scholarly journals Modelling the Effects of Ageing Time of Starch on the Enzymatic Activity of Three Amylolytic Enzymes

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Nelson P. Guerra ◽  
Lorenzo Pastrana Castro
Keyword(s):  
Enzymatic Activity ◽  
Conformational Changes ◽  
Active Site ◽  
Ageing Time ◽  
Enzymatic Reactions ◽  
Reaction Products ◽  
Inhibitory Effects ◽  
Amylolytic Enzymes ◽  
Modified Forms

The effect of increasing ageing time (t) of starch on the activity of three amylolytic enzymes (Termamyl, San Super, and BAN) was investigated. Although all the enzymatic reactions follow michaelian kinetics,vmaxdecreased significantly (P<0.05) andKMincreased (although not always significantly) with the increase int. The conformational changes produced in the starch chains as a consequence of the ageing seemed to affect negatively the diffusivity of the starch to the active site of the enzymes and the release of the reaction products to the medium. A similar effect was observed when the enzymatic reactions were carried out with unaged starches supplemented with different concentrations of gelatine [G]. The inhibition in the amylolytic activities was best mathematically described by using three modified forms of the Michaelis-Menten model, which included a term to consider, respectively, the linear, exponential, and hyperbolic inhibitory effects oftand [G].

scholarly journals Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1

2018 ◽  
Vol 62 (11) ◽  
Author(s):  
Hongmin Zhang ◽  
Guixing Ma ◽  
Yifan Zhu ◽  
Lingxiao Zeng ◽  
Ashfaq Ahmad ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Conformational Changes ◽  
Active Site ◽  
Bacterial Infections ◽  
Site Directed Mutagenesis ◽  
New Delhi ◽  
Native Form ◽  
Conformational Fluctuation ◽  
Almost All

ABSTRACT β-Lactam antibiotics are the mainstay for the treatment of bacterial infections. However, elevated resistance to these antibiotics mediated by metallo-β-lactamases (MBLs) has become a global concern. New Delhi metallo-β-lactamase-1 (NDM-1), a newly added member of the MBL family that can hydrolyze almost all β-lactam antibiotics, has rapidly spread all over the world and poses serious clinical threats. Broad-spectrum and mechanism-based inhibitors against all MBLs are highly desired, but the differential mechanisms of MBLs toward different antibiotics pose a great challenge. To facilitate the design of mechanism-based inhibitors, we investigated the active-site conformational changes of NDM-1 through the determination of a series of 15 high-resolution crystal structures in native form and in complex with products and by using biochemical and biophysical studies, site-directed mutagenesis, and molecular dynamics computation. The structural studies reveal the consistency of the active-site conformations in NDM-1/product complexes and the fluctuation in native NDM-1 structures. The enzymatic measurements indicate a correlation between enzymatic activity and the active-site fluctuation, with more fluctuation favoring higher activity. This correlation is further validated by structural and enzymatic studies of the Q123G mutant. Our combinational studies suggest that active-site conformational fluctuation promotes the enzymatic activity of NDM-1, which may guide further mechanism studies and inhibitor design.

Temperature Sensitivity of Myosin and Actomyosin

1973 ◽  
Vol 51 (1) ◽  
pp. 71-86 ◽  
Author(s):  
A. L. Jacobson ◽  
J. Henderson
Keyword(s):  
Enzymatic Activity ◽  
Conformational Changes ◽  
Temperature Sensitivity ◽  
Active Site ◽  
Temperature Effects ◽  
Thermal Denaturation ◽  
Site Analysis ◽  
Maximum Change ◽  
Temperature Inactivation

