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1.
Protein J ; 43(5): 935-948, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39179691

ABSTRACT

Dihydrofolate reductase (DHFR) is ubiquitously present in all living organisms and plays a crucial role in the growth of the fungal pathogen R.solani. Sequence alignment confirmed the evolutionary conservation of the essential lid domain, with the amino acid 'P' within the PEKN lid domain appearing with a frequency of 89.5% in higher organisms and 11.8% in lower organisms. Consequently, a K65P variant was introduced into R.solani DHFR (rDHFR). Subsequent enzymatic kinetics assays were conducted for human DHFR (hDHFR), rDHFR, E. coli DHFR (eDHFR), and the K65P variant. hDHFR exhibited the highest kcat of 0.95 s-1, followed by rDHFR with 0.14 s-1, while eDHFR displayed the lowest kcat of 0.09 s-1. Remarkably, the K65P variant induced a significant reduction in Km, resulting in a 1.8-fold enhancement in catalytic efficiency (kcat/Km) relative to the wild type. Differential scanning fluorimetry and binding free energy calculations confirmed the enhanced substrate affinity for both folate and NADPH in the K65P variant. These results suggest that the K65P mutation enhances substrate affinity and catalytic efficiency in DHFR, highlighting the evolutionary and functional importance of the K65 residue.


Subject(s)
Molecular Dynamics Simulation , Tetrahydrofolate Dehydrogenase , Tetrahydrofolate Dehydrogenase/genetics , Tetrahydrofolate Dehydrogenase/chemistry , Tetrahydrofolate Dehydrogenase/metabolism , Humans , Escherichia coli/genetics , Escherichia coli/metabolism , Fungal Proteins/genetics , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Kinetics , Amino Acid Substitution , Substrate Specificity , Folic Acid/metabolism , Folic Acid/chemistry , NADP/metabolism , NADP/chemistry
2.
J Agric Food Chem ; 71(49): 19385-19395, 2023 Dec 13.
Article in English | MEDLINE | ID: mdl-38038282

ABSTRACT

Dihydrofolate reductase (DHFR) is an essential enzyme in the folate pathway and has been recognized as a well-known target for antibacterial and antifungal drugs. We discovered eight compounds from the ZINC database using virtual screening to inhibit Rhizoctonia solani (R. solani), a fungal pathogen in crops. These compounds were evaluated with in vitro assays for enzymatic and antifungal activity. Among these, compound Hit8 is the most active R. solani DHFR inhibitor, with the IC50 of 10.2 µM. The selectivity of inhibition is 22.3 against human DHFR with the IC50 of 227.7 µM. Moreover, Hit8 has higher antifungal activity against R. solani (EC50 of 38.2 mg L-1) compared with validamycin A (EC50 of 67.6 mg L-1), a well-documented fungicide. These results suggest that Hit8 may be a potential fungicide. Our study exemplifies a computer-aided method to discover novel inhibitors that could target plant pathogenic fungi.


Subject(s)
Folic Acid Antagonists , Fungicides, Industrial , Humans , Fungicides, Industrial/pharmacology , Antifungal Agents/pharmacology , Folic Acid Antagonists/pharmacology , Rhizoctonia , Structure-Activity Relationship , Plant Diseases/microbiology
3.
Behav Brain Res ; 442: 114330, 2023 03 28.
Article in English | MEDLINE | ID: mdl-36746309

ABSTRACT

Extracellular matrix proteins appear to be necessary for the synaptic plasticity that underlies addiction memory. In the brain, matrix metalloproteinases (MMPs), especially matrix metalloproteinase-9 (MMP-9), have been recently implicated in processes involving alcohol reward and memory. Here, we showed for the first time, the positive effects of MMP-9 on alcohol-induced conditioned place preference (CPP) behavior and hippocampal neuron plasticity in C57BL/6 mice. Using recombinant adeno-associated viruses to overexpress MMP-9 in the hippocampus, we investigated the NMDAR, PSD-95, and cellular cytoskeleton proteins F-actin/G-actin in the modulation of alcohol reward behavior in mice exposed to CPP. We found that hippocampal infusions of MMP-9 decreased alcohol-induced place preference suggesting a reduction in alcohol reward. Western blot analysis demonstrated that protein expression of NMDA receptors (GluN1, GluN2A and GluN2B) in the hippocampus of alcohol-exposed mice were higher than that of the saline group. Further, the expression of these proteins was decreased in MMP-9 overexpressing mice. MMP-9 also regulated the ratio of F-actin/G-actin (dendritic spines cytoskeleton proteins), which might be the key mediator for behavioral changes in mice. Consequently, our results highlight new evidence that MMP-9 may play an important role in the molecular mechanism underlying alcohol reward and preference.


