Статті в журналах: "Enzyme interaction"

1

Gao, Qi, and Dangling Ming. "Protein-protein interactions enhance the thermal resilience of SpyRing-cyclized enzymes: A molecular dynamic simulation study." PLOS ONE 17, no. 2 (February 17, 2022): e0263792. http://dx.doi.org/10.1371/journal.pone.0263792.

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Recently a technique based on the interaction between adhesion proteins extracted from Streptococcus pyogenes, known as SpyRing, has been widely used to improve the thermal resilience of enzymes, the assembly of biostructures, cancer cell recognition and other fields. It was believed that the covalent cyclization of protein skeleton caused by SpyRing reduces the conformational entropy of biological structure and improves its rigidity, thus improving the thermal resilience of the target enzyme. However, the effects of SpyTag/ SpyCatcher interaction with this enzyme are poorly understood, and their regulation of enzyme properties remains unclear. Here, for simplicity, we took the single domain enzyme lichenase from Bacillus subtilis 168 as an example, studied the interface interactions in the SpyRing by molecular dynamics simulations, and examined the effects of the changes of electrostatic interaction and van der Waals interaction on the thermal resilience of target enzyme. The simulations showed that the interface between SpyTag/SpyCatcher and the target enzyme is different from that found by geometric matching method and highlighted key mutations at the interface that might have effect on the thermal resilience of the enzyme. Our calculations highlighted interfacial interactions between enzyme and SpyTag/SpyCatcher, which might be useful in rational designs of the SpyRing.

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2

Duskey, Jason Thomas, Federica da Ros, Ilaria Ottonelli, Barbara Zambelli, Maria Angela Vandelli, Giovanni Tosi, and Barbara Ruozi. "Enzyme Stability in Nanoparticle Preparations Part 1: Bovine Serum Albumin Improves Enzyme Function." Molecules 25, no. 20 (October 9, 2020): 4593. http://dx.doi.org/10.3390/molecules25204593.

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Enzymes have gained attention for their role in numerous disease states, calling for research for their efficient delivery. Loading enzymes into polymeric nanoparticles to improve biodistribution, stability, and targeting in vivo has led the field with promising results, but these enzymes still suffer from a degradation effect during the formulation process that leads to lower kinetics and specific activity leading to a loss of therapeutic potential. Stabilizers, such as bovine serum albumin (BSA), can be beneficial, but the knowledge and understanding of their interaction with enzymes are not fully elucidated. To this end, the interaction of BSA with a model enzyme B-Glu, part of the hydrolase class and linked to Gaucher disease, was analyzed. To quantify the natural interaction of beta-glucosidase (B-Glu,) and BSA in solution, isothermal titration calorimetry (ITC) analysis was performed. Afterwards, polymeric nanoparticles encapsulating these complexes were fully characterized, and the encapsulation efficiency, activity of the encapsulated enzyme, and release kinetics of the enzyme were compared. ITC results showed that a natural binding of 1:1 was seen between B-Glu and BSA. Complex concentrations did not affect nanoparticle characteristics which maintained a size between 250 and 350 nm, but increased loading capacity (from 6% to 30%), enzyme activity, and extended-release kinetics (from less than one day to six days) were observed for particles containing higher B-Glu:BSA ratios. These results highlight the importance of understanding enzyme:stabilizer interactions in various nanoparticle systems to improve not only enzyme activity but also biodistribution and release kinetics for improved therapeutic effects. These results will be critical to fully characterize and compare the effect of stabilizers, such as BSA with other, more relevant therapeutic enzymes for central nervous system (CNS) disease treatments.

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3

Yabutsuka, Takeshi, Masaya Yamamoto, Shigeomi Takai, and Takeshi Yao. "Enzyme Immobilization Behavior on the Surface of Hydroxyapatite Capsules under Alkaline Condition." Key Engineering Materials 782 (October 2018): 21–26. http://dx.doi.org/10.4028/www.scientific.net/kem.782.21.

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We prepared hydroxyapatite (HA) capsules encapsulating maghemite particles. In order to evaluate enzyme immobilization behavior of the HA capsules under alkaline condition, we immobilized five kinds of enzymes with different isoelectric point in carbonate/bicarbonate buffer (CBB, pH 10.0). When the enzymes in CBB were moderately charged, immobilization efficiency on the HA capsules showed the highest value. It was suggested that immobilization efficiency was affected according to both pI of enzyme and pH of the surrounding solution and that enzyme immobilized on the HA capsules by not only electrical double layer interactions but also ion interaction and other interactions.

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4

Grabarczyk, Daniel B., Paul E. Chappell, Steven Johnson, Lukas S. Stelzl, Susan M. Lea, and Ben C. Berks. "Structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle." Proceedings of the National Academy of Sciences 112, no. 52 (December 11, 2015): E7166—E7175. http://dx.doi.org/10.1073/pnas.1506386112.

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The bacterial Sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. Intermediates in the Sox pathway are covalently attached to the heterodimeric carrier protein SoxYZ through conjugation to a cysteine on a protein swinging arm. We have investigated how the carrier protein shuttles intermediates between the enzymes of the Sox pathway using the interaction between SoxYZ and the enzyme SoxB as our model. The carrier protein and enzyme interact only weakly, but we have trapped their complex by using a “suicide enzyme” strategy in which an engineered cysteine in the SoxB active site forms a disulfide bond with the incoming carrier arm cysteine. The structure of this trapped complex, together with calorimetric data, identifies sites of protein–protein interaction both at the entrance to the enzyme active site tunnel and at a second, distal, site. We find that the enzyme distinguishes between the substrate and product forms of the carrier protein through differences in their interaction kinetics and deduce that this behavior arises from substrate-specific stabilization of a conformational change in the enzyme active site. Our analysis also suggests how the carrier arm-bound substrate group is able to outcompete the adjacent C-terminal carboxylate of the carrier arm for binding to the active site metal ions. We infer that similar principles underlie carrier protein interactions with other enzymes of the Sox pathway.

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5

Goldman, Samuel, Ria Das, Kevin K. Yang, and Connor W. Coley. "Machine learning modeling of family wide enzyme-substrate specificity screens." PLOS Computational Biology 18, no. 2 (February 10, 2022): e1009853. http://dx.doi.org/10.1371/journal.pcbi.1009853.

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Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze their natural chemical transformation on non-natural substrates. While machine learning and in silico directed evolution are well-posed for this predictive modeling challenge, efforts to date have primarily aimed to increase activity against a single known substrate, rather than to identify enzymes capable of acting on new substrates of interest. To address this need, we curate 6 different high-quality enzyme family screens from the literature that each measure multiple enzymes against multiple substrates. We compare machine learning-based compound-protein interaction (CPI) modeling approaches from the literature used for predicting drug-target interactions. Surprisingly, comparing these interaction-based models against collections of independent (single task) enzyme-only or substrate-only models reveals that current CPI approaches are incapable of learning interactions between compounds and proteins in the current family level data regime. We further validate this observation by demonstrating that our no-interaction baseline can outperform CPI-based models from the literature used to guide the discovery of kinase inhibitors. Given the high performance of non-interaction based models, we introduce a new structure-based strategy for pooling residue representations across a protein sequence. Altogether, this work motivates a principled path forward in order to build and evaluate meaningful predictive models for biocatalysis and other drug discovery applications.

