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1.
Mol Cell ; 84(14): 2747-2764.e7, 2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39059371

ABSTRACT

A recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryoelectron microscopy (cryo-EM) structures of XBB.1.5, XBB.1.16, EG.5, and EG.5.1 spike (S) ectodomains to reveal reinforced 3-receptor binding domain (RBD)-down receptor-inaccessible closed states mediated by interprotomer RBD interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters, including stability, receptor binding, and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.


Subject(s)
COVID-19 , Cryoelectron Microscopy , Mutation , Protein Conformation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/metabolism , SARS-CoV-2/chemistry , Humans , COVID-19/virology , COVID-19/immunology , Protein Binding , Immune Evasion , Models, Molecular , Protein Domains , Binding Sites
2.
Mol Cell ; 81(7): 1384-1396.e6, 2021 04 01.
Article in English | MEDLINE | ID: mdl-33636126

ABSTRACT

G proteins play a central role in signal transduction and pharmacology. Signaling is initiated by cell-surface receptors, which promote guanosine triphosphate (GTP) binding and dissociation of Gα from the Gßγ subunits. Structural studies have revealed the molecular basis of subunit association with receptors, RGS proteins, and downstream effectors. In contrast, the mechanism of subunit dissociation is poorly understood. We use cell signaling assays, molecular dynamics (MD) simulations, and biochemistry and structural analyses to identify a conserved network of amino acids that dictates subunit release. In the presence of the terminal phosphate of GTP, a glycine forms a polar network with an arginine and glutamate, putting torsional strain on the subunit binding interface. This "G-R-E motif" secures GTP and, through an allosteric link, discharges the Gßγ dimer. Replacement of network residues prevents subunit dissociation regardless of agonist or GTP binding. These findings reveal the molecular basis of the final committed step of G protein activation.


Subject(s)
Guanosine Triphosphate , Heterotrimeric GTP-Binding Proteins , Molecular Dynamics Simulation , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/enzymology , Allosteric Regulation , Amino Acid Motifs , Guanosine Triphosphate/chemistry , Guanosine Triphosphate/metabolism , HEK293 Cells , Heterotrimeric GTP-Binding Proteins/chemistry , Heterotrimeric GTP-Binding Proteins/metabolism , Humans , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism
3.
Proc Natl Acad Sci U S A ; 120(49): e2309884120, 2023 Dec 05.
Article in English | MEDLINE | ID: mdl-38039271

ABSTRACT

Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal stability based on comparison of the amino acid sequences of homologous proteins derived from bacteria that grow at different temperatures. A key feature of the method is that it compares the sequences based not simply on the amino acid identity, but rather on the structural and physicochemical properties of the side chain. The method accurately identified stabilizing substitutions in three well-studied systems and was validated prospectively by experimentally testing predicted stabilizing substitutions in a polyamine oxidase. In each case, the method outperformed the widely used bioinformatic consensus approach. The method can also provide insight into fundamental aspects of protein structure, for example, by identifying how many sequence positions in a given protein are relevant to temperature adaptation.


Subject(s)
Machine Learning , Proteins , Protein Stability , Amino Acid Sequence , Mutation , Proteins/genetics , Enzyme Stability
4.
J Biol Chem ; 300(6): 107333, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38820650

ABSTRACT

The human Solute Carrier (SLC) family member, monocarboxylate transporter 1 (MCT1), transports lactic and pyruvic acid across biological membranes to regulate cellular pH and metabolism. Proper trafficking of MCT1 from the endoplasmic reticulum to the plasma membrane hinges on its interactions with the membrane-bound chaperone protein, CD147. Here, using AlphaFold2 modeling and copurification, we show how a conserved signature motif located in the flexible N-terminus of MCT1 is a crucial region of interaction between MCT1 and the C-terminus of CD147. Mutations to this motif-namely, the thymic cancer linked G19C and the highly conserved W20A-destabilize the MCT1-CD147 complex and lead to a loss of proper membrane localization and cellular substrate flux. Notably, the monomeric stability of MCT1 remains unaffected in mutants, thus supporting the role of CD147 in mediating the trafficking of the heterocomplex. Using the auxiliary chaperone, GP70, we demonstrated that W20A-MCT1 can be trafficked to the plasma membrane, while G19C-MCT1 remains internalized. Overall, our findings underscore the critical role of the MCT1 transmembrane one signature motif for engaging CD147 and identify altered chaperone binding mechanisms between the CD147 and GP70 glycoprotein chaperones.


