Recombination of 2Fe-2S Ferredoxins Reveals Differences in the Inheritance of Thermostability and Midpoint Potential
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Biochemistry & Molecular Biology↗
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Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase
Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.
archaea↗
Pyrodictium abyssi AbpX reveals a calcium-responsive family of microbial biomatrix proteins that form thermostable hydrogels
Evolutionary pressure on microbial communities propagating under extreme environmental conditions often results in unique structural adaptations to promote cell survival. In this work, we report an investigation of AbpX, a biomatrix protein identified in cultures of the hyperthermophilic archaeon Pyrodictium abyssi. Under ex vivo and in vitro conditions, AbpX assembles into a paracrystalline lattice composed of semiflexible fibrils. CryoEM analysis of recombinant AbpX fibrils reveals that the precursor protein polymerizes through donor strand complementation (DSC), a process previously reported for chaperone-usher fimbriae in Gram-negative bacteria. Unlike the latter DSC protein polymers, AbpX undergoes chaperone-free polymerization in the presence of calcium ions, which are sequestered at the donor strand-acceptor groove interface between protomers in the fibril. Using a combination of cryoEM and crystallographic information, a structural model is proposed for the AbpX lattice that provides insight into its potential role in biofilm formation. These findings suggest that calcium ion coordination may contribute to fibril assembly and preorganize fibrils for incorporation into the protein lattice. Bioinformatic analysis indicates that AbpX exemplifies a distinct and broadly distributed clade of calcium ion responsive biomatrix proteins within the TasA superfamily that can be fabricated into hydrogel biomaterials in vitro under environmentally benign conditions.
59 BASIC BIOLOGICAL SCIENCES↗
Fermentation Practices Select for Thermostable Endolysins in Phages
Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.
59 BASIC BIOLOGICAL SCIENCES↗
Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies
Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.
59 BASIC BIOLOGICAL SCIENCES↗
Observations on the specificity of a thermostable bacterial protease ''thermolysin.''
Substrate specificity of proteolytic enzyme thermolysin /Thermolase/ isolated from bacterial cultures
BIOCHEMISTRY↗
Observations on the specificity of a thermostable bacterial protease ''thermolysin''
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Jukes, T. H.↗
Thermostability of glycolytic enzymes from thermophilic clostridia
Thermal stability of glycolytic enzymes from thermophilic clostridia
Akagi, J. M.↗
Thermostable Shelf Life Study
The objective of this project is to determine the shelf life end-point of various food items by means of actual measurement or mathematical projection. The primary goal of the Advanced Food Technology Project in these long duration exploratory missions is to provide the crew with a palatable, nutritious and safe food system while minimizing volume, mass, and waste. The Mars missions could be as long as 2.5 years with the potential of the food being positioned prior to the crew arrival. Therefore, it is anticipated that foods that are used during the Mars missions will require a 5 year shelf life. Shelf life criteria are safety, nutrition, and acceptability. Any of these criteria can be the limiting factor in determining the food's shelf life. Due to the heat sterilization process used for the thermostabilized food items, safety will be preserved as long as the integrity of the package is maintained. Nutrition and acceptability will change over time. Since the food can be the sole source of nutrition to the crew, a significant loss in nutrition may determine when the shelf life endpoint has occurred. Shelf life can be defined when the food item is no longer acceptable. Acceptability can be defined in terms of appearance, flavor, texture, or aroma. Results from shelf life studies of the thermostabilized food items suggest that the shelf life of the foods range from 0 months to 8 years, depending on formulation.
Perchonok, M. H.↗
Synthesis and Structural Characterization of 2′‐Deoxy‐2′‐Methoxy‐ L ‐Cytidine Nucleic Acids
Abstract We report here for the first time the synthesis of a novel 2′‐methoxy‐modified L‐cytidine analog and its phosphoramidite, as well as its incorporation into oligonucleotides via solid‐phase synthesis. Our measure the thermostability of the modified L‐nucleic acids by UV‐melting studies, and find out the 2′‐methoxy‐derivatization enhances the thermostability of the L‐duplexes. Consistent with the thermostability result, our X‐ray crystal structure study reveals that the 2′‐methoxy‐L‐deoxycytidine forms the Watson‐Crick base pair with L‐guanosine virtually as the mirror‐image fashion of native pair. This novel chemically modified L‐cytidine provides a useful biochemical and structural strategy to create mirror‐image nucleic acid molecules with expanded functionalities.