The thermal denaturation of myosin and actomyosin was studied by active site analysis (enzymatic activity) and measurements were related to overall conformational changes (viscosity) over the temperature range 19–65 °C. The role of sulfhydryl (SH) groups on the temperature-induced denaturation of actomyosin was investigated. The temperature of maximum change in the overall conformation (the melting temperature, TM) was unaffected by the binding of F-actin to myosin. For both myosin and actomyosin the TM was 43 ± 2 °C. However, the range of temperature over which large conformational changes were observed was affected by the binding of F-actin to myosin. For myosin and dissociated actomyosin, changes were observed between 37 and 50 °C, while for actomyosin large changes were observed between 20 and 50 °C. With actomyosin there was an irreversible increase in titratable sulfhydryl groups from 19 to 60 °C. Temperature effects on the calcium-activated ATPase were studied. The temperature of maximum enzymatic activity for actomyosin was 45 ± 2 °C, which corresponds to the TM and the temperature at which increases in SH content were apparent. However, for myosin the temperature of maximum enzymatic activity was 33 °C, considerably below the TM. Overall conformational changes were reversible below the TM, while changes in enzymatic activity were reversible below the temperature of maximum enzymatic activity. Actin offers considerable protection to the temperature inactivation of the active site of myosin even though the F-actin–myosin complex is very highly dissociated in the presence of ATP. However, there is no significant stabilization of myosin by F-actin in terms of the temperature sensitivity of the overall conformation.

scholarly journals Active site lysine backbone undergoes conformational changes in the bacteriorhodopsin photocycle.

1994 ◽  
Vol 269 (10) ◽  
pp. 7387-7389
Author(s):  
H. Takei ◽  
Y. Gat ◽  
Z. Rothman ◽  
A. Lewis ◽  
M. Sheves
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Bacteriorhodopsin Photocycle

scholarly journals Enzymatic assay of d-mannose in serum

1997 ◽  
Vol 43 (3) ◽  
pp. 533-538 ◽  
Author(s):  
James R Etchison ◽  
Hudson H Freeze
Keyword(s):  
Bacillus Stearothermophilus ◽  
Anion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Enzymatic Assay ◽  
Enzymatic Reactions ◽  
Reaction Products ◽  
Serum Samples ◽  
Healthy Human ◽  
Human Volunteers ◽  
Chromatography Step

Abstract We describe a new and improved enzymatic assay for determining the concentration of d-mannose in sera. Serum d-glucose is selectively converted to glucose-6 phosphate with the highly specific thermostable glucokinase (EC 2.7.1.2) from Bacillus stearothermophilus. The anionic reaction products and excess substrates are removed by a rapid and simple anion-exchange chromatography step in microcentrifuge spin columns. d-Mannose in the glucose-depleted sample is then assayed spectrophotometrically by using coupled enzymatic reactions. The quantitative elimination of glucose from the serum samples allowed the accurate and reproducible assay of serum mannose in the 0–200 μmol/L range. Recovery of mannose added to serum (5–200 μmol/L) was 94% ± 4.4%. The intraassay CV was 6.7% at 40 μmol/L mannose (n = 5; 39.6 ± 1.6 μmol/L) and 4.4% at 80 μmol/L (n = 11; 75.0 ± 1.8 μmol/L); the interassay CV at these concentrations was 12.2% (n = 7; 36.9 ± 2.1 μmol/L) and 9.8% (n = 7; 74.2 ± 2.7 μmol/L), respectively. Sera from 11 healthy human volunteers contained an average of 54.1 ± 11.9 μmol/L mannose (range 36–81 μmol/L).

Protein Immobilization in Metal–Organic Frameworks by Covalent Binding

2014 ◽  
Vol 67 (11) ◽  
pp. 1629 ◽  
Author(s):  
Xuan Wang ◽  
Trevor A. Makal ◽  
Hong-Cai Zhou
Keyword(s):  
Enzymatic Activity ◽  
Enzyme Immobilization ◽  
Working Conditions ◽  
Active Site ◽  
Covalent Binding ◽  
Metal Organic Frameworks ◽  
Protein Immobilization ◽  
Immobilization Of Enzymes ◽  
Metal Organic ◽  
Biological Catalysis

Metal–organic frameworks (MOFs), possessing a well defined system of pores, demonstrate extensive potential serving as a platform in biological catalysis. Successful immobilization of enzymes in a MOF system retains the enzymatic activity, renders the active site more accessible to the substrate, and promises recyclability for reuse, and solvent adaptability in a broad range of working conditions. This highlight describes enzyme immobilization on MOFs via covalent binding and its significance.