Subject(s)
Amino Acid Motifs , Basigin , Monocarboxylic Acid Transporters , Protein Transport , Symporters , Basigin/metabolism , Basigin/genetics , Basigin/chemistry , Monocarboxylic Acid Transporters/metabolism , Monocarboxylic Acid Transporters/genetics , Monocarboxylic Acid Transporters/chemistry , Humans , Symporters/metabolism , Symporters/chemistry , Symporters/genetics , Cell Membrane/metabolism , Endoplasmic Reticulum/metabolism , HEK293 Cells , Mutation, Missense
5.
J Virol ; 98(4): e0024824, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38466094

ABSTRACT

The H9N2 avian influenza virus (AIV) represents a significant risk to both the poultry industry and public health. Our surveillance efforts in China have revealed a growing trend of recent H9N2 AIV strains exhibiting a loss of hemagglutination activity at 37°C, posing challenges to detection and monitoring protocols. This study identified a single K141N substitution in the hemagglutinin (HA) glycoprotein as the culprit behind this diminished hemagglutination activity. The study evaluated the evolutionary dynamics of residue HA141 and studied the impact of the N141K substitution on aspects such as virus growth, thermostability, receptor-binding properties, and antigenic properties. Our findings indicate a polymorphism at residue 141, with the N variant becoming increasingly prevalent in recent Chinese H9N2 isolates. Although both wild-type and N141K mutant strains exclusively target α,2-6 sialic acid receptors, the N141K mutation notably impedes the virus's ability to bind to these receptors. Despite the mutation exerting minimal influence on viral titers, antigenicity, and pathogenicity in chicken embryos, it significantly enhances viral thermostability and reduces plaque size on Madin-Darby canine kidney (MDCK) cells. Additionally, the N141K mutation leads to decreased expression levels of HA protein in both MDCK cells and eggs. These findings highlight the critical role of the K141N substitution in altering the hemagglutination characteristics of recent H9N2 AIV strains under elevated temperatures. This emphasizes the need for ongoing surveillance and genetic analysis of circulating H9N2 AIV strains to develop effective control and prevention measures.IMPORTANCEThe H9N2 subtype of avian influenza virus (AIV) is currently the most prevalent low-pathogenicity AIV circulating in domestic poultry globally. Recently, there has been an emerging trend of H9N2 AIV strains acquiring increased affinity for human-type receptors and even losing their ability to bind to avian-type receptors, which raises concerns about their pandemic potential. In China, there has been a growing number of H9N2 AIV strains that have lost their ability to agglutinate chicken red blood cells, leading to false-negative results during surveillance efforts. In this study, we identified a K141N mutation in the HA protein of H9N2 AIV to be responsible for the loss of hemagglutination activity. This finding provides insight into the development of effective surveillance, prevention, and control strategies to mitigate the threat posed by H9N2 AIV to both animal and human health.


Subject(s)
Amino Acid Substitution , Hemagglutination , Hemagglutinin Glycoproteins, Influenza Virus , Influenza A Virus, H9N2 Subtype , Influenza in Birds , Mutation , Animals , Chick Embryo , Dogs , Humans , Chickens/virology , Hemagglutinin Glycoproteins, Influenza Virus/chemistry , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Hemagglutinin Glycoproteins, Influenza Virus/metabolism , Influenza A Virus, H9N2 Subtype/genetics , Influenza A Virus, H9N2 Subtype/growth & development , Influenza A Virus, H9N2 Subtype/immunology , Influenza A Virus, H9N2 Subtype/metabolism , Influenza A Virus, H9N2 Subtype/pathogenicity , Influenza in Birds/virology , Poultry , Female , Mice , Cell Line , Evolution, Molecular , Temperature , Receptors, Virus/metabolism
6.
J Virol ; 98(3): e0182023, 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38329331