Subject(s)
Actins , Ethanol , Matrix Metalloproteinase 9 , Neuronal Plasticity , Animals , Mice , Actins/metabolism , Ethanol/pharmacology , Hippocampus/metabolism , Matrix Metalloproteinase 9/metabolism , Mice, Inbred C57BL , Neuronal Plasticity/physiology , Conditioning, Classical
4.
Zhongguo Ying Yong Sheng Li Xue Za Zhi ; 38(2): 97-101, 2022 Mar.
Article in Chinese | MEDLINE | ID: mdl-36031564

ABSTRACT

Objective: To study the effects of Synaptotagmin1 gene knockout (Syt1+/-) on emotional behavior in mice and explore its possible mechanisms. Methods: Five 8-week-old male Syt1+/-mice and five wild-type (WT) mice in the same litter were selected. The expressions of Syt1 in 6 mice brain regions of prelimbic cortex (PL), hippocampus (HIP), amygdala (AMY), accumbens nucleus (ACB), caudoputamen (CP) and ventral tegmental area (VTA) were detected by Immunofluorescence staining. Nine 8-week-old male Syt1+/-mice and ten WT mice were selected as controls. The anxiety-like behaviors of adult Syt1+/- mice and WT mice were detected by open field test, elevated plus maze test and forced swim test. In addition, five 8-week-old male Syt1+/-mice and five WT mice were selected to detect the glutamate content in prelimbic cortex, hippocampus and amygdala. Results: Compared with WT mice, the number of Syt1 positive cells in PL, HIP, AMY, ACB, CP and VTA were decreased significantly in Syt1+/- mice (P<0.01); Syt1+/- mice had less total movement distance in open field test (P<0.01), more preference for peripheral area (P<0.01) and less desire to explore the central platform (P<0.01), while Syt1+/- mice preferred to stay in a closed and safe environment (P<0.01); the number (P<0.05) and the time spent in open-arm explorations (P<0.01) were reduced significantly; the immobile time of Syt1+/- mice was increased in the forced swim test (P<0.01). Meanwhile, the concentration of glutamate in the amygdala of Syt1+/- mice was increased significantly (P<0.01). Conclusion: Syt1 gene knockout leads to significant anxiety-like behavior in mice, which is deduced that related to the increase of glutamate content in the amygdala.


Subject(s)
Amygdala , Anxiety , Animals , Behavior, Animal , Gene Knockout Techniques , Glutamic Acid , Male , Mice , Mice, Inbred C57BL , Mice, Knockout
6.
Postgrad Med ; 133(6): 626-638, 2021 Aug.
Article in English | MEDLINE | ID: mdl-33993838

ABSTRACT

BACKGROUND AND AIMS: Lipid metabolism is often disrupted in liver cirrhosis. The present study aimed to evaluate the impact of lipid profile on decompensation events, severity of liver dysfunction, and death in patients with liver cirrhosis. METHODS: In a cross-sectional study, 778 patients with lipid profile data were enrolled, and then were divided into 240 and 538 patients with and without liver cirrhosis, respectively. In a cohort study, 314 cirrhotic patients with lipid profile data, who were prospectively followed, were enrolled. Lipid profile included total cholesterol (TC), high-density lipoprotein-cholesterol (HDL-c), low-density lipoprotein-cholesterol (LDL-c), triglycerides (TG), and lipoprotein(a). RESULTS: In the cross-sectional study, cirrhotic patients with decompensation events had significantly lower levels of TC and lipoprotein(a) than those without; and cirrhotic patients with Child-Pugh class B and C had significantly lower levels of TC, HDL-c, LDL-c, and lipoprotein(a) than those with Child-Pugh class A. In the cohort study, there was an inverse association of survival with TC, HDL-c, and lipoprotein(a) levels; after adjusting for MELD score, TC (Hazard Ratio [HR] = 1.703, P = 0.034) and HDL-c (HR = 2.036, P = 0.005), but not lipoprotein(a) (HR = 1.377, P = 0.191), remained a significant predictor of death; when TC, HDL-c, lipoprotein(a), and MELD score were included in the multivariate Cox regression analysis, HDL-c (HR = 1.844, P = 0.024) was the only independent predictor of death. CONCLUSIONS: Decreased levels in specific components of lipid profile indicate more decompensation events, worse liver function, and reduced survival in liver cirrhosis. MELD score combined with HDL-c should be promising for the assessment of outcomes of cirrhotic patients.