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6

Staum, John M. "Enzyme Induction: Rifampin-Disopyramide Interaction." DICP 24, no. 7-8 (July 1990): 701–3. http://dx.doi.org/10.1177/106002809002400709.

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7

Mokhtar, Nur Fathiah, Raja Noor Zaliha Raja Abd. Rahman, Noor Dina Muhd Noor, Fairolniza Mohd Shariff, and Mohd Shukuri Mohamad Ali. "The Immobilization of Lipases on Porous Support by Adsorption and Hydrophobic Interaction Method." Catalysts 10, no. 7 (July 4, 2020): 744. http://dx.doi.org/10.3390/catal10070744.

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Four major enzymes commonly used in the market are lipases, proteases, amylases, and cellulases. For instance, in both academic and industrial levels, microbial lipases have been well studied for industrial and biotechnological applications compared to others. Immobilization is done to minimize the cost. The improvement of enzyme properties enables the reusability of enzymes and facilitates enzymes used in a continuous process. Immobilized enzymes are enzymes physically confined in a particularly defined region with retention to their catalytic activities. Immobilized enzymes can be used repeatedly compared to free enzymes, which are unable to catalyze reactions continuously in the system. Immobilization also provides a higher pH value and thermal stability for enzymes toward synthesis. The main parameter influencing the immobilization is the support used to immobilize the enzyme. The support should have a large surface area, high rigidity, suitable shape and particle size, reusability, and resistance to microbial attachment, which will enhance the stability of the enzyme. The diffusion of the substrate in the carrier is more favorable on hydrophobic supports instead of hydrophilic supports. The methods used for enzyme immobilization also play a crucial role in immobilization performance. The combination of immobilization methods will increase the binding force between enzymes and the support, thus reducing the leakage of the enzymes from the support. The adsorption of lipase on a hydrophobic support causes the interfacial activation of lipase during immobilization. The adsorption method also causes less or no change in enzyme conformation, especially on the active site of the enzyme. Thus, this method is the most used in the immobilization process for industrial applications.

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8

Abdi, Sayed Aliul Hasan, Abdulaziz Alzahrani, Saleh Alghamdi, Ali Alquraini, and Adel Alghamdi. "Hexaconazole exposure ravages biosynthesis pathway of steroid hormones: revealed by molecular dynamics and interaction." Toxicology Research 11, no. 1 (December 16, 2021): 60–76. http://dx.doi.org/10.1093/toxres/tfab113.

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Abstract Widespread application of hexaconazole for agriculture purpose poses a threat to human health by disrupting normal endocrine homeostasis. To avoid adverse health effects on human, it is crucial to identify the effects of hexaconazole on key enzymes responsible for steroidal hormone synthesis. In view of this, present study was conducted to investigate the interaction mechanisms of hexaconazole with key enzymes in comparison with their food drug administration (FDA) approved inhibitor by molecular docking and molecular dynamics simulations. Results indicate that hexaconazole contacts with the active site of the key enzymes required for steroidal hormonal synthesis. Results pertaining to root-mean-square deviation, root-mean-square calculation, radius of gyration, hydrogen bonding and solvent accessible surface area exhibited that the interaction pattern and stability of interaction of hexaconazole was similar to enzyme specific inhibitor. In addition, ligand and enzyme complex interaction energy of hexaconazole was almost similar to key enzyme and FDA-approved enzyme specific inhibitor complex. This study offers a molecular level of understanding of hexaconazole with different enzymes required for steroidal hormonal synthesis. Findings of the study clearly suggest that hexaconazole has efficacy to stably interact with various enzyme required to progress the pathway of hormonal synthesis. If incessant exposure of hexaconazole occurs during agricultural work it may lead to ravage hormonal synthesis or potent endocrine disruption. The result of binding energy and complex interaction energy is depicted in the graphical abstract.

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9

Higgins, G. "Concern over ibuprofen/pancreatic enzyme interaction." Reactions Weekly &NA;, no. 656 (June 1997): 2. http://dx.doi.org/10.2165/00128415-199706560-00001.

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10

Chadwick, Ben, Derek G. Waller, and J. Guy Edwards. "Potentially hazardous drug interactions with psychotropics." Advances in Psychiatric Treatment 11, no. 6 (November 2005): 440–49. http://dx.doi.org/10.1192/apt.11.6.440.

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Of the many interactions with psychotropic drugs, a minority are potentially hazardous. Most interactions are pharmacodynamic, resulting from augmented or antagonistic actions at a receptor or from different mechanisms in the same tissue. Most important pharmacokinetic interactions are due to effects on metabolism or renal excretion. The major enzymes involved in metabolism belong to the cytochrome P450 (CYP) system. Genetic variation in the CYP system produces people who are ‘poor’, ‘extensive’ or ‘ultra-rapid’ drug metabolisers. Hazardous interactions more often result from enzyme inhibition, but the probability of interaction depends on the initial level of enzyme activity and the availability of alternative metabolic routes for elimination of the drug. There is currently interest in interactions involving uridine diphosphate glucuronosyltransferases and the P-glycoprotein cell transport system, but their importance for psychotropics has yet to be defined. The most serious interactions with psychotropics result in profound sedation, central nervous system toxicity, large changes in blood pressure, ventricular arrhythmias, an increased risk of dangerous side-effects or a decreased therapeutic effect of one of the interacting drugs.

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11

Kuznetsov, Aleksei, and Jaak Järv. "Ligand structure controlled allostery in cAMP-dependent protein kinase catalytic subunit." Open Life Sciences 4, no. 2 (June 1, 2009): 131–41. http://dx.doi.org/10.2478/s11535-009-0012-6.

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AbstractProtein kinase A (cAMP dependent protein kinase catalytic subunit, EC 2.7.11.11) binds simultaneously ATP and a phosphorylatable peptide. These structurally dissimilar allosteric ligands influence the binding effectiveness of each other. The same situation is observed with substrate congeners, which reversibly inhibit the enzyme. In this review these allosteric effects are quantified using the interaction factor, which compares binding effectiveness of ligands with the free enzyme and the pre-loaded enzyme complex containing another ligand. This analysis revealed that the allosteric effect depends upon structure of the interacting ligands, and the principle “better binding: stronger allostery” observed can be formalized in terms of linear free-energy relationships, which point to similar mechanism of the allosteric interaction between the enzyme-bound substrates and/or inhibitor molecules. On the other hand, the type of effect is governed by ligand binding effectiveness and can be inverted from positive allostery to negative allostery if we move from effectively binding ligands to badly binding compounds. Thus the outcome of the allostery in this monomeric enzyme is the same as defined by classical theories for multimeric enzymes: making the enzyme response more efficient if appropriate ligands bind.

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12

SYGUSCH, Jurgen, and Danielle BEAUDRY. "Subunit interaction in mammalian aldolases." Biochemical Journal 323, no. 3 (May 1, 1997): 671–76. http://dx.doi.org/10.1042/bj3230671.