ABSTRACT

Multi-segmented viruses often multimerize their genomic segments to ensure efficient and stoichiometric packaging of the correct genetic cargo. In the bipartite Nodaviridae family, genome heterodimerization is also observed and conserved among different species. However, the nucleotide composition and biological function for this heterodimer remain unclear. Using Flock House virus as a model system, we developed a next-generation sequencing approach ("XL-ClickSeq") to probe heterodimer site sequences. We identified an intermolecular base-pairing site which contributed to heterodimerization in both wild-type and defective virus particles. Mutagenic disruption of this heterodimer site exhibited significant deficiencies in genome packaging and encapsidation specificity to viral genomic RNAs. Furthermore, the disruption of this intermolecular interaction directly impacts the thermostability of the mature virions. These results demonstrate that the intermolecular RNA-RNA interactions within the encapsidated genome of an RNA virus have an important role on virus particle integrity and thus may impact its transmission to a new host.IMPORTANCEFlock House virus is a member of Nodaviridae family of viruses, which provides a well-studied model virus for non-enveloped RNA virus assembly, cell entry, and replication. The Flock House virus genome consists of two separate RNA molecules, which can form a heterodimer upon heating of virus particles. Although similar RNA dimerization is utilized by other viruses (such as retroviruses) as a packaging mechanism and is conserved among Nodaviruses, the role of heterodimerization in the Nodavirus replication cycle is unclear. In this research, we identified the RNA sequences contributing to Flock House virus genome heterodimerization and discovered that such RNA-RNA interaction plays an essential role in virus packaging efficiency and particle integrity. This provides significant insight into how the interaction of packaged viral RNA may have a broader impact on the structural and functional properties of virus particles.


Subject(s)
Dimerization , Genome, Viral , Nodaviridae , RNA, Viral , Thermodynamics , Viral Genome Packaging , Virion , Animals , Base Pairing/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing , Mutation , Nodaviridae/chemistry , Nodaviridae/genetics , Nodaviridae/growth & development , RNA Virus Infections/transmission , RNA Virus Infections/veterinary , RNA Virus Infections/virology , RNA, Viral/chemistry , RNA, Viral/genetics , RNA, Viral/metabolism , Viral Genome Packaging/genetics , Virion/chemistry , Virion/genetics , Virion/metabolism
7.
Brief Bioinform ; 25(1)2023 11 22.
Article in English | MEDLINE | ID: mdl-38018911

ABSTRACT

Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable proteins often results in single-point mutations with a limited effect on protein stability. However, the construction of stable multiple-point mutants can prove difficult due to the possibility of antagonistic effects between individual mutations. FireProt protocol enables the automated computational design of highly stable multiple-point mutants. FireProt 2.0 builds on top of the previously published FireProt web, retaining the original functionality and expanding it with several new stabilization strategies. FireProt 2.0 integrates the AlphaFold database and the homology modeling for structure prediction, enabling calculations starting from a sequence. Multiple-point designs are constructed using the Bron-Kerbosch algorithm minimizing the antagonistic effect between the individual mutations. Users can newly limit the FireProt calculation to a set of user-defined mutations, run a saturation mutagenesis of the whole protein or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical user interface broadens the tool's availability even to users with older hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.


Subject(s)
Algorithms , Proteins , Proteins/genetics , Proteins/chemistry , Mutation , Protein Stability , Internet
8.
Proteins ; 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-39023292

ABSTRACT

Butanol dehydrogenase (BDH) plays a crucial role in butanol biosynthesis by catalyzing the conversion of butanal to butanol using the coenzyme NAD(P)H. In this study, we observed that BDH from Thermotoga maritima (TmBDH) exhibits dual coenzyme specificity and catalytic activity with NADPH as the coenzyme under highly alkaline conditions. Additionally, a thermal stability analysis on TmBDH demonstrated its excellent activity retention even at elevated temperatures of 80°C. These findings demonstrate the superior thermal stability of TmBDH and suggest that it is a promising candidate for large-scale industrial butanol production. Furthermore, we discovered that TmBDH effectively catalyzes the conversion of aldehydes to alcohols and exhibits a wide range of substrate specificities toward aldehydes, while excluding alcohols. The dimeric state of TmBDH was observed using rapid online buffer exchange native mass spectrometry. Additionally, we analyzed the coenzyme-binding sites and inferred the possible locations of the substrate-binding sites. These results provide insights that improve our understanding of BDHs.