Subject(s)
Cholesterol, HDL/blood , Cholesterol, LDL/blood , Cholesterol/blood , Lipoprotein(a)/blood , Liver Cirrhosis , Triglycerides/blood , China/epidemiology , Cross-Sectional Studies , Female , Humans , Lipid Metabolism , Liver Cirrhosis/complications , Liver Cirrhosis/diagnosis , Liver Cirrhosis/metabolism , Liver Cirrhosis/mortality , Liver Function Tests/methods , Male , Middle Aged , Outcome Assessment, Health Care , Predictive Value of Tests , Prognosis , Research Design , Survival Analysis
8.
Ann Palliat Med ; 10(2): 1145-1153, 2021 Feb.
Article in English | MEDLINE | ID: mdl-32954752

ABSTRACT

BACKGROUND: Anemia is one of the most common disorders in the world. Serum iron is an essential element for the synthesis of hemoglobin and contribution of the oxygen-carrying ability of red blood cells (RBCs). Iron sucrose injection may effectively correct iron deficiency, increase iron storage, and then improve anemia. The aim of the present study was to evaluate the therapeutic effect of iron sucrose injection in anemia patients with reduced serum iron concentration. METHODS: Overall, 95 anemia patients with digestive and/or liver diseases were included. They were divided according to the infusion of iron sucrose injection during hospitalization. The paired sample t test was used for comparison between last and baseline hemoglobin concentration. The independent sample t test was used for comparison of a dynamic change of hemoglobin concentration between patients who received and did not receive infusion of iron sucrose injection. RESULTS: Iron sucrose injection was infused in 74 (77.90%) patients. Mean hemoglobin concentration after infusion of iron sucrose injection was significantly increased (91.61 vs. 94.98 g/L, P=0.011). Δ Hemoglobin concentration was significantly different between patients who received and did not receive infusion of iron sucrose injection (P=0.007). Mean hemoglobin concentration after infusion of iron sucrose injection remained significantly increased in subgroup analyses of patients with cirrhosis (88.30 vs. 91.98 g/L, P=0.035) and gastrointestinal bleeding (85.70 vs. 92.63 g/L, P<0.01). CONCLUSIONS: Iron sucrose injection can significantly increase the hemoglobin concentration in anemia patients with serum iron concentration below the lower limit of the normal range.


Subject(s)
Anemia, Iron-Deficiency , Anemia , Liver Diseases , Anemia/drug therapy , Anemia, Iron-Deficiency/drug therapy , Ferric Compounds/therapeutic use , Ferric Oxide, Saccharated , Glucaric Acid , Hospitalization , Humans , Iron , Liver Diseases/drug therapy
9.
Bioresour Bioprocess ; 8(1): 102, 2021 Oct 17.
Article in English | MEDLINE | ID: mdl-38650272

ABSTRACT

ß-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic ß-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like ß-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.

10.
Gastroenterol Res Pract ; 2020: 4019289, 2020.
Article in English | MEDLINE | ID: mdl-33029132

ABSTRACT

METHODS: Cirrhotic patients who were consecutively hospitalized between January 2016 and March 2019 were screened. Serum cardiac biomarkers at admission, including N-Terminal pro-B-type natriuretic peptide (NT-pro BNP), high-sensitivity cardiac troponin T (hs-cTnT), creatine kinase (CK), creatine kinase MB (CK-MB), and lactate dehydrogenase (LDH), were collected. Acute decompensating events at admission, primarily including ascites, acute gastrointestinal hemorrhage, and acute-on-chronic liver failure (ACLF), were recorded. RESULTS: The NT-pro BNP level was significantly higher in cirrhotic patients with acute decompensating events than in those without any decompensating events (median: 140.75 pg/mL versus 41.86 pg/mL, P < 0.001). The NT-pro BNP level significantly correlated with ascites, acute gastrointestinal hemorrhage, and ACLF. The hs-cTnT level was significantly higher in cirrhotic patients with acute decompensating events than in those without decompensating events (median: 0.008 ng/mL versus 0.006 ng/mL, P = 0.007). The hs-cTnT level significantly correlated with acute gastrointestinal hemorrhage, but not ascites or ACLF. LDH (185.0 U/L versus 173.5 U/L, P = 0.281), CK (71 U/L versus 84 U/L, P = 0.157), and CK-MB (29.5 U/L versus 33.0 U/L, P = 0.604) levels were not significantly different between cirrhotic patients with and without acute decompensating events. CONCLUSION: The elevated NT-pro BNP level seems to be closely related to the development of acute decompensating events in liver cirrhosis.

