile,Val, and Leu could be related to the protein psychrophilicity. Further, ternary models were also developed that could classify psychrophilic, mesophilic, and thermophilic proteins effectively. The predictive accuracy of the ternary classification model using AAC descriptor via the support vector machine algorithm was 75.8%. These findings would enhance our insight into the cold-adaption mechanisms of psychrophilic proteins and aid in the design of engineered cold-active enzymes. Moreover, the proposed model could be used as a screening tool to identify novel cold-adapted proteins.

β-glucosidase, driven by porcine transthyretin promoter, specific expression in the liver of transgenic mice

Under the background of food security, using non-grain feed instead of corn-soybean-based feed is an effective measure to alleviate the food-feed competition. While, non-grain feeds are often rich in fiber, which cannot be digested by non-ruminants. Producing heterologous enzymes in non-ruminants to improve cellulose utilization rate is a new research strategy by transgenic technology. In this study, porcine transthyretin (TTR) promoter, signal peptide-coding sequence (CDS), Saccharomycopsis fibuligera β-glucosidase gene (BGL1)-CDS, 6×His sequences fragments were fused into pGL3-control vector to generate transgenic vector. Then, transgenic mice were generated by pronuclear microinjection of the linearized expression vectors. Transgenic mice and their offspring were examined by PCR-based genotyping and copy number variation. Results showed that BGL1 was successfully integrated into the mouse genome and transmitted stably. Furthermore, reverse transcription-polymerase chain reaction (RT-PCR), Western blotting, and β-glucosidase activity assay demonstrated that BGL1 was specifically expressed in the liver, and β-glucosidase activity significantly increased. In addition, liver weight index, cellular morphology, and collagen fiber content of the liver showed that exogenous gene insertion did not cause any lesions to live. Taken together, our findings suggest that β-glucosidase driven by TTR promoter was specifically expressed in the liver of transgenic mice.

Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic Enzyme

The polyextremophilic β-galactosidase enzyme of the haloarchaeon Halorubrum lacusprofundi functions in extremely cold and hypersaline conditions. To better understand the basis of polyextremophilic activity, the enzyme was studied using steady-state kinetics and molecular dynamics at temperatures ranging from 10 °C to 50 °C and salt concentrations from 1 M to 4 M KCl. Kinetic analysis showed that while catalytic efficiency (k_cat/K_m) improves with increasing temperature and salinity, K_m is reduced with decreasing temperatures and increasing salinity, consistent with improved substrate binding at low temperatures. In contrast, k_cat was similar from 2-4 M KCl across the temperature range, with the calculated enthalpic and entropic components indicating a threshold of 2 M KCl to lower the activation barrier for catalysis. With molecular dynamics simulations, the increase in per-residue root-mean-square fluctuation (RMSF) was observed with higher temperature and salinity, with trends like those seen with the catalytic efficiency, consistent with the enzyme's function being related to its flexibility. Domain A had the smallest change in flexibility across the conditions tested, suggesting the adaptation to extreme conditions occurs via regions distant to the active site and surface accessible residues. Increased flexibility was most apparent in the distal active sites, indicating their importance in conferring salinity and temperature-dependent effects.

Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks

The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation (TDHDX-MS) has emerged as a generic and efficient tool for the spatial resolution of protein networks that are proposed to function in the thermal activation of catalysis. In this work, we extend TDHDX from apo-enzyme structures to protein-ligand complexes. Using adenosine deaminase as a prototype, we compared the impacts of a substrate analog (1-deaza-adenosine or DAA) and a very tight-binding inhibitor/transition state analog (pentostatin) at single and multiple temperatures. At a single temperature, we observed different HDX-MS properties for the two ligands, as expected from their 10⁶-fold differences in strength of binding. By contrast, analogous patterns for TDHDX-MS emerge in the presence of both DAA and pentostatin, indicating similar impacts of either ligand on the enthalpic barriers for local protein unfolding. We extended TDHDX to a function-altering mutant of adenosine deaminase in the presence of pentostatin and revealed a protein thermal network that is highly similar to that previously reported for the apo-enzyme (Gao et al., 2020, JACS 142, 19936-19949). Finally, we discuss the differential impacts of pentostatin binding on overall protein flexibility vs. site-specific thermal transfer pathways in the context of models for substrate-induced changes to a distributed protein conformational landscape that act in synergy with embedded protein thermal networks to achieve efficient catalysis.

