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1.
Nat Commun ; 11(1): 4808, 2020 09 23.
Artigo em Inglês | MEDLINE | ID: mdl-32968058

RESUMO

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M-1s-1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M-1s-1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.


Assuntos
Simulação por Computador , Evolução Molecular Direcionada/métodos , Enzimas/química , Evolução Química , Liases/química , Catálise , Domínio Catalítico , Cristalografia por Raios X , Estabilidade Enzimática , Enzimas/genética , Enzimas/metabolismo , Cinética , Liases/genética , Liases/metabolismo , Simulação de Dinâmica Molecular , Mutação , Conformação Proteica , Engenharia de Proteínas
2.
Sheng Wu Gong Cheng Xue Bao ; 36(8): 1556-1567, 2020 Aug 25.
Artigo em Chinês | MEDLINE | ID: mdl-32924354

RESUMO

Improving the thermal stability of enzymes is a hot and difficult point in the field of biocatalysis. Compared with the traditional directed evolution, computational assisted rational design is more efficient, and is widely used in enzyme engineering. Using Bacillus subtilis LipA as the model protein, the structure cavity of the enzyme was analyzed by Rosetta-VIP design, the mutation which was beneficial to the filling of the structure cavity (ΔΔE<0) was selected, followed by the solvent accessible surface area and evolutionary conservation analysis. The thermal stabilities of six out of sixteen designed single-point mutants were improved, with a maximum ΔTm value of 3.18 °C. These six mutations were further used for iterative combination mutation, the maximum ΔTm of the two-point and three-point combination mutants were 4.04 °C and 5.13 °C, respectively. The Tm of the four-point combination mutant M11 (F17A/L114P/I135V/M137L) was increased by 7.30 °C. The Tm of the six-point combination mutant M10 (F17A/V74I/L114P/I135V/M137A/I157L) was increased by 7.43 °C. The thermal stability of mutation with lower energy value, reduced accessible surface area, while conformed to evolutionary conservatism, was more likely to be improved. Therefore, the multiple virtual screening strategy based on the enzyme structure cavity filling, solvent accessible surface area and amino acid sequence conservation analysis can effectively improve the thermal stability of enzyme.


Assuntos
Bacillus subtilis , Biologia Computacional , Estabilidade Enzimática , Lipase , Bacillus subtilis/enzimologia , Bacillus subtilis/genética , Lipase/química , Lipase/genética , Lipase/metabolismo , Mutação
3.
Sheng Wu Gong Cheng Xue Bao ; 36(8): 1568-1577, 2020 Aug 25.
Artigo em Chinês | MEDLINE | ID: mdl-32924355

RESUMO

Catalase catalyzes the decomposition of H2O2 to H2O and O2, and has a wide range of industrial applications. However, most catalases used in the textile and paper industries are often subjected to high-alkaline challenges which makes it necessary to develop alkaline catalase. In this study, a catalase from Corynebacterium glutamicum was expressed in Escherichia coli, and the expression conditions were optimized. The recombinant catalase was purified by Ni-chelating affinity chromatography, and the recombinant enzyme was characterized. The optimal conditions of producing the recombinant catalase were: an IPTG concentration of 0.2 mmol/L, a culturing temperature of 25 °C and a culturing time of 11 h. The purified catalase had a specific activity of 55 266 U/mg, and it had a high activity in the pH range of 4.0 to11.5, with the highest activity at pH 11.0. When treated in pH 11.0 for 3 h, the enzyme retained 93% of its activity, indicating that the enzyme was qualified with a favorable stability under high-alkaline condition. The recombinant catalase had maximal activity at 30 °C, and showed a satisfactory thermal stability at a range of 25 °C to 50 °C. The apparent Km and Vmax values of purified catalase were 25.89 mmol/L and 185.18 mmol/(minmg), respectively. Besides, different inhibitors, such as sodium dodecyl sulfate (SDS), urea, NaN2, ß-mercaptoethanol, and EDTA had different degrees of inhibition on enzyme activity. The catalase from C. glutamicum shows high catalytic efficiency and high alkaline stability, suggesting its potential utilization in industrial production.