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Enzyme inactivation was utilized to study subunit interaction in the homotetrameric glycolytic enzyme, aldolase. Isoenzymes from rabbit liver and skeletal muscle were inactivated in the presence of Pi and d-glyceraldehyde-P to a maximum stoichiometry of one modification per aldolase subunit. Subunit modification increased net negative charge on each subunit surface and was used to resolve modified aldolase isoenzymes into various chromatographic species. A combination of anion-(Mono Q) and cation- (Mono S) exchange chromatography separated the modified aldolase homotetramers into three distinct enzyme populations: unchanged enzyme, fully modified enzyme corresponding to one ligand molecule incorporated per subunit and partially modified enzyme in which only one subunit out of four is modified. Both fully and partially modified species were devoid of catalytic activity. Activity loss through modification of a single subunit in both aldolase isoenzymes indicates tightly coupled communication between subunit active sites and suggests simple functional regulation of aldolases.

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13

Aldred, Katie J., Tim R. Blower, Robert J. Kerns, James M. Berger, and Neil Osheroff. "Fluoroquinolone interactions withMycobacterium tuberculosisgyrase: Enhancing drug activity against wild-type and resistant gyrase." Proceedings of the National Academy of Sciences 113, no. 7 (January 20, 2016): E839—E846. http://dx.doi.org/10.1073/pnas.1525055113.

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Mycobacterium tuberculosisis a significant source of global morbidity and mortality. Moxifloxacin and other fluoroquinolones are important therapeutic agents for the treatment of tuberculosis, particularly multidrug-resistant infections. To guide the development of new quinolone-based agents, it is critical to understand the basis of drug action againstM. tuberculosisgyrase and how mutations in the enzyme cause resistance. Therefore, we characterized interactions of fluoroquinolones and related drugs with WT gyrase and enzymes carrying mutations at GyrAA90and GyrAD94.M. tuberculosisgyrase lacks a conserved serine that anchors a water–metal ion bridge that is critical for quinolone interactions with other bacterial type II topoisomerases. Despite the fact that the serine is replaced by an alanine (i.e., GyrAA90) inM. tuberculosisgyrase, the bridge still forms and plays a functional role in mediating quinolone–gyrase interactions. Clinically relevant mutations at GyrAA90and GyrAD94cause quinolone resistance by disrupting the bridge–enzyme interaction, thereby decreasing drug affinity. Fluoroquinolone activity against WT and resistant enzymes is enhanced by the introduction of specific groups at the C7 and C8 positions. By dissecting fluoroquinolone–enzyme interactions, we determined that an 8-methyl-moxifloxacin derivative induces high levels of stable cleavage complexes with WT gyrase and two common resistant enzymes, GyrAA90Vand GyrAD94G. 8-Methyl-moxifloxacin was more potent than moxifloxacin against WTM. tuberculosisgyrase and displayed higher activity against the mutant enzymes than moxifloxacin did against WT gyrase. This chemical biology approach to defining drug–enzyme interactions has the potential to identify novel drugs with improved activity against tuberculosis.

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14

Guo, Qing, Yufan He, and H. Peter Lu. "Manipulating and probing enzymatic conformational fluctuations and enzyme–substrate interactions by single-molecule FRET-magnetic tweezers microscopy." Phys. Chem. Chem. Phys. 16, no. 26 (2014): 13052–58. http://dx.doi.org/10.1039/c4cp01454e.

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To investigate the critical role of the enzyme–substrate interactions in enzymatic reactions, the enzymatic conformation and enzyme–substrate interaction at a single-molecule level are manipulated by magnetic tweezers, and the impact of the manipulation on enzyme–substrate interactions are simultaneously probed by single-molecule FRET spectroscopy.

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15

Li, Jian, Zhongyi Jiang, Hong Wu, Yanpeng Liang, Yufei Zhang, and Jiaxian Liu. "Enzyme–polysaccharide interaction and its influence on enzyme activity and stability." Carbohydrate Polymers 82, no. 1 (August 2010): 160–66. http://dx.doi.org/10.1016/j.carbpol.2010.04.045.

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16

Li, Congcong, Zhongkui Lu, Min Wang, Siao Chen, Lu Han, and Weiwei Han. "A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations." International Journal of Molecular Sciences 22, no. 19 (October 6, 2021): 10813. http://dx.doi.org/10.3390/ijms221910813.

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Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.

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17

Gerberding, Holger, and Frank Mayer. "Interaction and Compartmentalization of the Components of Bacterial Enzyme Systems Involved in Cell Energetics." Zeitschrift für Naturforschung C 48, no. 7-8 (August 1, 1993): 535–41. http://dx.doi.org/10.1515/znc-1993-7-801.

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Bacterial enzyme systems, especially those which are involved in cell energetics, often show a common characteristic feature: their constituents (either interacting enzymes or subunits of a given enzyme complex) are physically separated. They are located in different functional entities, such as cytoplasm or periplasmic space. This kind of cellular and macromolecular organization enables the cell to establish spatially separated but neighbouring zones in which distinct conditions are created or maintained. This intrinsic imbalance is one of the keys for the process of life. As the mediator between the two compartments, the cytoplasm and the periplasmic space, the cytoplasmic membrane -itself a functional entity -not only acts as a barrier, but carries a set of functional enzyme components, thus contributing to the interaction between compartments. Examples to illustrate this concept are enzyme systems involved in anaerobic glycine metabolism, aerobic utilization of carbon monoxide, proton or sodium translocation across the membrane, and intracellular hydrogen cycling used by the cell for the generation of a proton gradient.

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18

Stein, Matthias, Razif R. Gabdoulline, and Rebecca C. Wade. "Calculating enzyme kinetic parameters from protein structures." Biochemical Society Transactions 36, no. 1 (January 22, 2008): 51–54. http://dx.doi.org/10.1042/bst0360051.

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Enzyme kinetic parameters can differ between different species and isoenzymes for the same catalysed reaction. Computational approaches to calculate enzymatic kinetic parameters from the three-dimensional structures of proteins will be reviewed briefly here. Enzyme kinetic parameters may be derived by modelling and simulating the rate-determining process. An alternative, approximate, but more computationally efficient approach is the comparison of molecular interaction fields for experimentally characterized enzymes and those for which parameters should be determined. A correlation between differences in interaction fields and experimentally determined kinetic parameters can be used to determine parameters for orthologous enzymes from other species. The estimation of enzymatic kinetic parameters is an important step in setting up mathematical models of biochemical pathways in systems biology.

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19

Hyytiäinen, Heidi, Marcos Montesano, and E. Tapio Palva. "Global Regulators ExpA (GacA) and KdgR Modulate Extracellular Enzyme Gene Expression Through the RsmA-rsmB System in Erwinia carotovora subsp. carotovora." Molecular Plant-Microbe Interactions® 14, no. 8 (August 2001): 931–38. http://dx.doi.org/10.1094/mpmi.2001.14.8.931.

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The production of the main virulence determinants, the extracellular plant cell wall-degrading enzymes, and hence virulence of Erwinia carotovora subsp. carotovora is controlled by a complex regulatory network. One of the global regulators, the response regulator ExpA, a GacA homolog, is required for transcriptional activation of the extracellular enzyme genes of this soft-rot pathogen. To elucidate the mechanism of ExpA control as well as interactions with other regulatory systems, we isolated second-site transposon mutants that would suppress the enzyme-negative phenotype of an expA (gacA) mutant. Inactivation of kdgR resulted in partial restoration of extracellular enzyme production and virulence to the expA mutant, suggesting an interaction between the two regulatory pathways. This interaction was mediated by the RsmA-rsmB system. Northern analysis was used to show that the regulatory rsmB RNA was under positive control of ExpA. Conversely, the expression of rsmA encoding a global repressor was under negative control of ExpA and positive control of KdgR. This study indicates a central role for the RsmA-rsmB regulatory system during pathogenesis, integrating signals from the ExpA (GacA) and KdgR global regulators of extracellular enzyme production in E. carotovora subsp. carotovora.