11.
Ecotoxicol Environ Saf ; 189: 110003, 2020 Feb.
Article in English | MEDLINE | ID: mdl-31791728

ABSTRACT

When the amount of pesticide exceeds the self-purification ability of the environment, it will be enriched in the human body through the atmosphere, soil, water circulation, etc., threatening human health. Aryloxy-phenoxy-propionate (APP) herbicides are a class of acetyl-CoA carboxylase (ACCase) inhibitor herbicides, widely used in field-weeding of soybean, cabbage, peanut and other crops. However, due to the water circulation, surface runoff and the agronomic practices such as watering irrigation, APP herbicides have the risk of polluting water and destroying the living environment of aquatic organisms. In this paper, a multistep framework combining homology modeling, molecular docking and molecular dynamic simulations were adopted to explore the interactions between APP herbicides and zebrafish estrogen receptor α (ERα) to investigate the estrogenic activities of the herbicides. The structure of zebrafish ERα was modeled by homology modeling, using the human's estrogen receptor α (PDB ID:2YJA) as the template. Then, eight typical APP herbicides were selected to dock with the zebrafish ERα, and it was determined that there were clear interactions between the herbicides and the receptor. The binding patterns of Quizalofop-P-ethyl (QPE), Clodinafop-propargyl (CP) and Haloxyfop-P (HP) with ERα were further investigated by molecular dynamics and binding free energy calculation. The results showed the van der Waals force and electrostatic force were the main driving forces for maintaining the stability of the complex system. In order to verify the theoretical prediction, an exposed experiment was conducted to study the effects of different concentrations of herbicides on VTG level of zebrafish in vivo and the results were consistent with the computational method. The results of this study revealed the mechanism of the action between APP herbicides and zebrafish estrogen receptors, and also provided ideas for optimizing the herbicides.


Subject(s)
Estrogen Receptor alpha/chemistry , Herbicides/chemistry , Propionates/chemistry , Water Pollutants, Chemical/chemistry , Zebrafish/metabolism , Acetyl-CoA Carboxylase/antagonists & inhibitors , Acetyl-CoA Carboxylase/chemistry , Animals , Computer Simulation , Models, Molecular , Protein Binding
12.
New Phytol ; 2019 Aug 22.
Article in English | MEDLINE | ID: mdl-31436314

ABSTRACT

Oomycete pathogens secrete numerous effectors to manipulate host immunity. While some effectors share a conserved structural fold, it remains unclear if any have conserved host targets. Avr3a-like family effectors, which are related to Phytophthora infestans effector PiAvr3a and are widely distributed across diverse clades of Phytophthora species, were used to study this question. By using yeast-two-hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays, we identified members of the plant cinnamyl alcohol dehydrogenase 7 (CAD7) subfamily as targets of multiple Avr3a-like effectors from Phytophthora pathogens. The CAD7 subfamily has expanded in plant genomes but lost the lignin biosynthetic activity of canonical CAD subfamilies. In turn, we identified CAD7s as negative regulators of plant immunity that are induced by Phytophthora infection. Moreover, AtCAD7 was stabilized by Avr3a-like effectors and involved in suppression of pathogen-associated molecular pattern-triggered immunity, including callose deposition, reactive oxygen species burst and WRKY33 expression. Our results reveal CAD7 subfamily proteins as negative regulators of plant immunity that are exploited by multiple Avr3a-like effectors to promote infection in different host plants.