Assuntos
Catalase , Corynebacterium glutamicum , Regulação Enzimológica da Expressão Gênica , Catalase/genética , Catalase/isolamento & purificação , Catalase/metabolismo , Corynebacterium glutamicum/enzimologia , Ativação Enzimática , Estabilidade Enzimática , Concentração de Íons de Hidrogênio
4.
Nature ; 584(7821): 479-483, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32788728

RESUMO

Lipopolysaccharide (LPS) resides in the outer membrane of Gram-negative bacteria where it is responsible for barrier function1,2. LPS can cause death as a result of septic shock, and its lipid A core is the target of polymyxin antibiotics3,4. Despite the clinical importance of polymyxins and the emergence of multidrug resistant strains5, our understanding of the bacterial factors that regulate LPS biogenesis is incomplete. Here we characterize the inner membrane protein PbgA and report that its depletion attenuates the virulence of Escherichia coli by reducing levels of LPS and outer membrane integrity. In contrast to previous claims that PbgA functions as a cardiolipin transporter6-9, our structural analyses and physiological studies identify a lipid A-binding motif along the periplasmic leaflet of the inner membrane. Synthetic PbgA-derived peptides selectively bind to LPS in vitro and inhibit the growth of diverse Gram-negative bacteria, including polymyxin-resistant strains. Proteomic, genetic and pharmacological experiments uncover a model in which direct periplasmic sensing of LPS by PbgA coordinates the biosynthesis of lipid A by regulating the stability of LpxC, a key cytoplasmic biosynthetic enzyme10-12. In summary, we find that PbgA has an unexpected but essential role in the regulation of LPS biogenesis, presents a new structural basis for the selective recognition of lipids, and provides opportunities for future antibiotic discovery.


Assuntos
Membrana Celular/química , Escherichia coli/química , Escherichia coli/patogenicidade , Lipopolissacarídeos/química , Lipopolissacarídeos/metabolismo , Amidoidrolases/química , Amidoidrolases/metabolismo , Motivos de Aminoácidos , Membrana Externa Bacteriana/química , Membrana Externa Bacteriana/metabolismo , Sítios de Ligação , Membrana Celular/metabolismo , Estabilidade Enzimática , Escherichia coli/citologia , Escherichia coli/efeitos dos fármacos , Genes Essenciais , Hidrolases/química , Hidrolases/metabolismo , Lipídeo A/química , Lipídeo A/metabolismo , Lipopolissacarídeos/biossíntese , Testes de Sensibilidade Microbiana , Viabilidade Microbiana/efeitos dos fármacos , Modelos Moleculares , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/metabolismo , Fragmentos de Peptídeos/farmacologia , Periplasma/química , Periplasma/metabolismo , Ligação Proteica , Virulência
5.
Bioresour Technol ; 317: 124020, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32827973

RESUMO

In view of the potential applications of immobilized enzymes, partially purified Lignin Peroxidase (LiP) from Pseudomonas fluorescens LiP-RL5 was immobilized on Graphene Oxide functionalized MnFe2O4 nanoparticles (10 nm, synthesized by sol-gel auto-combustion) to fabricate a new hyperactive and thermostable nanobiocatalyst and thereafter characterized by using standard techniques. Immobilized LiP was quite stable at 50 °C with the half-life of 14 h and showed higher tolerance towards various metal ions and solvents than free LiP. Immobilized LiP retained 50% of enzyme activity even after nine consecutive runs. When tested against various textile dyes, the immobilized LiP was found quite effective with higher dye decolourization efficiency (up to 88%) within 1 h of incubation at 30 °C. The results of this research effort confirmed that the immobilization of LiP and fabrication of nanobiocatalyst increase the efficacy, stability, and reusability of the enzyme which could be efficiently utilized under harsh industrial conditions.