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20

Hauzer, Karel, Tomislav Barth, Linda Hauzerová, Jana Barthová, Pavel Hrbas, Jiřina Slaninová, and Karel Jošt. "Post-proline endopeptidase. Interaction of the enzyme with substrates containing disulfide and thioether bond." Collection of Czechoslovak Chemical Communications 51, no. 1 (1986): 234–40. http://dx.doi.org/10.1135/cccc19860234.

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The free thiol group of post-proline endopeptidase (EC 3.4.21.26) can interact with the disulfide bridge contained in some of the substrates of this enzyme (neurohypophysial hormones and some of their analogues). The influence of these interactions on the activity of this enzyme was studied using several substances modelling individual types of interactions: thiol-disulfide exchange, catalytic interaction and a complex interaction including the two preceding types. Deamino-1-carba-oxytocin is catalytically hydrolysed in the concentration range up to 10-3mol/l, oxytocin and arginine-vasopressin are catalytically hydrolysed in concentrations of 10-5 to 10-8 mol/l. A reaction leading to inactivation of the enzyme prevails at concentrations of 10-3 to 10-4 mol/l. When inactivated by lower concentrations of arginine-vasopressin (up to a molar ratio of 1 : 1), the enzyme can be reactivated by incubation with dithiothreitol, higher concentrations of arginine-vasopresson cause irreversible enzyme inactivation.

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21

Hofmann, M., S. Witt, and R. Guckenberger. "Probing Enzyme - Protein Interaction with Force - Spectroscopy." Single Molecules 2, no. 2 (July 2001): 133–34. http://dx.doi.org/10.1002/1438-5171(200107)2:2<133::aid-simo133>3.0.co;2-x.

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22

Konash, Anastassija, Michael J. Cooney, Bor Yann Liaw, and David M. Jameson. "Characterization of enzyme–polymer interaction using fluorescence." J. Mater. Chem. 16, no. 42 (2006): 4107–9. http://dx.doi.org/10.1039/b611686h.

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23

Palaniandavar, Mallayan. "Models for enzyme-copper-nucleic acid interaction." Biological Trace Element Research 21, no. 1 (July 1989): 41–48. http://dx.doi.org/10.1007/bf02917235.

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24

Sowa, Mathew E., Eric J. Bennett, Steven P. Gygi, and J. Wade Harper. "Defining the Human Deubiquitinating Enzyme Interaction Landscape." Cell 138, no. 2 (July 2009): 389–403. http://dx.doi.org/10.1016/j.cell.2009.04.042.

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25

Babbi, Giulia, Davide Baldazzi, Castrense Savojardo, Martelli Pier Luigi, and Rita Casadio. "Highlighting Human Enzymes Active in Different Metabolic Pathways and Diseases: The Case Study of EC 1.2.3.1 and EC 2.3.1.9." Biomedicines 8, no. 8 (July 29, 2020): 250. http://dx.doi.org/10.3390/biomedicines8080250.

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Enzymes are key proteins performing the basic functional activities in cells. In humans, enzymes can be also responsible for diseases, and the molecular mechanisms underlying the genotype to phenotype relationship are under investigation for diagnosis and medical care. Here, we focus on highlighting enzymes that are active in different metabolic pathways and become relevant hubs in protein interaction networks. We perform a statistics to derive our present knowledge on human metabolic pathways (the Kyoto Encyclopaedia of Genes and Genomes (KEGG)), and we found that activity aldehyde dehydrogenase (NAD(+)), described by Enzyme Commission number EC 1.2.1.3, and activity acetyl-CoA C-acetyltransferase (EC 2.3.1.9) are the ones most frequently involved. By associating functional activities (EC numbers) to enzyme proteins, we found the proteins most frequently involved in metabolic pathways. With our analysis, we found that these proteins are endowed with the highest numbers of interaction partners when compared to all the enzymes in the pathways and with the highest numbers of predicted interaction sites. As specific enzyme protein test cases, we focus on Alpha-Aminoadipic Semialdehyde Dehydrogenase (ALDH7A1, EC 2.3.1.9) and Acetyl-CoA acetyltransferase, cytosolic and mitochondrial (gene products of ACAT2 and ACAT1, respectively; EC 2.3.1.9). With computational approaches we show that it is possible, by starting from the enzyme structure, to highlight clues of their multiple roles in different pathways and of putative mechanisms promoting the association of genes to disease.

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26

Szűcs, G., P. Laczay, Judit Bajnógel, and Zsuzsa Móra. "StudIES oN the Toxic Interaction between Monensin and Tiamulin in Rats: EFFECTS ON P450 ACTIVITIES." Acta Veterinaria Hungarica 48, no. 3 (July 1, 2000): 361–68. http://dx.doi.org/10.1556/avet.48.2000.3.13.

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Studies were carried out to investigate the effects of monensin and tiamulin, and the simultaneous administration of both compounds on microsomal enzymes in rats. In Phase I of the experiments the effects of monensin and tiamulin were studied separately (monensin 10, 30, and 50 mg/kg or tiamulin 40, 120, and 200 mg/kg body weight, respectively), while in Phase II the two compounds were administered simultaneously (monensin 10 mg/kg and tiamulin 40 mg/kg b.w., respectively). When monensin was administered by itself, it exerted no significant effect on microsomal liver enzymes. In a few cases, slight inhibition of certain enzyme activities was seen. Tiamulin provoked a dose-dependent hepatic enzyme induction. The combined administration of monensin and tiamulin at low doses (10 and 40 mg/kg, respectively) resulted in marked elevation of P450-related enzyme activities. The enzyme induction was more pronounced in females than in males. The results suggest that the simultaneous administration of tiamulin may influence the biotransformation of monensin, possibly increasing the amount of reactive metabolite(s) of the ionophore antibiotic.

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27

Merugu, Ramchander, Uttam Kumar Neerudu, Karunakar Dasa, and Kalpana V. Singh. "Molecular docking studies of deacetylbisacodyl with intestinal sucrase-maltase enzyme." International Journal of Advances in Scientific Research 2, no. 12 (January 1, 2017): 191. http://dx.doi.org/10.7439/ijasr.v2i12.3821.

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Анотація:

Molecular docking of sucrase-isomaltase with ligand deacetylbisacodyl when subjected to docking analysis using docking server, predicted in-silico result with a free energy of -3.36 Kcal/mol which was agreed well with physiological range for protein-ligand interaction, making bisacodyl probable potent anti-isomaltase molecule. According to docking server Inhibition constant is 5.98Mm. which predicts that the ligand is going to inhibits enzyme and result in a clinically relevant drug interaction with a substrate for the enzyme. Hydrogen bond with bond length 3.45is formed between Pro 64 (A) of target and of ligand, which is again indicative of the docking between target and ligand. Excellent electrostatic interactions of polar, hydrophobic, pi-pi and Van der walls are observed. The proteinligand interaction study showed 6 amino acid residues interaction with the ligand.