Enzymatic Production of Chondroitin Oligosaccharides and Its Sulfate Derivatives

Chondroitin sulfate (CS) has a wide range of physiological functions and clinical applications. However, the biosynthesis of chondroitin oligosaccharides (o-CHs) and sulfate derivatives with specific length is always challenging. Herein, we report enzymatic strategies for producing homogeneous o-CHs and its sulfate derivatives from microbial sourced chondroitin. Chondroitin disaccharides, tetrasaccharides, hexasaccharides, octasaccharides, and decasaccharides with defined structure were produced by controllably depolymerizing microbial sourced chondroitin with an engineered chondroitinase ABC I. The highest conversion rates of the above corresponding o-CHs were 65.5%, 32.1%, 12.7%, 7.2%, and 16.3%, respectively. A new efficient enzymatic sulfation system that directly initiates from adenosine 5′-triphosphate (ATP) and sulfate was developed and improved the sulfation of chondroitin from 8.3% to 85.8% by optimizing the temperature, sulfate and ATP concentration. o-CHs decasaccharide, octasaccharide, hexasaccharide, tetrasaccharide and disaccharide were modified and the corresponding sulfate derivatives with one sulfate group were prepared. The enzymatic approaches constructed here for preparing o-CHs and its sulfate derivatives pave the way for the study of structure-activity relationship and applications.

Targeting the alternative oxidase (AOX) for human health and food security, a pharmaceutical and agrochemical target or a rescue mechanism?

Some of the most threatening human diseases are due to a blockage of the mitochondrial electron transport chain (ETC). In a variety of plants, fungi, and prokaryotes, there is a naturally evolved mechanism for such threats to viability, namely a bypassing of the blocked portion of the ETC by alternative enzymes of the respiratory chain. One such enzyme is the alternative oxidase (AOX). When AOX is expressed, it enables its host to survive life-threatening conditions or, as in parasites, to evade host defenses. In vertebrates, this mechanism has been lost during evolution. However, we and others have shown that transfer of AOX into the genome of the fruit fly and mouse results in a catalytically engaged AOX. This implies that not only is the AOX a promising target for combating human or agricultural pathogens but also a novel approach to elucidate disease mechanisms or, in several cases, potentially a therapeutic cure for human diseases. In this review, we highlight the varying functions of AOX in their natural hosts and upon xenotopic expression, and discuss the resulting need to develop species-specific AOX inhibitors.

Physiological responses and adjustments of corals to strong seasonal temperature variations (20-28°C)

Temperature is a key driver of metabolic rates. So far, we know little about potential physiological adjustments of subtropical corals to seasonal temperature changes (>8°) that substantially exceed temperature fluctuation experienced by their counterparts in the tropics. This study investigated the effect of temperature reductions on Montastrea cavernosa and Porites astreoides in Bermuda (32°N; SST: ∼19-29°C) over 5 weeks applying the following treatments: (i) constant control temperature at 28°C, and (ii) temperature reduction (0.5 °C/day) followed by constant temperature (20 days; acclimatization period) at 24 °C and (iii) at 20 °C. Both species decreased photosynthesis and respiration during temperature reduction as expected, which continued to decrease during the acclimatization period, indicating adjustment to a low energy turnover rather than thermal compensation. Trajectories of physiological adjustments and level of thermal compensation, however, differed between species: M. cavernosa zooxanthellae metrics showed a strong initial response to temperature reduction, followed by a return to close to control values during the acclimatization period, reflecting a high physiological flexibility and low thermal compensation. P. astreoides zooxanthellae, in contrast, showed no initial response, but an increase in pigment concentration zooxanthellae-1 and similar photosynthesis rates at 24° and 20°C at the end of the experiment, indicating low acute thermal sensitivity and the ability for thermal compensation at the lowest temperature. Respiration decreased more strongly than photosynthesis leading to significant build-up of biomass in both species (energy reserves). Results are important in the light of potential poleward migration of corals and of potential latitudinal and species-specific differences in coral thermal tolerance.