13.
Plant Dis ; 103(10): 2599-2605, 2019 Oct.
Article in English | MEDLINE | ID: mdl-31339441

ABSTRACT

Tobacco black shank, caused by Phytophthora parasitica, is one of the most notorious tobacco diseases and causes huge economic losses worldwide. Understanding the genetic variation of P. parasitica populations is essential to the development of disease control measures. In this research, 210 simple sequence repeat (SSR) markers for P. parasitica were identified, 10 of which were polymorphic among nine reference strains. We further performed population genetic analysis of 245 P. parasitica isolates randomly collected from tobacco fields in Chongqing for mating type, molecular variation at 14 SSR loci (four of which were identified previously), and sensitivity to the fungicide metalaxyl. The results showed that the A2 mating type was dominant and no A1 mating type isolate was discovered. SSR genotyping distinguished 245 P. parasitica isolates into 46 genotypes, four of which were dominant in the population. Low genotypic diversity and excess heterozygosity were common in nearly all of the populations from Chongqing. Population analysis showed that no differentiation existed among different populations. All isolates tested were highly sensitive to metalaxyl. Taken together, our results showed that the P. parasitica populations from tobacco fields in Chongqing belonged to a clonal lineage and were highly sensitive to metalaxyl.


Subject(s)
Genetics, Population , Nicotiana , Phytophthora , Alanine/analogs & derivatives , Alanine/pharmacology , China , Genotype , Microsatellite Repeats/genetics , Phytophthora/drug effects , Phytophthora/genetics , Nicotiana/parasitology
14.
J Mol Model ; 25(6): 175, 2019 Jun 01.
Article in English | MEDLINE | ID: mdl-31154518

ABSTRACT

In this study, molecular docking studies were carried out to explore the binding interactions of sodium glucose co-transporter 2 (SGLT2) with its inhibitors. A correlation between the docking scores and the experimental bioactivity was observed (R2 = 0.8368, N = 24). The new inhibitors were designed using the 3D quantitative structure activity relationship (3D-QSAR) method, and the activities were predicted by the docking method. In order to understand the structure-activity correlation of compound 1 m (the highest score of docking) and compound 1 t (the lowest score), we carried out a combined molecular dynamics simulation and MM-GBSA method. It was found that, in the system of SGLT2-1 m, the interaction between Gln271 and Val272 exhibited significant effects, which were absent in the SGLT2-1 t system. This study is expected to shed light on the mechanism of action of compound 1 m, leading to development of active drug candidates targeting SGLT2.


Subject(s)
Molecular Docking Simulation , Molecular Dynamics Simulation , Sodium-Glucose Transporter 2 Inhibitors/chemistry , Sodium-Glucose Transporter 2/chemistry , Binding Sites , Drug Discovery , Molecular Conformation , Molecular Structure , Protein Binding , Quantitative Structure-Activity Relationship , Sodium-Glucose Transporter 2 Inhibitors/pharmacology
15.
Front Chem ; 7: 235, 2019.
Article in English | MEDLINE | ID: mdl-31111026

ABSTRACT

ß-N-acetyl-D-hexosaminidases have attracted significant attention due to their crucial role in diverse physiological functions including antibacterial synergists, pathogen defense, virus infection, lysosomal storage, and protein glycosylation. In particular, the GH3 ß-N-acetyl-D-hexosaminidase of V. cholerae (VcNagZ), human GH20 ß-N-acetyl-D-hexosaminidase B (HsHexB), and human GH84 ß-N-acetyl-D-hexosaminidase (hOGA) are three important representative glycosidases. These have been found to be implicated in ß-lactam resistance (VcNagZ), lysosomal storage disorders (HsHexB) and Alzheimer's disease (hOGA). Considering the profound effects of these three enzymes, many small molecule inhibitors with good potency and selectivity have been reported to regulate the corresponding physiological functions. In this paper, the best-known inhibitors PUGNAc and two of its derivatives (N-valeryl-PUGNAc and EtBuPUG) were selected as model compounds and docked into the active pockets of VcNagZ, HsHexB, and hOGA, respectively. Subsequently, molecular dynamics simulations of the nine systems were performed to systematically compare their binding modes from active pocket architecture and individual interactions. Furthermore, the binding free energy and free energy decomposition are calculated using the MM/GBSA methods to predict the binding affinities of enzyme-inhibitor systems and to quantitatively analyze the contribution of each residue. The results show that PUGNAc is deeply-buried in the active pockets of all three enzymes, which indicates its potency (but not selectivity) against VcNagZ, HsHexB, and hOGA. However, EtBuPUG, bearing branched 2-isobutamido, adopted strained conformations and was only located in the active pocket of VcNagZ. It has completely moved out of the pocket of HsHexB and lacks interactions with HsHexB. This indicates why the selectivity of EtBuPUG to VcNagZ/HsHexB is the largest, reaching 968-fold. In addition, the contributions of the catalytic residue Asp253 (VcNagZ), Asp254 (VcNagZ), Asp175 (hOGA), and Asp354 (HsHexB) are important to distinguish the activity and selectivity of these inhibitors. The results of this study provide a helpful structural guideline to promote the development of novel and selective inhibitors against specific ß-N-acetyl-D-hexosaminidases.