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28

JAGATH, Junutula Reddy, Naropantul APPAJI RAO, and Handanahal SubbaRao SAVITHRI. "Role of Arg-401 of cytosolic serine hydroxymethyltransferase in subunit assembly and interaction with the substrate carboxy group." Biochemical Journal 327, no. 3 (November 1, 1997): 877–82. http://dx.doi.org/10.1042/bj3270877.

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In an attempt to identify the arginine residue involved in binding of the carboxylate group of serine to mammalian serine hydroxymethyltransferase, a highly conserved Arg-401 was mutated to Ala by site-directed mutagenesis. The mutant enzyme had a characteristic visible absorbance at 425 nm indicative of the presence of bound pyridoxal 5ʹ-phosphate as an internal aldimine with a lysine residue. However, it had only 0.003% of the catalytic activity of the wild-type enzyme. It was also unable to perform reactions with glycine, β-phenylserine or D-alanine, suggesting that the binding of these substrates to the mutant enzyme was affected. This was also evident from the interaction of amino-oxyacetic acid, which was very slow (8.4×10-4 s-1 at 50 μM) for the R401A mutant enzyme compared with the wild-type enzyme (44.6 s-1 at 50 μM). In contrast, methoxyamine (which lacks the carboxy group) reacted with the mutant enzyme (1.72 s-1 at 250 μM) more rapidly than the wild-type enzyme (0.2 s-1 at 250 μM). Further, both wild-type and the mutant enzymes were capable of forming unique quinonoid intermediates absorbing at 440 and 464 nm on interaction with thiosemicarbazide, which also does not have a carboxy group. These results implicate Arg-401 in the binding of the substrate carboxy group. In addition, gel-filtration profiles of the apoenzyme and the reconstituted holoenzyme of R401A and the wild-type enzyme showed that the mutant enzyme remained in a tetrameric form even when the cofactor had been removed. However, the wild-type enzyme underwent partial dissociation to a dimer, suggesting that the oligomeric structure was rendered more stable by the mutation of Arg-401. The increased stability of the mutant enzyme was also reflected in the higher apparent melting temperature (Tm) (61 °C) than that of the wild-type enzyme (56 °C). The addition of serine or serinamide did not change the apparent Tm of R401A mutant enzyme. These results suggest that the mutant enzyme might be in a permanently ‘open’ form and the increased apparent Tm could be due to enhanced subunit interactions.

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29

Budipramana, Krisyanti, Junaidin Junaidin, Komar Ruslan Wirasutisna, Yanatra Budi Pramana та Sukrasno Sukrasno. "An Integrated In Silico and In Vitro Assays of Dipeptidyl Peptidase-4 and α-Glucosidase Inhibition by Stellasterol from Ganoderma australe". Scientia Pharmaceutica 87, № 3 (14 серпня 2019): 21. http://dx.doi.org/10.3390/scipharm87030021.

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Background: Ganoderma fungus is rich in terpenoids. These compounds are known for their anti-hyperglycemic activities. However, the study of terpenoids as the secondary metabolite from Ganoderma as a dipeptidyl peptidase-4 (DPP-4) inhibitor remains unexplored. In addition, we examined the α-glucosidase inhibition activity. Objective: This study aimed to isolate the major terpenoid from non-laccate Ganoderma and examined its inhibitor activity on DPP-4 and α-glucosidase enzymes, and its interaction. Methods: The compound was isolated using column chromatography from Ganoderma australe. The structure of the isolated compound was confirmed by 1H and 13C nuclear magnetic resonance spectroscopy, while the inhibitory activity was evaluated using an enzymatic assay. The interaction of the isolated compound with DPP-4 and α-glucosidase enzymes was investigated using an in silico study. Results: The isolated compound was identified as stellasterol; IC50 values for DPP-4 and α-glucosidase inhibitor were 427.39 µM and 314.54 µM, respectively. This study revealed that the inhibitory effect of stellasterol on DPP-4 enzyme is through hydrophobic interaction, while the α-glucosidase enzyme is due to the interaction with six amino acids of the enzyme. Conclusion: Stellasterol is the major component of the steroid from G. australe. Enzyme inhibitory assay and in silico study suggest that stellasterol may contribute antidiabetic activity with a mechanism closer to acarbose rather than to sitagliptin.

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30

Patumcharoenpol, Preecha, Narumol Doungpan, Asawin Meechai, Bairong Shen, Jonathan H. Chan, and Wanwipa Vongsangnak. "An integrated text mining framework for metabolic interaction network reconstruction." PeerJ 4 (March 21, 2016): e1811. http://dx.doi.org/10.7717/peerj.1811.

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Анотація:

Text mining (TM) in the field of biology is fast becoming a routine analysis for the extraction and curation of biological entities (e.g., genes, proteins, simple chemicals) as well as their relationships. Due to the wide applicability of TM in situations involving complex relationships, it is valuable to apply TM to the extraction of metabolic interactions (i.e., enzyme and metabolite interactions) through metabolic events. Here we present an integrated TM framework containing two modules for the extraction of metabolic events (Metabolic Event Extraction module—MEE) and for the construction of a metabolic interaction network (Metabolic Interaction Network Reconstruction module—MINR). The proposed integrated TM framework performed well based on standard measures of recall, precision and F-score. Evaluation of the MEE module using the constructed Metabolic Entities (ME) corpus yielded F-scores of 59.15% and 48.59% for the detection of metabolic events for production and consumption, respectively. As for the testing of the entity tagger for Gene and Protein (GP) and metabolite with the test corpus, the obtained F-score was greater than 80% for the Superpathway of leucine, valine, and isoleucine biosynthesis. Mapping of enzyme and metabolite interactions through network reconstruction showed a fair performance for the MINR module on the test corpus with F-score >70%. Finally, an application of our integrated TM framework on a big-scale data (i.e., EcoCyc extraction data) for reconstructing a metabolic interaction network showed reasonable precisions at 69.93%, 70.63% and 46.71% for enzyme, metabolite and enzyme–metabolite interaction, respectively. This study presents the first open-source integrated TM framework for reconstructing a metabolic interaction network. This framework can be a powerful tool that helps biologists to extract metabolic events for further reconstruction of a metabolic interaction network. The ME corpus, test corpus, source code, and virtual machine image with pre-configured software are available atwww.sbi.kmutt.ac.th/ preecha/metrecon.

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31

Sarvesh, Sabarathinam, Preethi L, Haripritha Meganathan, M. Arjun Gokulan, Dhivya Dhanasekaran, Nila Ganamurali, and Rahul Radhakrishnan. "HCIP: An Online database for prediction CYP450 Enzyme Inhibition potential of bioactive compounds." Journal of Drug Delivery and Therapeutics 11, no. 2 (April 1, 2021): 253–55. http://dx.doi.org/10.22270/jddt.v11i2.4637.