2′-Methoxy↗
Concentration‐Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering
Abstract Enzyme‐based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis ( Is PETase) is capable of PET hydrolysis under mild conditions but suffers from concentration‐dependent inhibition. In this study, this inhibition is found to be dependent on incubation time, the solution conditions, and PET surface area. Furthermore, this inhibition is evident in other mesophilic PET‐degrading enzymes to varying degrees, independent of the level of PET depolymerization activity. The inhibition has no clear structural basis, but moderately thermostable Is PETase variants exhibit reduced inhibition, and the property is completely absent in the highly thermostable HotPETase, previously engineered by directed evolution, which simulations suggest results from reduced flexibility around the active site. This work highlights a limitation in applying natural mesophilic hydrolases for PET hydrolysis and reveals an unexpected positive outcome of engineering these enzymes for enhanced thermostability.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Engineered living materials for capture, conversion, and recycling technologies
Continued dependence on crude oil and natural gas resources for fossil fuels has caused global atmospheric carbon dioxide (CO 2 ) emissions to increase to record-setting proportions. There is an urgent need for efficient and inexpensive carbon sequestration systems to mitigate large-scale CO 2 emissions from industrial flue gas. Carbonic anhydrase (CA) has shown high potential for enhanced CO 2 capture applications compared to conventional absorption-based methods currently utilized in various industrial settings. This study aims to understand structural aspects that contribute to the stability of CA enzymes critical for their applications in industrial processes, which require the ability to withstand conditions different from their native environments. Here, we evaluated the thermostability and enzyme activity of mesophilic and thermophilic CA variants at different temperature conditions and in the presence of atmospheric gas pollutants like nitrogen oxides (NO x ) and sulphur oxides (SO x ). Based on our enzyme activity assays and molecular dynamics simulations, we see increased conformational stability and CA activity levels in thermostable CA variants incubated week-long at different temperature conditions. The thermostable CA variants also retained high levels of CA activity despite changes in solution pH due to increasing NO x and SO x concentrations. Furthermore, a loss of CA activity was observed only at high concentrations of NO x /SO x that possibly can be minimized with appropriate buffered solutions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Fire-retardant decorative inks for aircraft interiors
Commercial and experimental fire retardants were screened for possible use wiith acrylic printing inks on aircraft interior sandwich panels. The fire retardants were selected according to their physical properties and thermostabilities. Thermostabilities were determined by thermogravimetric analysis and differential scanning calorimetry. A criterion was then established for selecting the more stable agent. Results show that some of the bromine-containing fire retardants are more thermostable than the acrylic ink, alone, used as a control. Also, the bromine-containing fire retardants yield even better limiting oxygen index values when tested after adding carboxy-terminated butadiene acrylonitrile (CTBN) rubber.
Nir, Z.↗
Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome
Xylanase is efficient for xylan degradation and widely applied in industries. We found a GH11 family xylanase (Xyn11A) with high thermostability and catalytic activity from compost metatranscriptome. This xylanase has the optimal reaction temperature at 80 °C with the activity of 2907.3 U/mg. The X-ray crystallographic structure shows a typical “right hand” architecture, which is the characteristics of the GH11 family enzymes. Comparing it with the mesophilic XYN II, a well-studied GH11 xylanase from Trichoderma reesei, Xyn11A is more compact with more H-bonds. Our mutagenic results show that the electrostatic interactions in the thumb and palm region of Xyn11A could result in its high thermostability and activity. Introducing a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 °C with augmented activity.