Assuntos
Grafite , Nanopartículas de Magnetita , Estabilidade Enzimática , Enzimas Imobilizadas , Concentração de Íons de Hidrogênio , Peroxidases , Temperatura
6.
J Oleo Sci ; 69(8): 893-905, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32759550

RESUMO

In this study, lipase from Thermomyces lanuginosus (TLL) was immobilized onto the parent and organic groups modified SBA-15, and the enzymatic properties of the obtained immobilized TLL samples were investigated. 1) Activity of SBA-15-TLL at 2862.78 ± 293.24 U/g was obtained. 2) Most of the organic groups modification favored a great improvement in activity, and higher activity over 12000 U/g was observed for N-phenylaminomethyl and phenyl group modification. 3) Most of the supported TLL showed better thermostability in air while poor in phosphate buffer, with over 80% vers less than 20% of their initial activity retained after 4 h incubation at 70℃. 4) The n-dodecyl, phenyl and N-phenylaminomethyl group functionalization decreased the sensitivity of immobilized TLL in extreme pH values. 5) The n-octyl and 2-(propoxymethyl)oxirane group modification confered the supported TLL good reusability, and over 60% of their initial activity was retained after five successive cycles of reuse.


Assuntos
Ascomicetos/enzimologia , Enzimas Imobilizadas/química , Lipase/química , Dióxido de Silício/química , Estabilidade Enzimática , Óxido de Etileno/química , Concentração de Íons de Hidrogênio , Fenômenos de Química Orgânica , Espaço Pessoal , Fosfatos
7.
EBioMedicine ; 59: 102980, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32862101

RESUMO

BACKGROUND: Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease as well as Lou Gehrig's disease, is a progressive neurological disorder selectively affecting motor neurons with no currently known cure. Around 20% of the familial ALS cases arise from dominant mutations in the sod1 gene encoding superoxide dismutase1 (SOD1) enzyme. Aggregation of mutant SOD1 in familial cases and of wild-type SOD1 in at least some sporadic ALS cases is one of the known causes of the disease. Riluzole, approved in 1995 and edaravone in 2017 remain the only drugs with limited therapeutic benefits. METHODS: We have utilised the ebselen template to develop novel compounds that redeem stability of mutant SOD1 dimer and prevent aggregation. Binding modes of compounds have been visualised by crystallography. In vitro neuroprotection and toxicity of lead compounds have been performed in mouse neuronal cells and disease onset delay of ebselen has been demonstrated in transgenic ALS mice model. FINDING: We have developed a number of ebselen-based compounds with improvements in A4V SOD1 stabilisation and in vitro therapeutic effects with significantly better potency than edaravone. Structure-activity relationship of hits has been guided by high resolution structures of ligand-bound A4V SOD1. We also show clear disease onset delay of ebselen in transgenic ALS mice model holding encouraging promise for potential therapeutic compounds. INTERPRETATION: Our finding established the new generation of organo-selenium compounds with better in vitro neuroprotective activity than edaravone. The potential of this class of compounds may offer an alternative therapeutic agent for ALS treatment. The ability of these compounds to target cysteine 111 in SOD may have wider therapeutic applications targeting cysteines of enzymes involved in pathogenic and viral diseases including main protease of SARS-Cov-2 (COVID-19). FUNDING: Project funding was supported by the ALS Association grant (WA1128) and Fostering Joint International Research (19KK0214) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.


Assuntos
Esclerose Amiotrófica Lateral/tratamento farmacológico , Compostos Organosselênicos/uso terapêutico , Superóxido Dismutase-1/metabolismo , Esclerose Amiotrófica Lateral/mortalidade , Esclerose Amiotrófica Lateral/patologia , Animais , Azóis/química , Azóis/metabolismo , Azóis/uso terapêutico , Betacoronavirus/metabolismo , Sítios de Ligação , Linhagem Celular Tumoral , Cristalografia por Raios X , Dimerização , Modelos Animais de Doenças , Estabilidade Enzimática , Camundongos , Camundongos Transgênicos , Simulação de Dinâmica Molecular , Fármacos Neuroprotetores/química , Fármacos Neuroprotetores/metabolismo , Fármacos Neuroprotetores/uso terapêutico , Compostos Organosselênicos/química , Compostos Organosselênicos/metabolismo , Estrutura Terciária de Proteína , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Superóxido Dismutase-1/genética , Taxa de Sobrevida , Proteínas da Matriz Viral/química , Proteínas da Matriz Viral/metabolismo
8.
PLoS One ; 15(7): e0235687, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32678825