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Background: Concomitant administration of herbal medicine and conventional may lead to severe metabolism-oriented herb-drug interactions. However, detecting herb-drug interaction is expensive and higher time-consuming. Several computer-aided techniques have been proposed in recent years to predict drug interactions. However, most of the methods cannot predict herb-drug interactions effectively. Methods: Canonical SMILES of bioactive compounds was gathered from the PubChem online database, and its inhibition details were gathered PKCSM from the webserver. Results: By searching the bioactive compound name in the search bar of “The Herb-CYP450 Enzyme Inhibition Predictor online database” (HCIP- http://hcip.in/), it will provide the liver enzyme inhibition profile of the selected bioactive compound. For example; Guggulsterone: CYP3A4 inhibitor. Conclusion: The Herb-CYP450 Enzyme Inhibition Predictor online database is very peculiar and easy to determine the inhibition profile of the targeted bioactive compound. Keywords: CYP450; Enzyme inhibition; Bioactive Compounds; Online database; Herb-Drug Interaction

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32

VISHWANATH, Bannikuppe S., Waldemar EICHENBERGER, Felix J. FREY, and Brigitte M. FREY. "Interaction of plant lipids with 14 kDa phospholipase A2 enzymes." Biochemical Journal 320, no. 1 (November 15, 1996): 93–99. http://dx.doi.org/10.1042/bj3200093.

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Several structurally related plant lipids were isolated and their effect was assessed on the enzyme activity of group I (pancreatic and Naja mocambique venom) and group II (Crotalus atrox venom) phospholipase A2 (PLA2) enzymes, with labelled Escherichia coli as an enzyme substrate. The neutral monogalactosyldiacylglycerol (MGDG) and negatively charged diacylglyceryl α-D-glucuronide (DGGA) did not influence the enzyme activity of either group. Digalactosyldiacylglycerol (DGDG), another uncharged glycolipid, inhibited PLA2 activity in a dose-dependent manner to 60–70% of the control. Sulphoquinovosyldiacylglycerol (SQDG), which is also anionic, activated both groups of PLA2 enzyme. A similar activation was observed with the zwitterionic diacylglyceryl-O-(N,N,N-trimethylhomoserine) (DGTS) and diacylglyceryl-O-(hydroxymethyl)(N,N,N-trimethyl)-β-alanine (DGTA). DGDG, SQDG and DGTS are dispersed homogeneously with low critical micelle concentrations (CMCs). The hydrodynamic radius of neutral DGDG is an order of magnitude larger than the charged lipids SQDG and DGTS. The inhibition of pig pancreatic PLA2 by DGDG was dependent on substrate concentration. The intrinsic fluorescence spectra of the enzyme was not changed in the presence of native or hydrogenated DGDG. Thus the inhibition is most probably due to a non-specific interaction of plant lipids with the substrate. Different lengths and saturations of the fatty acyl chains of DGDG did not alter the inhibition of PLA2, whereas deacylation abrogated the inhibitory effect. Both SQDG and DGTS activated pig pancreatic PLA2 in a dose-dependent manner. Saturation of the double bonds of these lipids decreased the activating effect. The fluorescence of pig pancreatic PLA2 incubated with SQDG and DGTS was enhanced by 2-fold and 3-fold respectively, suggesting the formation of a complex between enzyme and lipids. In conclusion, the effect of different plant lipids on PLA2 activity depends on different structural elements of the polar head group and their charge as well as the degree of unsaturation of the fatty acyl chains.

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33

Sinurat, Arnold Parlindungan, Tuti Haryati, Nurul Pratiwi, and Tresnawati Purwadaria. "Effectivity of Dry and Liquid BS4 Enzymes in Improving Performance of Broiler Chickens Fed Different Nutrient Density Diet." Jurnal Ilmu Ternak dan Veteriner 27, no. 2 (August 11, 2022): 84–92. http://dx.doi.org/10.14334/jitv.v27i2.3051.

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Supplementation of enzymes in feed is now commonly practiced to increase the nutrient availability of feed and the performance of poultry. A new enzyme called BS4 was produced by cultivating Eupenicilium javanicum. It is necessary to test the efficacy of this enzyme since the effectiveness of enzyme supplementation depends on many factors. An experiment was conducted to study the effect of dietary BS4 enzyme supplementation in improving the performance of broiler chickens. A number of 300 broilers DOC was distributed into 30 pens and reared until 35 d. Six experimental diets i.e., factorial of 2 (Standard diet, and low nutrient density diet) X 3 (Control, BS4 liquid enzyme, and BS4 powder enzyme) were formulated with 5 replications. The performance (feed intake, body weight, FCR, and survival rates) were observed during the starter (1-21 d) and whole (1-35 d) periods. At the end of the trial, measurements were also made on the carcass yield, abdominal fat, liver, and gizzard weights. Results showed that performances of broilers from 1-35 d were not significantly affected by interaction between nutrient density and enzyme supplement. The nutrient density also did not affect performances of broilers. However, dietary enzyme supplementation significantly reduced feed intake and improved FCR of broilers as compared to the control. Supplementation of BS4 in liquid or powder form, reduced feed intake by 3.6%. Supplementation of liquid and powder BS4 enzymes improved FCR by 6.4% and 8.9%, respectively, but no different effect between liquid and powder BS4 enzymes on performance of broilers. Nutrient density, enzyme supplementation, and interactions between the two factors did not significantly influence carcass yield, abdominal fat, liver, and gizzard relative weights of broilers.

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34

Pérez de la Lastra, José Manuel, Victoria Baca-González, Sergio González-Acosta, Patricia Asensio-Calavia, Andrea Otazo-Pérez, and Antonio Morales-delaNuez. "Antibodies targeting enzyme inhibition as potential tools for research and drug development." Biomolecular Concepts 12, no. 1 (January 1, 2021): 215–32. http://dx.doi.org/10.1515/bmc-2021-0021.

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Abstract Antibodies have transformed biomedical research and are now being used for different experimental applications. Generally, the interaction of enzymes with their specific antibodies can lead to a reduction in their enzymatic activity. The effect of the antibody is dependent on its narrow i.e. the regions of the enzyme to which it is directed. The mechanism of this inhibition is rarely a direct combination of the antibodies with the catalytic site, but is rather due to steric hindrance, barring the substrate access to the active site. In several systems, however, the interaction with the antibody induces conformational changes on the enzyme that can either inhibit or enhance its catalytic activity. The extent of enzyme inhibition or enhancement is, therefore, a reflection of the nature and distribution of the various antigenic determinants on the enzyme molecule. Currently, the mode of action of many enzymes has been elucidated at the molecular level. We here review the molecular mechanisms and recent trends by which antibodies inhibit the catalytic activity of enzymes and provide examples of how specific antibodies can be useful for the neutralization of biologically active molecules

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35

BOUGIE, Isabelle, Amélie PARENT, and Martin BISAILLON. "Thermodynamics of ligand binding by the yeast mRNA-capping enzyme reveals different modes of binding." Biochemical Journal 384, no. 2 (November 23, 2004): 411–20. http://dx.doi.org/10.1042/bj20041112.