9.
Proteins ; 2024 Sep 18.
Article in English | MEDLINE | ID: mdl-39291641

ABSTRACT

High thermostability of the enzymes is one of the distinguishing characteristics that increase their industrial utility. In the current research work, rigidifying the flexible amino acid residues of a lysophospholipase (Pa-LPL) from Pyrococcus abyssi was used as a protein engineering approach to improve its thermostability. A truncated variant of Pa-LPL (t-LPL∆12) was constructed by trimming its 12 amino acid residues (50-61) through overlap extension PCR. The truncated enzyme worked optimally at 65°C and pH 6.5 with remarkable thermostability at 65°C-85°C. In comparison to wild-type Pa-LPL, 5.8 and 1.2-fold increase in half-life (t1/2) of t-LPL∆12 was observed at 65 (optimum temperature) and 95°C, respectively. The activity of t-LPL∆12 was stimulated by 1 mM Cu2+ followed by Ca2+, Ni2+, Co2+, and Mg2+. Both substrate docking and experimental results indicated that the truncated enzyme could hydrolyze a variety of p-nitrophenyl esters. Km, Vmax, and Kcat for enzymatic hydrolysis of p-nitrophenyl butyrate were calculated to be 1 ± 0.087 mM, 1456 ± 36.474 U/mg, and 1.397 × 1011 min-1, respectively. In short, broad substrate specificity and thermostability of t-LPL∆12 are some of the distinctive features that make it an ideal candidate for degumming of vegetable oils.

10.
Biochem Biophys Res Commun ; 732: 150405, 2024 Nov 05.
Article in English | MEDLINE | ID: mdl-39033552

ABSTRACT

ß-Glucosidase is a crucial cellulase, as its activity determines the efficiency of cellulose hydrolysis into glucose. This study addresses the functional and structural characteristics of Thermotoga profunda ß-glucosidase (Tp-BGL). Tp-BGL exhibited a Km of 0.3798 mM for p-nitrophenyl-ß-d-glucopyranoside (pNPGlc) and 4.44 mM for cellobiose, with kcat/Km of 1211.16 and 4.18 s-1 mM-1, respectively. In addition, Tp-BGL showed significant pH adaptability and thermal stability, with a Tm of 85.7 °C and retaining >90 % of its activity after incubation at 80 °C for 90 min. The crystal structure of Tp-BGL was resolved at 1.95 Å resolution, and reveals a typical TIM barrel structure. Comparative structural analysis highlighted that the major distinction between Tp-BGL and the other glucosidases lies in their loop regions.


Subject(s)
Models, Molecular , Thermotoga , beta-Glucosidase , beta-Glucosidase/chemistry , beta-Glucosidase/metabolism , Crystallography, X-Ray , Thermotoga/enzymology , Thermotoga/chemistry , Thermotoga/metabolism , Enzyme Stability , Protein Conformation , Hydrogen-Ion Concentration , Kinetics , Substrate Specificity , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/genetics
11.
Chembiochem ; 25(1): e202300700, 2024 01 02.
Article in English | MEDLINE | ID: mdl-37917145

ABSTRACT

Flavin-dependent halogenases allow halogenation of electron-rich aromatic compounds under mild reaction conditions even at electronically unfavored positions with high regioselectivity. In order to expand the application of halogenases, the enzymes need to be improved in terms of stability and efficiency. A previous study with the tryptophan 6-halogenase Thal demonstrated that thermostable Thal variants tend to form dimers in solution while the wild type is present as a monomer. Based on this a dimeric Thal variant was generated that is covalently linked by disulfide bonds. Introducing two cysteine residues at the dimer interface resulted in the variant Thal CC with significantly increased thermostability (▵T50 =15.7 K) and stability over time at elevated temperature compared to the wild type. By introducing the homologous mutations into the tryptophan 5-halogenase PyrH, we were able to show that the stabilization by covalent dimerization can also be transferred to other halogenases. Moreover, it was possible to further increase the thermostability of PyrH by inserting cysteine mutations at alternative sites of the dimer interface.


Subject(s)
Cysteine , Tryptophan , Tryptophan/metabolism , Halogenation , Flavins/metabolism
12.
Chembiochem ; 25(2): e202300578, 2024 01 15.
Article in English | MEDLINE | ID: mdl-37960968

ABSTRACT

Poly (ethylene terephthalate) (PET) is one of the most commonly used plastics in daily life and various industries. Enzymatic depolymerization and recycling of post-consumer PET (pc-PET) provides a promising strategy for the sustainable circular economy of polymers. Great protein engineering efforts have been devoted to improving the depolymerization performance of PET hydrolytic enzymes (PHEs). In this review, we first discuss the mechanisms and challenges of enzymatic PET depolymerization. Subsequently, we summarize the state-of-the-art engineering of PHEs including rational design, machine learning, and directed evolution for improved depolymerization performance, and highlight the advances in screening methods of PHEs. We further discuss several factors that affect the enzymatic depolymerization efficiency. We conclude with our perspective on the opportunities and challenges in bio-recycling and bio-upcycling of PET wastes.