RESUMO

Lactobacillus amylolyticus L6, a gram-positive amylolytic bacterium isolated from naturally fermented tofu whey (NFTW), was able to hydrolyze raffinose and stachyose for the production of α-galactosidase. The cell-free extract of L. amylolyticus L6 was found to exhibit glycosyltransferase activity to synthesize α-galacto-oligosaccharides (GOS) with melibiose as substrate. The coding genes of α-galactosidase were identified in the genome of L. amylolyticus L6. The α-galactosidase (AglB) was placed into GH36 family by amino acid sequence alignments with other α-galactosidases from lactobacilli. The optimal reaction conditions of pH and temperature for AglB were pH 6.0 and 37°C, respectively. Besides, potassium ion was found to improve the activity of AglB while divalent mercury ion, copper ion and zinc ion displayed different degrees of inhibition effect. Under the optimum reaction condition, AglB could catalyze the synthesis of GOS with degree of polymerization (DP) ≥5 by using 300 mM melibiose concentration as substrate. The maximum yield of GOS with (DP) ≥3 could reach 31.56% (w/w). Transgalactosyl properties made AglB a potential candidate for application in the production of GOS.


Assuntos
Proteínas de Bactérias/metabolismo , Clonagem Molecular , Lactobacillus/enzimologia , alfa-Galactosidase/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Estabilidade Enzimática , Glicosilação , Concentração de Íons de Hidrogênio , Hidrólise , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/isolamento & purificação , Alinhamento de Sequência , Temperatura , alfa-Galactosidase/química , alfa-Galactosidase/genética
9.
Food Chem ; 332: 127438, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32645671

RESUMO

ß-N-acetylhexosaminidases have attracted much attention in recent years due to their potential application in oligosaccharide production, in particular lacto-N-triose II (LNT2) and lacto-N-neotetraose (LNnT) synthesis, which can be further used as backbone precursors for human milk oligosaccharides. A novel ß-N-acetylhexosaminidase gene from Tyzzerella nexilis (TnHex189) was heterologously expressed in Bacillus subtilis. The highest ß-N-acetylhexosaminidase activity of 14.5 U mL-1 was obtained in a 5-L fermentor by fed-batch fermentation for 27 h. TnHex189 was optimally active at pH 5.0 and 45 °C. It efficiently synthesized LNT2 with a conversion ratio of 57.2% (4.7 g L-1). The synthesized LNT2 was further converted to LNnT by a reported ß-galactosidase (BgaD-D) in 8 h, with a conversion ratio of 17.3% (6.1 g L-1). These unique synthesis activities may make this enzyme a good candidate for the food industry.


Assuntos
Proteínas de Bactérias/metabolismo , Clostridiales/enzimologia , Trissacarídeos/biossíntese , beta-N-Acetil-Hexosaminidases/metabolismo , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Clostridiales/genética , Estabilidade Enzimática , Fermentação , Expressão Gênica , Concentração de Íons de Hidrogênio , Oligossacarídeos/metabolismo , beta-N-Acetil-Hexosaminidases/química , beta-N-Acetil-Hexosaminidases/genética
10.
PLoS One ; 15(7): e0236518, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32702033

RESUMO

Thermophilic microorganisms and their enzymes have been utilized in various industrial applications. In this work, we isolated and characterized thermophilic anaerobic bacteria with the cellulose and hemicellulose degrading activities from a tropical dry deciduous forest in northern Thailand. Out of 502 isolated thermophilic anaerobic soil bacteria, 6 isolates, identified as Thermoanaerobacterium sp., displayed an ability to utilize a wide range of oligosaccharides and lignocellulosic substrates. The isolates exhibited significant cellulase and xylanase activities at high temperature (65°C). Among all isolates, Thermoanaerobacterium sp. strain R63 exhibited remarkable hydrolytic properties with the highest cellulase and xylanase activities at 1.15 U/mg and 6.17 U/mg, respectively. Extracellular extract of Thermoanaerobacterium sp. strain R63 was thermostable with an optimal temperature at 65°C and could exhibit enzymatic activities on pH range 5.0-9.0. Our findings suggest promising applications of these thermoanaerobic bacteria and their potent enzymes for industrial purposes.