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RNA-capping enzymes are involved in the synthesis of the cap structure found at the 5′-end of eukaryotic mRNAs. The present study reports a detailed study on the thermodynamic parameters involved in the interaction of an RNA-capping enzyme with its ligands. Analysis of the interaction of the Saccharomyces cerevisiae RNA-capping enzyme (Ceg1) with GTP, RNA and manganese ions revealed significant differences between the binding forces that drive the interaction of the enzyme with its RNA and GTP substrates. Our thermodynamic analyses indicate that the initial association of GTP with the Ceg1 protein is driven by a favourable enthalpy change (ΔH=−80.9 kJ/mol), but is also clearly associated with an unfavourable entropy change (TΔS=−62.9 kJ/mol). However, the interaction between Ceg1 and RNA revealed a completely different mode of binding, where binding to RNA is clearly dominated by a favourable entropic effect (TΔS=20.5 kJ/mol), with a minor contribution from a favourable enthalpy change (ΔH=−5.3 kJ/mol). Fluorescence spectroscopy also allowed us to evaluate the initial binding of GTP to such an enzyme, thereby separating the GTP binding step from the concomitant metal-dependent hydrolysis of GTP that results in the formation of a covalent GMP–protein intermediate. In addition to the determination of the energetics of ligand binding, our study leads to a better understanding of the molecular basis of substrate recognition by RNA-capping enzymes.

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36

Chen, Jinghua, Peilu Xie, Yujia Huang, and Haichun Gao. "Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide." International Journal of Molecular Sciences 23, no. 2 (January 17, 2022): 979. http://dx.doi.org/10.3390/ijms23020979.

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Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.

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37

Chan, Catherine S., Limei Chang, Kenton L. Rommens, and Raymond J. Turner. "Differential Interactions between Tat-Specific Redox Enzyme Peptides and Their Chaperones." Journal of Bacteriology 191, no. 7 (January 16, 2009): 2091–101. http://dx.doi.org/10.1128/jb.00949-08.

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ABSTRACT The twin-arginine translocase (Tat) system is used by many bacteria to move proteins across the cytoplasmic membrane. Tat substrates are prefolded and contain a conserved SRRxFLK twin-arginine (RR) motif at their N termini. Many Tat substrates in Escherichia coli are cofactor-containing redox enzymes that have specific chaperones called redox enzyme maturation proteins (REMPs). Here we characterized the interactions between 10 REMPs and 15 RR peptides of known and predicted Tat-specific redox enzyme subunits. A combination of in vitro and in vivo experiments demonstrated that some REMPs were specific to a redox enzyme(s) of similar function, whereas others were less specific and bound peptides of unrelated enzymes. Results from Biacore surface plasmon resonance (SPR) and bacterial two-hybrid experiments identified interactions in addition to those found in far-Western experiments, suggesting that conformational freedom and/or other cellular factors may be required. Furthermore, we show that the interaction of the two prevents both from being proteolytically degraded in vivo, and kinetic data from SPR show up to 10-fold-tighter binding to the expected RR substrate when multiple binding partners existed. Investigations using full-length sequences of the RR proteins showed that the mature portion for some redox enzyme subunits is required for detection of the interactions. Sequence alignments among the REMPs and RR peptides indicated that homology between the REMPs and the hydrophobic regions following the RR motifs in the peptides correlates to cross-recognition.

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38

Uday, R. V. Sriram, Rajdip Misra, Annaram Harika, Sandip Dolui, Achintya Saha, Uttam Pal, V. Ravichandiran, and Nakul C. Maiti. "Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease." PLOS ONE 16, no. 9 (September 10, 2021): e0257206. http://dx.doi.org/10.1371/journal.pone.0257206.

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Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.

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39

Dunn, Ben M. "Anatomy and pathology of HIV-1 peptidase." Essays in Biochemistry 38 (October 1, 2002): 113–27. http://dx.doi.org/10.1042/bse0380113.

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The peptidase of the HIV type 1 (HIV PR) is required for the replication of and further infection by the virus. A concerted effort has taken place in the past 15 years to understand the properties of this enzyme, as it serves as an excellent drug target for control of the virus. Owing to drug pressure, many mutations arise during turnover of the virus and some of these lead to resistance to the effects of the inhibitors. Recent advances in the understanding of the changes these mutations cause to the enzyme and its interaction with substrates and inhibitors have been described. In addition, studies of closely related retroviral enzymes from simian immunodeficiency virus, feline immunodeficiency virus and HIV-2 have expanded the structure-function paradigm. The role of the flexibility of ligands and of the enzyme in active-site interactions is discussed.

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40

İş, Yusuf Serhat. "Elucidation of Ligand/Protein Interactions between BCR-ABL Tyrosine Kinase and Some Commercial Anticancer Drugs Via DFT Methods." Journal of Computational Biophysics and Chemistry 20, no. 04 (June 2021): 433–47. http://dx.doi.org/10.1142/s273741652150023x.

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Анотація:

In this study, the interactions of 7 commercially available BCR-ABL tyrosine kinase enzyme inhibitors with amino acids in the active site of the relevant enzyme were investigated quantum mechanically. Here a per-residue study was carried out. Interaction energies were calculated by using the coordinates of the critical residues in the binding site of the enzyme and the drug molecules docked in this region. DFT methods were used during the QM processes. All interaction energies were calculated via M06-2X functional and 6-31G (d,p) basis set in vacuum. Based on the results obtained, it was tried to be determined which of the important residues in the binding cavity of the enzyme could better interact with the examined ligands. It is thought that this study may contribute to the development of tyrosine kinase enzyme inhibitors.

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41

Bakhdar, Fatmah. "The Role of CYP 450 Isozymes in Drug-Drug Interaction." Journal of Umm Al-Qura University for Medical Sciences 6, no. 1 (June 1, 2020): 36–40. http://dx.doi.org/10.54940/ms53396452.

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The main focus of the pharmacokinetic process is hepatic metabolism, which is responsible for biotransformation and elimination of xenobiotics such as drugs. This step depends primarily on the CYP450 system, which plays a role in drug metabolism and changes their therapeutic responses. CYP450 enzyme system includes many notable points such as major families, their functions and also the factors that can alter their activity and cause significant interaction. According to previous studies, the most important factor affecting this enzyme system is the medications that can enhance or inhibit its activity. The aim of this article is to discuss the detailed mechanism of the interaction between CYP450 enzyme and other drugs. This mechanism is very important when prescribing various medications to avoid the problem of drug-drug interaction. We must remember that many drugs undergo metabolism through more than just isozyme interactions or may pass through dual metabolism pathways. Examples of such drugs are anticonvulsants, antidepressant, anti-infectives, immunosuppressant, and cardiovascular drugs.

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42

D.C., Okafor, Agunwah I.M., Ezegbe C.C., Ekeoma C.L., and Onuegbu N.C. "Sugar Spectra of Syrups Produced from Different Tuber Starches via Crude Enzymes and Amyloglucosidase Sources." Food Science and Nutrition Studies 3, no. 3 (August 19, 2019): p96. http://dx.doi.org/10.22158/fsns.v3n3p96.