16.
J Biomater Sci Polym Ed ; 29(12): 1463-1481, 2018 08.
Article in English | MEDLINE | ID: mdl-29734864

ABSTRACT

Polyvinyl alcohol (PVA) hydrogels have been widely studied for biomedical applications due to their water solubility, non-toxicity, non-carcinogenicity, and biocompatibility. However, PVA hydrogels prepared by the physical crosslinking method usually do not exhibit a macroporous structure, which limits their application when PVA hydrogels are used alone as a wound dressing. Here, we reported a sponge-like macroporous PVA hydrogel (SPH) prepared by employing polyethylene glycol and nano-hydroxyapatite (n-HA) to enhance phase separation. After being fabricated through cyclic freezing/thawing, the resulting PVA hydrogels possessed macroporous structures. The swelling ratio could reach nearly 1500%, resulting from the excellent water absorption capacity, and the sample could rapidly restore to the original state after being pressed, suggesting a sponge-like characteristic. Furthermore, cell experiments showed that macroporous PVA hydrogels exhibited good biocompatibility and the results of wound closure and H&E analysis consistently indicated that SPHs could significantly promote the wound healing process.


Subject(s)
Bandages , Durapatite/chemistry , Nanoparticles/chemistry , Polyvinyl Alcohol/chemistry , Wound Healing/drug effects , Animals , Biocompatible Materials , Cell Line , Cell Survival/drug effects , Female , Fibroblasts/cytology , Humans , Mechanical Phenomena , Phase Transition , Polyethylene Glycols/chemistry , Porosity , Rabbits , Solubility , Surface Properties
17.
J Mol Model ; 24(4): 86, 2018 Mar 06.
Article in English | MEDLINE | ID: mdl-29511885

ABSTRACT

Human sodium-dependent glucose co-transporter 2 (hSGLT2) is a crucial therapeutic target in the treatment of type 2 diabetes. In this study, both comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to generate three-dimensional quantitative structure-activity relationship (3D-QSAR) models. In the most accurate CoMFA-based and CoMSIA-based QSAR models, the cross-validated coefficients (r2cv) were 0.646 and 0.577, respectively, while the non-cross-validated coefficients (r2) were 0.997 and 0.991, respectively, indicating that both models were reliable. In addition, we constructed a homology model of hSGLT2 in the absence of a crystal structure. Molecular docking was performed to explore the bonding mode of inhibitors to the active site of hSGLT2. Molecular dynamics (MD) simulations and binding free energy calculations using MM-PBSA and MM-GBSA were carried out to further elucidate the interaction mechanism. With regards to binding affinity, we found that hydrogen-bond interactions of Asn51 and Glu75, located in the active site of hSGLT2, with compound 40 were critical. Hydrophobic and electrostatic interactions were shown to enhance activity, in agreement with the results obtained from docking and 3D-QSAR analysis. Our study results shed light on the interaction mode between inhibitors and hSGLT2 and may aid in the development of C-aryl glucoside SGLT2 inhibitors.


Subject(s)
Drug Discovery , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Sodium-Glucose Transporter 2/chemistry , Binding Sites , Catalytic Domain , Drug Discovery/methods , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Inhibitory Concentration 50 , Molecular Conformation , Protein Binding , Quantitative Structure-Activity Relationship , Reproducibility of Results , Sodium-Glucose Transporter 2 Inhibitors
18.
Enzyme Microb Technol ; 91: 59-65, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27444330