Assuntos
Celulose/metabolismo , Polissacarídeos/metabolismo , Microbiologia do Solo , Thermoanaerobacterium/metabolismo , Proteínas de Bactérias/metabolismo , Biomassa , Celulase/metabolismo , Endo-1,4-beta-Xilanases/metabolismo , Estabilidade Enzimática , Temperatura Alta , Concentração de Íons de Hidrogênio , Filogenia , Especificidade por Substrato , Thermoanaerobacterium/classificação , Thermoanaerobacterium/enzimologia , Thermoanaerobacterium/isolamento & purificação
11.
Artigo em Inglês | MEDLINE | ID: mdl-32664813

RESUMO

Alkaline proteases having activity and stability at alkaline pH possess a large variety of applications in many industries. Growing renewed interest urges the need to find a single alkaline protease with promising properties to be used in different industrial processes. Herein, alkaline proteases produced through fermentation of cheap and easily available organic municipal solid wastes by Bacillus subtilis AKAL7 and Exiguobacterium indicum AKAL11 were purified to investigate their kinetic and thermodynamic parameters, detergent compatibility, dehairing and feather-degrading capability. Sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed that the purified protease from B. subtilis and E. indicum had molecular mass of ∼45 and 75 kDa, respectively. The protease from B. subtilis and E. indicum showed highest activity at 55 and 50 °C having low K m 1.17 and 0.567 mg/mL and high V max 416.67 and 333.33 µmole/min, respectively. The activation energy and temperature quotient of protease from B. subtilis and E. indicum were 26.52 and 65.75 kJ/mole, and 1.0004 and 1.0003 at 20-55 and 20-50 °C, respectively. Thermodynamics analysis revealed the formation of more ordered enzyme-substrate complexes along with spontenity of enzyme reaction. The protease from E. indicum exhibited better compatibility at higher concentration of detergents compared to that from B. subtilis. However, both proteases could retain more than 80% of the activity in the presence of 0.1% commercial laundry detergents. The purified protease from the both sources could degrade almost 90% of barbs and 40% of dry weight of the native feather and that from E. indicum could dehair cow skin. Results reported herein suggest that the alkaline protease from B. subtilis AKAL7 and E. indicum AKAL11 has biotechnological implications in detergent, leather and poultry feather processing industries.


Assuntos
Bacillales/enzimologia , Bacillus subtilis/enzimologia , Proteínas de Bactérias/metabolismo , Endopeptidases/metabolismo , Resíduos Sólidos , Animais , Detergentes/química , Estabilidade Enzimática , Plumas , Fermentação , Cinética , Peso Molecular , Temperatura
12.
PLoS One ; 15(6): e0234958, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32574185

RESUMO

Proteases play an essential role in living organisms and represent one of the largest groups of industrial enzymes. The aim of this work was recombinant production and characterization of a newly identified thermostable protease 1147 from thermophilum indigenous Cohnella sp. A01. Phylogenetic tree analysis showed that protease 1147 is closely related to the cysteine proteases from DJ-1/ThiJ/PfpI superfamily, with the conserved catalytic tetrad. Structural prediction using MODELLER 9v7 indicated that protease 1147 has an overall α/ß sandwich tertiary structure. The gene of protease 1147 was cloned and expressed in Escherichia coli (E. coli) BL21. The recombinant protease 1147 appeared as a homogenous band of 18 kDa in SDS-PAGE, which was verified by western blot and zymography. The recombinant protein was purified with a yield of approximately 88% in a single step using Ni-NTA affinity chromatography. Furthermore, a rapid one-step thermal shock procedure was successfully implemented to purify the protein with a yield of 73%. Using casein as the substrate, Km, and kcat, kcat/Km values of 13.72 mM, 3.143 × 10-3 (s-1), and 0.381 (M-1 S-1) were obtained, respectively. The maximum protease activity was detected at pH = 7 and 60°C with the inactivation rate constant (kin) of 2.10 × 10-3 (m-1), and half-life (t1/2) of 330.07 min. Protease 1147 exhibited excellent stability to organic solvent, metal ions, and 1% SDS. The protease activity was significantly enhanced by Tween 20 and Tween 80 and suppressed by cysteine protease specific inhibitors. Docking results and molecular dynamics (MD) simulation revealed that Tween 20 interacted with protease 1147 via hydrogen bonds and made the structure more stable. CD and fluorescence spectra indicated structural changes taking place at 100°C, very basic and acidic pH, and in the presence of Tween 20. These properties make this newly characterized protease a potential candidate for various biotechnological applications.