Subject(s)
Machine Learning , Polyethylene Terephthalates , Hydrolysis , Polymers , Protein Engineering , Plastics
13.
Chembiochem ; 25(2): e202300459, 2024 01 15.
Article in English | MEDLINE | ID: mdl-37872746

ABSTRACT

Measurements of membrane protein thermostability reflect ligand binding. Current thermostability assays often require protein purification or rely on pre-existing radiolabelled or fluorescent ligands, limiting their application to established targets. Alternative methods, such as fluorescence-detection size exclusion chromatography thermal shift, detect protein aggregation but are not amenable to high-throughput screening. Here, we present a ThermoBRET method to quantify the relative thermostability of G protein coupled receptors (GPCRs), using cannabinoid receptors (CB1 and CB2 ) and the ß2 -adrenoceptor (ß2 AR) as model systems. ThermoBRET reports receptor unfolding, does not need labelled ligands and can be used with non-purified proteins. It uses Bioluminescence Resonance Energy Transfer (BRET) between Nanoluciferase (Nluc) and a thiol-reactive fluorescent dye that binds cysteines exposed by unfolding. We demonstrate that the melting point (Tm ) of Nluc-fused GPCRs can be determined in non-purified detergent solubilised membrane preparations or solubilised whole cells, revealing differences in thermostability for different solubilising conditions and in the presence of stabilising ligands. We extended the range of the assay by developing the thermostable tsNLuc by incorporating mutations from the fragments of split-Nluc (Tm of 87 °C versus 59 °C). ThermoBRET allows the determination of GPCR thermostability, which is useful for protein purification optimisation and drug discovery screening.


Subject(s)
Carrier Proteins , Receptors, G-Protein-Coupled , Ligands , Protein Binding , Membrane Proteins/chemistry
14.
Appl Environ Microbiol ; 90(3): e0224223, 2024 03 20.
Article in English | MEDLINE | ID: mdl-38358247

ABSTRACT

The extensive accumulation of polyethylene terephthalate (PET) has become a critical environmental issue. PET hydrolases can break down PET into its building blocks. Recently, we identified a glacial PET hydrolase GlacPETase sharing less than 31% amino acid identity with any known PET hydrolases. In this study, the crystal structure of GlacPETase was determined at 1.8 Å resolution, revealing unique structural features including a distinctive N-terminal disulfide bond and a specific salt bridge network. Site-directed mutagenesis demonstrated that the disruption of the N-terminal disulfide bond did not reduce GlacPETase's thermostability or its catalytic activity on PET. However, mutations in the salt bridges resulted in changes in melting temperature ranging from -8°C to +2°C and the activity on PET ranging from 17.5% to 145.5% compared to the wild type. Molecular dynamics simulations revealed that these salt bridges stabilized the GlacPETase's structure by maintaining their surrounding structure. Phylogenetic analysis indicated that GlacPETase represented a distinct branch within PET hydrolases-like proteins, with the salt bridges and disulfide bonds in this branch being relatively conserved. This research contributed to the improvement of our comprehension of the structural mechanisms that dictate the thermostability of PET hydrolases, highlighting the diverse characteristics and adaptability observed within PET hydrolases.IMPORTANCEThe pervasive problem of polyethylene terephthalate (PET) pollution in various terrestrial and marine environments is widely acknowledged and continues to escalate. PET hydrolases, such as GlacPETase in this study, offered a solution for breaking down PET. Its unique origin and less than 31% identity with any known PET hydrolases have driven us to resolve its structure. Here, we report the correlation between its unique structure and biochemical properties, focusing on an N-terminal disulfide bond and specific salt bridges. Through site-directed mutagenesis experiments and molecular dynamics simulations, the roles of the N-terminal disulfide bond and salt bridges were elucidated in GlacPETase. This research enhanced our understanding of the role of salt bridges in the thermostability of PET hydrolases, providing a valuable reference for the future engineering of PET hydrolases.