ABSTRACT

In the present work, NAD(+)-dependent formate dehydrogenase (FDH), encoded by fdh gene from Candida boidinii was successfully displayed on Escherichia coli cell surface using ice nucleation protein (INP) from Pseudomonas borealis DL7 as an anchoring protein. Localization of matlose binding protein (MBP)-INP-FDH fusion protein on the E. coli cell surface was characterized by SDS-PAGE and enzymatic activity assay. FDH activity was monitored through the oxidation of formate catalyzed by cell-surface-displayed FDH with its cofactor NAD(+), and the production of NADH can be detected spectrometrically at 340nm. After induction for 24h in Luria-Bertani medium containing isopropyl-ß-d-thiogalactopyranoside, over 80% of MBP-INP-FDH fusion protein present on the surface of E. coli cells. The cell-surface-displayed FDH showed optimal temperature of 50°C and optimal pH of 9.0. Additionally, the cell-surface-displayed FDH retained its original enzymatic activity after incubation at 4°C for one month with the half-life of 17days at 40°C and 38h at 50°C. The FDH activity could be inhibited to different extents by some transition metal ions and anions. Moreover, the E. coli cells expressing FDH showed different tolerance to solvents. The recombinant whole cell exhibited high formate specificity. Finally, the E. coli cell expressing FDH was used to assay formate with a wide linear range of 5-700µM and a low limit of detection of 2µM. It is anticipated that the genetically engineered cells may have a broad application in biosensors, biofuels and cofactor regeneration system.


Subject(s)
Formate Dehydrogenases/metabolism , Formates/analysis , Fungal Proteins/metabolism , Bacterial Outer Membrane Proteins/genetics , Bacterial Outer Membrane Proteins/metabolism , Candida/enzymology , Candida/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Formate Dehydrogenases/genetics , Fungal Proteins/genetics , Genes, Fungal , Kinetics , Limit of Detection , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Spectrophotometry, Ultraviolet , Substrate Specificity
19.
Enzyme Microb Technol ; 84: 78-85, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26827777

ABSTRACT

In this paper, the construction of 3D model structure of xylose dehydrogenase (XDH) by using homology modeling to guide the rational design of the enzyme for improving thermostability was reported. Three XDH mutants of NA-1 (+249L), NA-2 (G149P) and NA-3 (+249L/G149P) were designed and displayed on the surface of bacteria. Among them, bacteria displaying NA-1 (NA-1-bacteria) exhibited superior thermostability without compromising its activity and substrate specificity in comparison with its wild-type counterpart. NA-1-bacteria retained its original activity after incubation at room temperature for one-month with the half-life of 9.8 days at 40°C. Finally, the NA-1-bacteria were applied to construct xylose/O2 based biofuel cell with good performance including enhanced operational stability. Thus, the approach described here could be explored for engineering of other enzymes for improving certain characters without three-dimensional structure identified by experimental methods.


Subject(s)
Alcohol Oxidoreductases/chemistry , Alcohol Oxidoreductases/metabolism , Bioelectric Energy Sources , Alcohol Oxidoreductases/genetics , Amino Acid Sequence , Enzyme Stability , Kinetics , Models, Molecular , Molecular Sequence Data , Mutagenesis, Site-Directed , Protein Conformation , Protein Engineering , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid , Structural Homology, Protein , Substrate Specificity
20.
Bioresour Technol ; 192: 821-5, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26051524

ABSTRACT

In this work, a bacterial surface displaying enzyme based two-compartment biofuel cell for the direct electrical energy conversion from degradation products of lignocellulosic biomass is reported. Considering that the main degradation products of the lignocellulose are glucose and xylose, xylose dehydrogenase (XDH) displayed bacteria (XDH-bacteria) and glucose dehydrogenase (GDH) displayed bacteria (GDH-bacteria) were used as anode catalysts in anode chamber with methylene blue as electron transfer mediator. While the cathode chamber was constructed with laccase/multi-walled-carbon nanotube/glassy-carbon-electrode. XDH-bacteria exhibited 1.75 times higher catalytic efficiency than GDH-bacteria. This assembled enzymatic fuel cell exhibited a high open-circuit potential of 0.80 V, acceptable stability and energy conversion efficiency. Moreover, the maximum power density of the cell could reach 53 µW cm(-2) when fueled with degradation products of corn stalk. Thus, this finding holds great potential to directly convert degradation products of biomass into electrical energy.


Subject(s)
Bacterial Physiological Phenomena , Bioelectric Energy Sources/microbiology , Carbohydrate Dehydrogenases/metabolism , Lignin/metabolism , Refuse Disposal/instrumentation , Biodegradation, Environmental , Energy Transfer , Equipment Design , Equipment Failure Analysis
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