Assuntos
Bacillales/enzimologia , Proteínas de Bactérias/química , Peptídeo Hidrolases/química , Proteínas de Bactérias/isolamento & purificação , Proteínas de Bactérias/ultraestrutura , Clonagem Molecular , Ensaios Enzimáticos , Estabilidade Enzimática , Concentração de Íons de Hidrogênio , Simulação de Dinâmica Molecular , Peso Molecular , Peptídeo Hidrolases/isolamento & purificação , Peptídeo Hidrolases/ultraestrutura , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/ultraestrutura , Especificidade por Substrato
13.
Nat Commun ; 11(1): 3219, 2020 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-32591542

RESUMO

The receptor-linked protein tyrosine phosphatases (RPTPs) are key regulators of cell-cell communication through the control of cellular phosphotyrosine levels. Most human RPTPs possess an extracellular receptor domain and tandem intracellular phosphatase domains: comprising an active membrane proximal (D1) domain and an inactive distal (D2) pseudophosphatase domain. Here we demonstrate that PTPRU is unique amongst the RPTPs in possessing two pseudophosphatase domains. The PTPRU-D1 displays no detectable catalytic activity against a range of phosphorylated substrates and we show that this is due to multiple structural rearrangements that destabilise the active site pocket and block the catalytic cysteine. Upon oxidation, this cysteine forms an intramolecular disulphide bond with a vicinal "backdoor" cysteine, a process thought to reversibly inactivate related phosphatases. Importantly, despite the absence of catalytic activity, PTPRU binds substrates of related phosphatases strongly suggesting that this pseudophosphatase functions in tyrosine phosphorylation by competing with active phosphatases for the binding of substrates.


Assuntos
Proteínas Tirosina Fosfatases Classe 2 Semelhantes a Receptores/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Biocatálise , Linhagem Celular , Dissulfetos/metabolismo , Estabilidade Enzimática , Humanos , Modelos Moleculares , Oxirredução , Ligação Proteica , Domínios Proteicos , Proteínas Tirosina Fosfatases Classe 2 Semelhantes a Receptores/química , Especificidade por Substrato
14.
Proc Natl Acad Sci U S A ; 117(25): 14127-14138, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-32522879

RESUMO

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG's role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.


Assuntos
Síndrome de Cockayne/genética , Proteínas de Ligação a DNA/química , Endonucleases/química , Proteínas Nucleares/química , Mutação Puntual , Fatores de Transcrição/química , Xeroderma Pigmentoso/genética , Sítios de Ligação , Sequência Conservada , DNA/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Endonucleases/genética , Endonucleases/metabolismo , Estabilidade Enzimática , Humanos , Simulação de Dinâmica Molecular , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Fenótipo , Ligação Proteica , Dobramento de Proteína , Multimerização Proteica , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
15.
Nat Commun ; 11(1): 2689, 2020 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-32483206

RESUMO

The antiandrogen enzalutamide (Enz) has improved survival in castration resistant prostate cancer (CRPC) patients. However, most patients eventually develop Enz resistance that may involve inducing the androgen receptor (AR) splicing variant 7 (ARv7). Here we report that high expression of monoamine oxidase-A (MAO-A) is associated with positive ARv7 detection in CRPC patients following Enz treatment. Targeting MAO-A with phenelzine or clorgyline, the FDA-approved drugs for antidepression, resensitize the Enz resistant (EnzR) cells to Enz treatment and further suppress EnzR cell growth in vitro and in vivo. Our findings suggest that Enz-increased ARv7 expression can transcriptionally enhance MAO-A expression resulting in Enz resistance via altering the hypoxia HIF-1α signals. Together, our results show that targeting the Enz/ARv7/MAO-A signaling with the antidepressants phenelzine or clorgyline can restore Enz sensitivity to suppress EnzR cell growth, which may indicate that these antidepression drugs can overcome the Enz resistance to further suppress the EnzR CRPC.