59 BASIC BIOLOGICAL SCIENCES↗
Giant piezoelectricity in fluoropolymer fiber mats achieved by corona poling in water
Polymer piezoelectrics hold great potential for energy harvesting and wearable electronics. Efforts have been dedicated to enhancing piezoelectric coefficients and thermostability for several decades, but most of these have not been successful. In this report, we demonstrate a straightforward way to achieve high piezoelectric coefficients and output voltages while maintaining high thermostability at temperatures over 110 °C. Poly(vinylidene fluoride-co-trifluoroethylene) [P(VDF-TrFE)] 80/20 mol.% nanofiber mats (made by electrospinning) with extremely high crystallinity and Curie temperatures were obtained via a two-step annealing process, from which large ferroelectric domains were formed in extended-chain crystals. After corona poling using water, which is a high dielectric constant medium, giant piezoelectricity (apparent d 33 = 1045 ± 20 pC/N) and high output voltages (29.9 ± 0.5 V) were achieved. It is found that the dimensional effect induced significant polarization changes, which is the key requirement for piezoelectricity. Our finding in this work paves a way to further improve high-performance polymer piezoelectrics.
36 MATERIALS SCIENCE↗
Engineering PHL7 for Improved Poly(Ethylene Terephthalate) Depolymerization via Rational Design and Directed Evolution
Enzymatic depolymerization of poly(ethylene terephthalate) (PET) has emerged as a promising approach for polyester recycling, and, to date, many natural and engineered PET hydrolase enzymes have been reported. For industrial use, PET hydrolases must achieve high depolymerization extent and exhibit excellent thermostability. Here, we engineered a natural PET hydrolase, Polyester Hydrolase Leipzig #7 (PHL7), through rational design and directed evolution using a high-throughput screening platform. Four new enzymes were engineered with enhanced properties compared with the parent enzyme, wild-type PHL7 (PHL7-WT), and other benchmark PET hydrolases, under the tested conditions. In bioreactors, the exemplary engineered enzyme, PHL7-Jemez, exhibited improved ability to depolymerize amorphous PET film compared with PHL7-WT at 2.9% and 20% substrate loadings, with 37% and 270% higher hydrolysis, respectively, after 48 h. This study develops several state-of-the-art PET hydrolases and demonstrates a directed evolution platform to engineer high-performance enzymes, which can accelerate enzyme discovery toward improved biocatalytic recycling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Three-Dimensional Printable, Extremely Soft, Stretchable, and Reversible Elastomers from Molecular Architecture-Directed Assembly
3D printing elastomers enables the fabrication of many technologically important structures and devices such as tissue scaffolds, sensors, actuators, and soft robots. However, conventional 3D printable elastomers are intrinsically stiff; moreover, the process of printing often requires external mechanical support and/or post-treatment. In this work, we exploit the self-assembly of a responsive linear-bottlebrush-linear triblock copolymer to create stimuli-reversible, extremely soft, and stretchable elastomers and demonstrate their applicability as inks for in situ direct-write printing 3D structures without the aid of external mechanical support or post-treatment. By developing a procedure for controlled synthesis of such architecturally designed block copolymers, we create elastomers with extensibility up to 600% and Young’s moduli down to ~10 2 Pa, 10 6 times softer than plastics and more than 102 times softer than all existing 3D printable elastomers. Moreover, the elastomers are thermostable and remain to be solid up to 180 °C, yet they are 100% solvent-reprocessable. Their extreme softness, stretchability, thermostability, and solvent-reprocessability bode well for future applications.
36 MATERIALS SCIENCE↗
Discovering and Designing a Chimeric Hyperthermophilic Chitinase for Crystalline Chitin Degradation
Chitin is one of the most abundant renewable biopolymers on earth. However, it is highly crystalline and recalcitrant to degrade. Here, we report a hyperthermophilic chitinase (ActChi) to directly hydrolyze crystalline chitin at its optimal temperature of 80 °C. It contains a malectin domain, a fibronectin type-III (Fn3) domain, and a catalytic domain (CD chi ). Both Fn3 and malectin have the function of chitin binding domain (ChBD) to increase the activity. Fn3 also significantly increases thermostability, but malectin decreases it. To enhance both activity and thermostability, here we introduced a heterogeneous and hyperthermophilic ChBD at the N-terminus of CD chi to obtain ChBD-CD chi . The activity of this hybrid enzyme is 201 U/μmol for crystalline chitin, which has increased 400% compared with that of ActChi. In addition, ChBD-CD chi can continuously degrade crystalline chitin for more than 4 days at 70 °C to increase the overall hydrolysis rate. The strategy is a good example of green sustainable degradation for crystalline biopolymer in nature.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