Some Clues about Enzymes from Psychrophilic Microorganisms

Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.

The Effects of Temperature on Cellular Physiology

Temperature impacts biological systems across all length and timescales. Cells and the enzymes that comprise them respond to temperature fluctuations on short timescales, and temperature can affect protein folding, the molecular composition of cells, and volume expansion. Entire ecosystems exhibit temperature-dependent behaviors, and global warming threatens to disrupt thermal homeostasis in microbes that are important for human and planetary health. Intriguingly, the growth rate of most species follows the Arrhenius law of equilibrium thermodynamics, with an activation energy similar to that of individual enzymes but with maximal growth rates and over temperature ranges that are species specific. In this review, we discuss how the temperature dependence of critical cellular processes, such as the central dogma and membrane fluidity, contributes to the temperature dependence of growth. We conclude with a discussion of adaptation to temperature shifts and the effects of temperature on evolution and on the properties of microbial ecosystems.

Double mutations far from the active site affect cold activity in an Antarctic halophilic β-galactosidase

The Antarctic haloarchaeon, Halorubrum lacusprofundi, contains a polyextremophilic family 42 β-galactosidase, which we are using as a model for cold-active enzymes. Divergent amino acid residues in this 78 kDa protein were identified through comparative genomics and hypothesized to be important for cold activity. Six amino acid residues were previously mutated and five were shown by steady-state kinetic analysis to have altered temperature-dependent catalytic activity profiles via effects on K_m and/or k_cat compared to the wild-type enzyme. In this follow-up study, double-mutated enzymes were constructed and tested for temperature effects, including two new tandem residue pairs (N180T/A181T and T383A/S384A), and pairwise combination of the single residue mutations (N251D, F387L, I476V, and V482L). All double-mutated enzymes were found to be more catalytically active at moderate and/or less active at colder temperatures than wild-type, with both K_m and k_cat effects observed for the two tandem mutations. For pairwise combinations, a K_m effect was seen when the surface exposed F387L mutation located in a domain A TIM barrel α helix 19 Å from the active site was combined with two internal residues, N251D or V482L. When another surface exposed mutation I476V located in a coiled region of domain B 25 Å from the active site was paired with N251D or V482L, a k_cat effect was observed. These results indicate that temperature-dependent kinetic effects may be complex and subtle and are mediated by a combination of a small number of residues distant from the active site via changes to the hydration shell and/or perturbation of internal packing.

Functional characterization of Legionella pneumophila Cu+ transport ATPase. The activation by Cu+ and ATP

Cu⁺-ATPases are integral membrane proteins belonging to the IB subfamily of the P-type ATPases that couple Cu⁺ transport to the hydrolysis of ATP. As some structural and functional particularities arise for Cu⁺-ATPases, several authors suggest that some of the reaction steps of the Albers-Post model postulated for other P-ATPases may be different. In this work we describe a functional characterization of Legionella pneumophila Cu⁺-ATPase (LpCopA), the first P_IB-ATPase whose structure was determined by X-ray crystallography. Cu⁺-ATPase activity of the enzyme presents a maximum at ∼37 °C and pH 6.6-6.8. Phospholipids enhance LpCopA Cu⁺-ATPase activity in a non-essential mode where optimal activity is achieved at an asolectin molar fraction of 0.15 and an amphiphile-protein ratio of ~30,000. As described for other P-ATPases, Mg²⁺ acts as an essential activator. Furthermore, Cu⁺-ATPase activity dependence on [Cu⁺] and [ATP] can both be described by a sum of two hyperbolic functions. Based on that, and the [Cu⁺] and [ATP] dependencies of the best fitting parameters of the hyperbolae pointed above, we propose a minimal reaction scheme for the catalytic mechanism that shares the basic reaction steps of the Albers-Post model for P-type ATPases. The reaction scheme postulated contemplates two different binding affinities for a single ATP (apparent affinities of 0.66 and 550 μM at [Cu⁺] → ∞) and binding of at least 2 Cu⁺ with different affinities as well (apparent affinities of 1.4 and 102.5 μM at [ATP] → ∞).