Assuntos
Clorgilina/farmacologia , Inibidores da Monoaminoxidase/farmacologia , Fenelzina/farmacologia , Feniltioidantoína/análogos & derivados , Neoplasias de Próstata Resistentes à Castração/tratamento farmacológico , Processamento Alternativo , Animais , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/genética , Estabilidade Enzimática , Regulação Enzimológica da Expressão Gênica/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Masculino , Camundongos , Camundongos Nus , Camundongos SCID , Monoaminoxidase/química , Monoaminoxidase/genética , Monoaminoxidase/metabolismo , Células Neoplásicas Circulantes/metabolismo , Feniltioidantoína/farmacologia , Neoplasias de Próstata Resistentes à Castração/genética , Neoplasias de Próstata Resistentes à Castração/metabolismo , Receptores Androgênicos/genética , Receptores Androgênicos/metabolismo , Transdução de Sinais/efeitos dos fármacos , Regulação para Cima/efeitos dos fármacos , Ensaios Antitumorais Modelo de Xenoenxerto
16.
Food Chem ; 331: 127322, 2020 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-32569968

RESUMO

Here we report a novel strategy for the immobilization of invertase using amyloid-like fibrils as a support. Optimal conditions to get Tyr-Tyr covalent binding between invertase and the support were determined using a photocrosslinking approach. The biological fibrils with invertase activity turn into microstructured catalysts according to electron microscopy outcomes. Thermal and storage stability as well as optimal pH and temperature of the enzyme were conserved. Moreover, the immobilized enzyme recovered by low g-force centrifugation retained 83% of its initial enzymatic activity after 15 reuse cycles. Considering that enzyme cost is the most significant part of the overall fee of enzymatic biomass conversion, the highly efficient recovery/reuse strategy described herein becomes relevant. Besides, it can also be applied to the immobilization of other enzymes for industrial biocatalysis.


Assuntos
Biocatálise , Enzimas Imobilizadas/química , Enzimas Imobilizadas/metabolismo , beta-Frutofuranosidase/química , beta-Frutofuranosidase/metabolismo , Estabilidade Enzimática , Concentração de Íons de Hidrogênio , Agregados Proteicos , Temperatura
17.
J Vis Exp ; (159)2020 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-32510498

RESUMO

Numerous somatic mutations occurring in the epidermal growth factor receptor (EGFR) family (ErbB) of receptor tyrosine kinases (RTK) have been reported from cancer patients, although relatively few have been tested and shown to cause functional changes in ErbBs. The ErbB receptors are dimerized and activated upon ligand binding, and dynamic conformational changes of the receptors are inherent for induction of downstream signaling. For two mutations shown experimentally to alter EGFR function, A702V and the Δ746ELREA750 deletion mutation, we illustrate in the following protocol how molecular dynamics (MD) simulations can probe the (1) conformational stability of the mutant tyrosine kinase structure in comparison with wild-type EGFR; (2) structural consequences and conformational transitions and their relationship to observed functional changes; (3) effects of mutations on the strength of binding ATP as well as for binding between the kinase domains in the activated asymmetric dimer; and (4) effects of the mutations on key interactions within the EGFR binding site associated with the activated enzyme. The protocol provides a detailed step-by-step procedure as well as guidance that can be more generally useful for investigation of protein structures using MD simulations as a means to probe structural dynamics and the relationship to biological function.