scholarly journals Three Conserved Regions in Baculovirus Sulfhydryl Oxidase P33 Are Critical for Enzymatic Activity and Function

2017 ◽  
Vol 91 (23) ◽  
Author(s):  
Wenhua Kuang ◽  
Huanyu Zhang ◽  
Manli Wang ◽  
Ning-Yi Zhou ◽  
Fei Deng ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Active Site ◽  
Salt Bridge ◽  
Sulfhydryl Oxidase ◽  
Dimer Interface ◽  
Conserved Regions ◽  
Occlusion Bodies ◽  
Budded Virus ◽  
And Function ◽  
Substrate Proteins

ABSTRACT Baculoviruses encode a conserved sulfhydryl oxidase, P33, which is necessary for budded virus (BV) production and multinucleocapsid occlusion-derived virus (ODV) formation. Here, the structural and functional relationship of P33 was revealed by X-ray crystallography, site-directed mutagenesis, and functional analysis. Based on crystallographic characterization and structural analysis, a series of P33 mutants within three conserved regions, i.e., the active site, the dimer interface, and the R127-E183 salt bridge, were constructed. In vitro experiments showed that mutations within the active site and dimer interface severely impaired the sulfhydryl oxidase activity of P33, while the mutations in the salt bridge had a relatively minor influence. Recombinant viruses containing mutated P33 were constructed and assayed in vivo. Except for the active-site mutant AXXA, all other mutants produced infectious BVs, although certain mutants had a decreased BV production. The active-site mutant H114A, the dimer interface mutant H227D, and the salt bridge mutant R127A-E183A were further analyzed by electron microscopy and bioassays. The occlusion bodies (OBs) of mutants H114A and R127A-E183A had a ragged surface and contained mostly ODVs with a single nucleocapsid. The OBs of all three mutants contained lower numbers of ODVs and had a significantly reduced oral infectivity in comparison to control virus. Crystallographic analyses further revealed that all three regions may coordinate with one another to achieve optimal function of P33. Taken together, our data revealed that all the three conserved regions are involved in P33 activity and are crucial for virus morphogenesis and peroral infectivity. IMPORTANCE Sulfhydryl oxidase catalyzes disulfide bond formation of substrate proteins. P33, a baculovirus-encoded sulfhydryl oxidase, is different from other cellular and viral sulfhydryl oxidases, bearing unique features in tertiary and quaternary structure organizations. In this study, we found that three conserved regions, i.e., the active site, dimer interface, and the R127-E183 salt bridge, play important roles in the enzymatic activity and function of P33. Previous observations showed that deletion of p33 results in a total loss of budded virus (BV) production and in morphological changes in occlusion-derived virus (ODV). Our study revealed that certain P33 mutants lead to occlusion bodies (OBs) with a ragged surface, decreased embedded ODVs, and reduced oral infectivity. Interestingly, some P33 mutants with impaired ODV/OB still retained BV productivity, indicating that the impacts on BV and on ODV/OB are two distinctly different functions of P33, which are likely to be performed via different substrate proteins.

Combined blockade of thrombin anion binding exosite-1 and PAR4 produces synergistic antiplatelet effect in human platelets

2011 ◽  
Vol 105 (01) ◽  
pp. 88-95 ◽  
Author(s):  
Wei-Ya Wang ◽  
Chien-Kei Wei ◽  
Che-Ming Teng ◽  
Chin-Chung Wu
Keyword(s):  
Platelet Aggregation ◽  
Active Site ◽  
Antithrombotic Therapy ◽  
Specific Binding ◽  
Anticoagulant Activity ◽  
Human Platelets ◽  
Anion Binding ◽  
Inhibitory Effects ◽  
Clotting Time ◽  
Potential Strategy