Subject(s)
Hydrolases , Polyethylene Terephthalates , Polyethylene Terephthalates/metabolism , Phylogeny , Enzyme Stability , Hydrolases/metabolism , Disulfides , Temperature
15.
Chemistry ; 30(53): e202401737, 2024 Sep 19.
Article in English | MEDLINE | ID: mdl-39224068

ABSTRACT

Molecular photoswitches provide interesting tools to reversibly control various biological functions with light. Thanks to its small size and easy introduction into the biomolecules, azobenzene derivatives have been widely employed in the field of photopharmacology. All visible-light switchable azobenzenes with controllable thermostability are highly demanded. Based on the reported tetra-o-chloroazobenzenes, we synthesized push-pull systems, by introducing dialkyl amine and nitro groups as strong electron-donating and electron-withdrawing groups on the para-positions, and then transformed to push-push systems by a simple reduction step. The developed push-pull and push-push tetra-o-chloroazobenzene derivatives displayed excellent photoswitching properties, as previously reported. The half-life of the Z-isomers can be tuned from milliseconds for the push-pull system to several hours for the push-push system. The n-π* and π-π* transitions have better resolution in the push-push molecules, and excitation at different wavelengths can tune the E/Z ratio at the photostationary state. For one push-pull molecule, structure and absorption spectra obtained from theoretical calculations are compared with experimental data, along with data on the push-push counterpart.

16.
Arch Biochem Biophys ; 756: 109996, 2024 06.
Article in English | MEDLINE | ID: mdl-38621445

ABSTRACT

Hyperthermostable enzymes are highly desirable biocatalysts due to their exceptional stability at extreme temperatures. Recently, a hyperthermostable carboxylesterase EstD9 from Anoxybacillus geothermalis D9 was biochemically characterized. The enzyme exhibited remarkable stability at high temperature. In this study, we attempted to probe the conformational adaptability of EstD9 under extreme conditions via in silico approaches. Circular dichroism revealed that EstD9 generated new ß-sheets at 80 °C, making the core of the hydrolase fold more stable. Interestingly, the profiles of molecular dynamics simulation showed the lowest scores of radius of gyration and solvent accessible surface area (SASA) at 80 °C. Three loops were responsible for protecting the catalytic site, which resided at the interface between the large and cap domains. To further investigate the structural adaptation in extreme conditions, the intramolecular interactions of the native structure were investigated. EstD9 revealed 18 hydrogen bond networks, 7 salt bridges, and 9 hydrophobic clusters, which is higher than the previously reported thermostable Est30. Collectively, the analysis indicates that intramolecular interactions and structural dynamics play distinct roles in preserving the overall EstD9 structure at elevated temperatures. This work is relevant to both fundamental and applied research involving protein engineering of industrial thermostable enzymes.


Subject(s)
Anoxybacillus , Carboxylesterase , Enzyme Stability , Molecular Dynamics Simulation , Thermodynamics , Anoxybacillus/enzymology , Carboxylesterase/chemistry , Carboxylesterase/metabolism , Hot Temperature , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism
17.
Arch Biochem Biophys ; 760: 110126, 2024 10.
Article in English | MEDLINE | ID: mdl-39154817

ABSTRACT

Nattokinase (NK) is an enzyme that has been recognized as a new potential thrombolytic drug due to its strong thrombolytic activity. However, it is difficult to maintain the enzyme activity of NK during high temperature environment of industrial production. In this study, we constructed six NK mutants with potential for higher thermostability using a rational protein engineering strategy integrating free energy-based methods and molecular dynamics (MD) simulation. Then, wild-type NK and NK mutants were expressed in Escherichia coli (E. coli), and their thermostability and thrombolytic activity were tested. The results showed that, compared with wild-type NK, the mutants Y256P, Q206L and E156F all had improved thermostability. The optimal mutant Y256P showed a higher melting temperature (Tm) of 77.4 °C, an increase of 4 °C in maximum heat-resistant temperature and an increase of 51.8 % in activity at 37 °C compared with wild-type NK. Moreover, we also explored the mechanism of the increased thermostability of these mutants by analysing the MD trajectories under different simulation temperatures.