Metabolic regulation of subcellular sucrose cleavage inferred from quantitative analysis of metabolic functions

Quantitative analysis of experimental metabolic data is frequently challenged by non-intuitive, complex patterns which emerge from regulatory networks. The complex output of metabolic regulation can be summarised by metabolic functions which comprise information about dynamics of metabolite concentrations. In a system of ordinary differential equations, metabolic functions reflect the sum of biochemical reactions which affect a metabolite concentration, and their integration over time reveals metabolite concentrations. Further, derivatives of metabolic functions provide essential information about system dynamics and elasticities. Here, invertase-driven sucrose hydrolysis was simulated in kinetic models on a cellular and subcellular level. Both Jacobian and Hessian matrices of metabolic functions were derived for quantitative analysis of kinetic regulation of sucrose metabolism. Model simulations suggest that transport of sucrose into the vacuole represents a central regulatory element in plant metabolism during cold acclimation which preserves control of metabolic functions and limits feedback-inhibition of cytosolic invertases by elevated hexose concentrations.

Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover

Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔC _P ^‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme-substrate interactions and the global dynamics of the protein. We find that changes in ΔC _P ^‡ and protein dynamics can be mapped to specific substrate-enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.

Evaluating the Arrhenius equation for developmental processes

The famous Arrhenius equation is well suited to describing the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how well the simple Arrhenius equation predicts complex multi-step biological processes, using frog and fruit fly embryogenesis as two canonical models. We find that the Arrhenius equation provides a good approximation for the temperature dependence of embryogenesis, even though individual developmental intervals scale differently with temperature. At low and high temperatures, however, we observed significant departures from idealized Arrhenius Law behavior. When we model multi-step reactions of idealized chemical networks, we are unable to generate comparable deviations from linearity. In contrast, we find the two enzymes GAPDH and β-galactosidase show non-linearity in the Arrhenius plot similar to our observations of embryonic development. Thus, we find that complex embryonic development can be well approximated by the simple Arrhenius equation regardless of non-uniform developmental scaling and propose that the observed departure from this law likely results more from non-idealized individual steps rather than from the complexity of the system.

Machine Learning for Chemical Reactions

Machine learning (ML) techniques applied to chemical reactions have a long history. The present contribution discusses applications ranging from small molecule reaction dynamics to computational platforms for reaction planning. ML-based techniques can be particularly relevant for problems involving both computation and experiments. For one, Bayesian inference is a powerful approach to develop models consistent with knowledge from experiments. Second, ML-based methods can also be used to handle problems that are formally intractable using conventional approaches, such as exhaustive characterization of state-to-state information in reactive collisions. Finally, the explicit simulation of reactive networks as they occur in combustion has become possible using machine-learned neural network potentials. This review provides an overview of the questions that can and have been addressed using machine learning techniques, and an outlook discusses challenges in this diverse and stimulating field. It is concluded that ML applied to chemistry problems as practiced and conceived today has the potential to transform the way with which the field approaches problems involving chemical reactions, in both research and academic teaching.

pH-Independent Heat Capacity Changes during Phosphorolysis Catalyzed by the Pyrimidine Nucleoside Phosphorylase from Geobacillus thermoglucosidasius

Enzyme-catalyzed reactions sometimes display curvature in their Eyring plots in the absence of denaturation, indicative of a change in activation heat capacity. However, the effects of pH and (de)protonation on this phenomenon have remained unexplored. Herein, we report a kinetic characterization of the thermophilic pyrimidine nucleoside phosphorylase from Geobacillus thermoglucosidasius across a two-dimensional working space covering 35 °C and 3 pH units with two substrates displaying different pK_a values. Our analysis revealed the presence of a measurable activation heat capacity change ΔC_p^⧧ in this reaction system, which showed no significant dependence on medium pH or substrate charge. Our results further describe the remarkable effects of a single halide substitution that has a minor influence on ΔC_p^⧧ but conveys a significant kinetic effect by decreasing the activation enthalpy, causing a >10-fold rate increase. Collectively, our results present an important piece in the understanding of enzymatic systems across multidimensional working spaces where the choice of reaction conditions can affect the rate, affinity, and thermodynamic phenomena independently of one another.