Assuntos
Simulação de Dinâmica Molecular , Mutação , Trifosfato de Adenosina/metabolismo , Estabilidade Enzimática , Receptores ErbB/química , Receptores ErbB/genética , Receptores ErbB/metabolismo , Humanos , Ligação Proteica , Conformação Proteica , Transdução de Sinais
18.
Biochim Biophys Acta Bioenerg ; 1861(9): 148236, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32479753

RESUMO

Galdieria phlegrea is a polyextremophilic red alga belonging to Cyanidiophyceae. Galdieria phlegrea C-phycocyanin (GpPC), an abundant light-harvesting pigment with an important role in energy capture and transfer to photosystems, is the C-phycocyanin (C-PC) with the highest thermal stability described so far. GpPC also presents interesting antioxidant and anticancer activities. The X-ray structure of the protein was here solved. GpPC is a [(αß)3]2 hexamer, with the phycocyanobilin chromophore attached to Cys84α, Cys82ß and Cys153ß. Details of geometry and interaction with solvent of the chromophores are reported. Comparison with the structure of a C-PC in the entire Porphyridium purpureum phycobilisome system reveals that linker polypeptides have a significant effect on the local structure of the chromophores environment. Comparative analyses with the structures of other purified C-PCs, which were carried out including re-refined models of G. sulphuraria C-PC, reveal that GpPC presents a significantly higher number of inter-trimer salt bridges. Notably, the higher number of salt bridges at the (αß)3/(αß)3 interface is not due to an increased number of charged residues in this region, but to subtle conformational variations of their side chains, which are the result of mutations of close polar and non-polar residues.


Assuntos
Ficocianina/química , Rodófitas/enzimologia , Temperatura , Cristalografia por Raios X , Estabilidade Enzimática , Metilação , Modelos Moleculares , Ficocianina/metabolismo , Conformação Proteica
19.
Biochim Biophys Acta Proteins Proteom ; 1868(9): 140461, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32474108

RESUMO

d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (kcat/Km) of TTHA1643 toward d- and l-Glu was comparable; however, the kcat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.


Assuntos
Isomerases de Aminoácido/química , Isomerases de Aminoácido/genética , Isomerases de Aminoácido/metabolismo , Thermus thermophilus/enzimologia , Sequência de Aminoácidos , Aminoácidos/metabolismo , Parede Celular/química , Clonagem Molecular , Estabilidade Enzimática , Escherichia coli/metabolismo , Deleção de Genes , Genoma Bacteriano , Ácido Glutâmico/metabolismo , Concentração de Íons de Hidrogênio , Cinética , Proteínas Recombinantes , Especificidade por Substrato , Temperatura , Thermus thermophilus/genética , Thermus thermophilus/crescimento & desenvolvimento , Thermus thermophilus/fisiologia , Transcriptoma
20.
Biochim Biophys Acta Bioenerg ; 1861(10): 148234, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32485158

RESUMO

Photosystem II (PS II) catalyzes the light-driven process of water splitting in oxygenic photosynthesis. Four core membrane-spanning proteins, including D1 that binds the majority of the redox-active co-factors, are surrounded by 13 low-molecular-weight (LMW) proteins. We previously observed that deletion of the LMW PsbT protein in the cyanobacterium Synechocystis sp. PCC 6803 slowed electron transfer between the primary and secondary plastoquinone electron acceptors QA and QB and increased the susceptibility of PS II to photodamage. Here we show that photodamaged ∆PsbT cells exhibit unimpaired rates of oxygen evolution if electron transport is supported by HCO3- even though the cells exhibit negligible variable fluorescence. We find that the protein environment in the vicinity of QA and QB is altered upon removal of PsbT resulting in inhibition of QA- oxidation in the presence of 2,5-dimethyl-1,4-benzoquinone, an artificial PS II-specific electron acceptor. Thermoluminescence measurements revealed an increase in charge recombination between the S2 oxidation state of the water-oxidizing complex and QA- by the indirect radiative pathway in ∆PsbT cells and this is accompanied by increased 1O2 production. At the protein level, both D1 removal and replacement, as well as PS II biogenesis, were accelerated in the ∆PsbT strain. Our results demonstrate that PsbT plays a key role in optimizing the electron acceptor complex of the acceptor side of PS II and support the view that repair and biogenesis of PS II share an assembly pathway that incorporates both de novo synthesis and recycling of the assembly modules associated with the core membrane-spanning proteins.


Assuntos
Proteínas de Bactérias/metabolismo , Complexo de Proteína do Fotossistema II/metabolismo , Synechocystis/metabolismo , Synechocystis/efeitos da radiação , Estabilidade Enzimática/efeitos da radiação , Luz/efeitos adversos , Oxigênio Singlete/metabolismo
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