Subject(s)
Enzyme Stability , Escherichia coli , Molecular Dynamics Simulation , Protein Engineering , Recombinant Proteins , Subtilisins , Escherichia coli/genetics , Subtilisins/genetics , Subtilisins/chemistry , Subtilisins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Protein Engineering/methods , Mutation , Temperature , Fibrinolytic Agents/chemistry
18.
Chemphyschem ; 25(15): e202400332, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38690751

ABSTRACT

A series of NaGd1-x-ySiO4: y Dy3+-x Eu3+ phosphors were synthesized by a high-temperature solid-phase method. The optimal doping ion concentration of Dy3+ ions for this phosphor was determined to be 1 % from the emission spectra. The energy transfer between Dy3+ and Eu3+ ions at 351 nm was investigated by photoluminescence spectra and fluorescence decay curves. At the excitation wavelengths of 275 nm, 351 nm, 366 nm, and 394 nm, a change from yellow to white to red light can be realized by adjusting the doping concentration of Eu/Dy ions. Particularly, by testing the temperature-dependent fluorescence spectrum of the phosphor, it can be found that the luminous intensity of the phosphor is as high as 96 % when 394 nm excitation is employed at 413 K. It was the maximum at this temperature comparing with other phosphors as far as we know. The color coordinate values show that the NaGd1-x-ySiO4:×Dy3+-y Eu3+ phosphors are very close to the white light color coordinates (x=0.33, y=0.33) under 351 nm excitation. Meanwhile, the correlated color temperature is between 5062-7104 K. These results indicate that this phosphor is a promising candidate for high-quality WLED.

19.
Biotechnol Bioeng ; 121(5): 1532-1542, 2024 May.
Article in English | MEDLINE | ID: mdl-38265115

ABSTRACT

Carbonyl reductases are useful for producing optically active alcohols from their corresponding prochiral ketones. Herein, we applied a computer-assisted strategy to increase the thermostability of a previously constructed carbonyl reductase, LsCRM4 (N101D/A117G/F147L/E145A), which showed an outstanding activity in the synthesis of the ticagrelor precursor (1S)-2-chloro-1-(3,4-difluorophenyl)ethanol. The stability changes introduced by mutations at the flexible sites were predicted using the computational tools FoldX, I-Mutant 3.0, and DeepDDG, which demonstrated that 12 virtually screened mutants could be thermally stable; 11 of these mutants exhibited increased thermostability. Then a superior mutant LsCRM4-V99L/D150F was screened out from the library that was constructed by iteratively combining the beneficial sites, which showed a 78% increase in activity and a 17.4°C increase in melting temperature compared to LsCRM4. Our computer-assisted design and combinatorial strategy dramatically increased the efficiency of thermostable enzyme production.


Subject(s)
Alcohol Oxidoreductases , Ethanol , Ticagrelor , Enzyme Stability , Alcohol Oxidoreductases/genetics , Temperature , Computers
20.
Mol Pharm ; 21(3): 1015-1026, 2024 Mar 04.
Article in English | MEDLINE | ID: mdl-38288698

ABSTRACT

Vaccines have historically faced challenges regarding stability, especially in regions lacking a robust cold chain infrastructure. This review delves into established and emergent techniques to improve the thermostability of vaccines. We discuss the widely practiced lyophilization method, effectively transforming liquid vaccine formulations into a solid powdered state, enhancing storage and transportation ability. However, potential protein denaturation during lyophilization necessitates alternative stabilization methods. Cryoprotectants, namely, starch and sugar molecules, have shown promise in protecting vaccine antigens and adjuvants from denaturation and augmenting the stability of biologics during freeze-drying. Biomineralization, a less studied yet innovative approach, utilizes inorganic or organic-inorganic hybrids to encapsulate biological components of vaccines with a particular emphasis on metal-organic coordination polymers. Encapsulation in organic matrices to form particles or microneedles have also been studied in the context of vaccine thermostability, showing some ability to store outside the cold-chain. Unfortunately, few of these techniques have advanced to clinical trials that evaluate differences in storage conditions. Nonetheless, early trials suggest that alternative storage techniques are viable and emphasize the need for more comprehensive studies. This review underscores the pressing need for heat-stable vaccines, especially in light of the increasing global distribution challenges. Combining traditional methods with novel approaches holds promise for the future adaptability of vaccine distribution and use.


Subject(s)
Hot Temperature , Vaccines , Humans , Drug Stability , Drug Compounding/methods , Vaccination , Freeze Drying/methods
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