On Catalytic Kinetics of Enzymes

Classical enzyme kinetic theories are summarized and linked with modern discoveries here. The sequential catalytic events along time axis by enzyme are analyzed at the molecular level, and by using master equations, this writing tries to connect the microscopic molecular behavior of enzyme to kinetic data (like velocity and catalytic coefficient k) obtained in experiment: 1/k = t equals to the sum of the times taken by the constituent individual steps. The relationships between catalytic coefficient k, catalytic rate or velocity, the amount of time taken by each step and physical or biochemical conditions of the system are discussed, and the perspective and hypothetic equations proposed here regarding diffusion, conformational change, chemical conversion, product release steps and the whole catalytic cycle provide an interpretation of previous experimental observations and can be testified by future experiments.

Designing better enzymes: Insights from directed evolution

De novo enzymes can be created by computational design and directed evolution. Here, we review recent insights into the origins of catalytic power in evolved designer enzymes to pinpoint opportunities for next-generation designs: Evolution precisely organizes active sites, introduces catalytic H-bonding networks, invokes electrostatic catalysis, and creates dynamical networks embedding the active site in a reactive protein scaffold. Such insights foster our fundamental knowledge of enzyme catalysis and fuel the future design of tailor-made enzymes.

Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.

Short-Term Temperature Response of Leaf Respiration in Different Subtropical Urban Tree Species

Plant leaf respiration is one of the critical components of the carbon cycle in terrestrial ecosystems. To predict changes of carbon emissions from leaves to the atmosphere under a warming climate, it is, therefore, important to understand the thermodynamics of the temperature response of leaf respiration. In this study, we measured the short-term temperature response of leaf respiration from five different urban tree species in a subtropical region of southern China. We applied two models, including an empirical model (the Kavanau model) and a mechanistic model (Macromolecular Rate Theory, MMRT), to investigate the thermodynamic properties in different plant species. Both models are equivalent in fitting measurements of the temperature response of leaf respiration with no significant difference (p = 0.67) in model efficiency, while MMRT provides an easy way to determine the thermodynamic properties, i.e., enthalpy, entropy, and Gibbs free energy of activation, for plant respiration. We found a conserved temperature response in the five studied plant species, showing no difference in thermodynamic properties and the relative temperature sensitivity for different species at low temperatures (<42°C). However, divergent temperature response among species happened at high temperatures over 42°C, showing more than two-fold differences in relative respiration rate compared to that below 42°C, although the causes of the divergent temperature response remain unclear. Notably, the convergent temperature response at low temperatures could provide useful information for land surface models to improve predictions of climate change effects on plant respiration.

Thermal adaptation in the honeybee (Apis mellifera) via changes to the structure of malate dehydrogenase

In honeybees there are three alleles of cytosolic malate dehydrogenase gene: F, M and S. Allele frequencies are correlated with environmental temperature, suggesting that the alleles have temperature-dependent fitness benefits. We determined the enzyme activity of each allele across a range of temperatures in vitro The F and S alleles have higher activity and are less sensitive to high temperatures than the M allele, which loses activity after incubation at temperatures found in the thorax of foraging bees in hot climates. Next, we predicted the protein structure of each allele and used molecular dynamics simulations to investigate their molecular flexibility. The M allozyme is more flexible than the S and F allozymes at 50°C, suggesting a plausible explanation for its loss of activity at high temperatures, and has the greatest structural flexibility at 15°C, suggesting that it can retain some enzyme activity at cooler temperatures. MM bees recovered from 2 h of cold narcosis significantly better than all other genotypes. Combined, these results explain clinal variation in malate dehydrogenase allele frequencies in the honeybee at the molecular level.