SummaryThrombin exosite-1 mediates the specific binding of thrombin with fibrinogen and protease-activated receptor (PAR) 1. Exosite-1 inhibitors have been shown to effectively decrease the clotting activity of thrombin, while their antiplatelet effects are relatively weak. In the present study, the inhibitory effects of two exosite-1 inhibitors, hirugen and HD1, but not the exosite-2 inhibitor HD22, on thrombin-induced platelet aggregation and P-selectin expression were dramatically enhanced by a PAR4 antagonist, YD-3. In contrast, the PAR1 antagonist SCH-79797 did not affect the antiplatelet effects of exosite-1 inhibitors. The exosite-1 inhibitors and YD-3 prevented the Ca2+ spike and the prolonged Ca2+ response in thrombin-stimulated platelets, respectively; and combination of these two classes of agents led to abolishment of Ca2+ signal. Unlike exosite-1 inhibitors, the antiplatelet effects of the active site inhibitor PPACK and the bivalent inhibitor bivalirudin were not significantly enhanced by YD-3. In addition, the platelet-stimulating activity of γ-thrombin, an autolytic product of α-thrombin which lacks exosite-1, was inhibited by YD-3. These results suggest that the synergistic antiplatelet effects of exosite-1 inhibitor and PAR4 antagonist are resulted from combined blockade of PAR1 and PAR4 in platelets. In fibrinogen or plasma clotting assay, YD-3 neither prolonged the clotting time on its own nor enhanced the anticoagulant activity of exosite-1 inhibitors. Therefore, the combined blockade of exosite-1 and PAR4 may offer a potential strategy for improving the balance of benefits and risks of antithrombotic therapy.

scholarly journals Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15.

2014 ◽  
Vol 61 (4) ◽  
Author(s):  
Mohd Adilin Yaacob ◽  
Wan Atiqah Najiah Wan Hasan ◽  
Mohd Shukuri Mohamad Ali ◽  
Raja Noor Zaliha Raja Abdul Rahman ◽  
Abu Bakar Salleh ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Conformational Changes ◽  
Specific Activity ◽  
3D Structure ◽  
Coli Strain ◽  
Exchange Chromatography ◽  
Molecular Dynamic Simulations ◽  
Type I ◽  
Enzymatic Reactions ◽  
Dynamic Simulations

Genome mining revealed a 1011 nucleotide-long fragment encoding a type I L-asparaginase (J15 asparaginase) from the halo-tolerant Photobacterium sp. strain J15. The gene was overexpressed in pET-32b (+) vector in E. coli strain Rosetta-gami B (DE3) pLysS and purified using two-step chromatographic methods: Ni(2+)-Sepharose affinity chromatography and Q-Sepharose anion exchange chromatography. The final specific activity and yield of the enzyme achieved from these steps were 20 U/mg and 49.2%, respectively. The functional dimeric form of J15-asparaginase was characterised with a molecular weight of ~70 kDa. The optimum temperature and pH were 25°C and pH 7.0, respectively. This protein was stable in the presence of 1 mM Ni(2+) and Mg(2+), but it was inhibited by Mn(2+), Fe(3+) and Zn(2+) at the same concentration. J15 asparaginase actively hydrolysed its native substrate, l-asparagine, but had low activity towards l-glutamine. The melting temperature of J15 asparaginase was ~51°C, which was determined using denatured protein analysis of CD spectra. The Km, Kcat, Kcat/Km of J15 asparaginase were 0.76 mM, 3.2 s(-1), and 4.21 s(-1) mM(-1), respectively. Conformational changes of the J15 asparaginase 3D structure at different temperatures (25°C, 45°C, and 65°C) were analysed using Molecular Dynamic simulations. From the analysis, residues Tyr₂₄ , His₂₂, Gly₂₃, Val₂₅ and Pro₂₆ may be directly involved in the 'open' and 'closed' lid-loop conformation, facilitating the conversion of substrates during enzymatic reactions. The properties of J15 asparaginase, which can work at physiological pH and has low glutaminase activity, suggest that this could be a good candidate for reducing toxic effects during cancer treatment.

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