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Syrup production was done via enzyme hydrolysis. Enzymes used were crude enzymes from malted sorghum, wheat and millet and exogenous enzyme by name amyloglucosidase (AMG) which hydrolyzed Cassava (Manihot esculenta,), water yam (Dioscorea alata) and potato white (Ipomoea batatas L) starches. Syrup sugars were determined using high performance liquid chromatography (HPLC) and the sugar profile found are fructose; glucose, sucrose, maltose, D-xylose, and D-Raffinose which manifested as a result of the interaction between starches and enzymes. The sugar Fructose was in the range of 17.34 ± 0.651 g/l to 28.16 ± 0.982 g/l, Glucose sugar was in the range of 6.09 ± 0.165 g/l to 177.04 ± 1.229 g/l. The highest glucose yield (177.04 ± 1.229 g/l) was observed in Cassava starch reaction with the commercial enzyme –AMG. Sucrose content was in the range of 5.78 ± 0.180 g/l to 21.59 ± 0.536 g/l, Maltose (23.71 ± 0.125 g/l to 48.04 ± 0.125 g/l) was the most predominant sugar in all syrups gotten from the starch and crude enzymes interaction. The hydrolysis of starches using different enzyme sources yielded sugar spectra of different sugars concentrations with each starch source predisposed to the natural activity of the enzyme peculiar to their variety or cell structure. D-xylose and D-Raffinose were in the range of 0.004-0.225 g/l which is very small in quantity compared to other sugars seen while no D-stachyose was detected.

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43

Reyes-Espinosa, Francisco, Domingo Méndez-Álvarez, Miguel A. Pérez-Rodríguez, Verónica Herrera-Mayorga, Alfredo Juárez-Saldivar, María A. Cruz-Hernández, and Gildardo Rivera. "In Silico Study of the Resistance to Organophosphorus Pesticides Associated with Point Mutations in Acetylcholinesterase of Lepidoptera: B. mandarina, B. mori, C. auricilius, C. suppressalis, C. pomonella, H. armígera, P. xylostella, S. frugiperda, and S. litura." International Journal of Molecular Sciences 20, no. 10 (May 15, 2019): 2404. http://dx.doi.org/10.3390/ijms20102404.

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An in silico analysis of the interaction between the complex-ligands of nine acetylcholinesterase (AChE) structures of Lepidopteran organisms and 43 organophosphorus (OPs) pesticides with previous resistance reports was carried out. To predict the potential resistance by structural modifications in Lepidoptera insects, due to proposed point mutations in AChE, a broad analysis was performed using computational tools, such as homology modeling and molecular docking. Two relevant findings were revealed: (1) Docking results give a configuration of the most probable spatial orientation of two interacting molecules (AChE enzyme and OP pesticide) and (2) a predicted ΔGb. The mutations evaluated in the form 1 acetylcholinesterase (AChE-1) and form 2 acetylcholinesterase (AChE-2) structures of enzymes do not affect in any way (there is no regularity of change or significant deviations) the values of the binding energy (ΔGb) recorded in the AChE–OPs complexes. However, the mutations analyzed in AChE are associated with a structural modification that causes an inadequate interaction to complete the phosphorylation of the enzyme.

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44

Chi, Zhenxing, Rutao Liu, and Hao Zhang. "Noncovalent Interaction of Oxytetracycline with the Enzyme Trypsin." Biomacromolecules 11, no. 9 (September 13, 2010): 2454–59. http://dx.doi.org/10.1021/bm100633h.

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45

Cheng, Ling-Li, Mei Wang, Ming-Hong Wu, Si-De Yao, Zheng Jiao, and Shi-Long Wang. "Interaction mechanism between berberine and the enzyme lysozyme." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 97 (November 2012): 209–14. http://dx.doi.org/10.1016/j.saa.2012.05.035.

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46

Mann, D. M., and T. C. Vanaman. "Topographical mapping of calmodulin-target enzyme interaction domains." Journal of Biological Chemistry 264, no. 4 (February 1989): 2373–78. http://dx.doi.org/10.1016/s0021-9258(18)94187-6.

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47

Etminan, M. "Interaction Between Angiotensin-Converting Enzyme Inhibitors and Aspirin." Archives of Internal Medicine 161, no. 16 (September 10, 2001): 2048–49. http://dx.doi.org/10.1001/archinte.161.16.2048.

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48

Lessenger, James E. "Postulated Interaction Between Hydroxychloroquine and Cholinesterase Enzyme Activity:." Journal of Agromedicine 2, no. 2 (June 27, 1995): 5–12. http://dx.doi.org/10.1300/j096v02n02_02.

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49

ROJO-NIERSBACH, Eileen, Debra MORLEY, Stephanie HECK, and Norbert LEHMING. "A new method for the selection of protein interactions in mammalian cells." Biochemical Journal 348, no. 3 (June 7, 2000): 585–90. http://dx.doi.org/10.1042/bj3480585.

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In the present study we present a new method that allows for the selection of protein interactions in mammalian cells. We have used this system to verify two interactions previously characterized in vitro. (1) The interaction between human TATA-binding protein 1 and nuclear factor ĸB and (2) the association of Homo sapiens nuclear autoantigen SP100B with human heterochromatin protein 1α, a protein implicated in chromatin remodelling. We observe for the first time that these interactions also occur in vivo. One protein was fused to the N-terminal half of ubiquitin, while the interacting partner was fused to the C-terminal half of ubiquitin, that was itself linked to guanine phosphoryltransferase 2 (gpt2) modified to begin with an arginine residue. Upon interaction of both proteins, ubiquitin is reconstituted, and its association with the Rgpt2 reporter is subsequently cleaved off by ubiquitin-processing enzymes. The presence of arginine in the Rgpt2 gene product leads to the degradation of the product by the N-end rule pathway. In the human fibroblast cell line HT1080HPRT- (that is deficient in the enzyme for hypoxanthine-guanine phosphoribosyltransferase) cells in which interaction between both proteins of interest occurs can then be selected for by hypoxanthine/aminopterin/thymine medium and counterselected against by 6-thioguanine medium. This method provides a suitable alternative to the yeast two-hybrid system and is generally applicable.

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50

Lindahl, P., E. Raub-Segall, S. T. Olson, and I. Björk. "Papain labelled with fluorescent thiol-specific reagents as a probe for characterization of interactions between cysteine proteinases and their protein inhibitors by competitive titrations." Biochemical Journal 276, no. 2 (June 1, 1991): 387–94. http://dx.doi.org/10.1042/bj2760387.

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Papain was labelled by attachment of the fluorescent groups 2-(4′-acetamidoanilino)naphthalene-6-sulphonic acid (AANS) or N-(acetylaminoethyl)-8-naphthylamine-1-sulphonic acid (AEDANS) to the active-site cysteine residue, with the aim of using the labelled papains as probes in competitive titrations of unlabelled cysteine proteinases with their inhibitors. The interaction between the labelled papains and cystatins was accompanied by an increase in fluorescence emission of up to 38-fold for AANS-papain and approximately 3.5-fold for AEDANS-papain. Fluorescence titrations gave dissociation equilibrium constants of 3.1 and 0.6 microM for the binding of chicken cystatin and recombinant human cystatin C respectively to AANS-papain and of 11.9 microM for the binding of chicken cystatin to AEDANS-papain. The kinetics of interaction of chicken cystatin with AANS-papain showed an unusual biphasic dependence of the observed pseudo-first-order rate constant on inhibitor concentration, consistent with the reaction occurring via both pathways of a general two-step binding mechanism. AANS-papain was selected as the most suitable probe for competitive titrations of unlabelled active or inactivated cysteine proteinases with inhibitors. This technique, which provides stoichiometries and dissociation constants for the interaction between unlabelled enzyme and inhibitor, allows monitoring of the interactions by a large fluorescent signal in a wavelength region where the interacting proteins do not contribute to the observed fluorescence. Such competitive titrations of active papain or actinidin with chicken cystatin or recombinant human cystatin C all gave inhibitor/enzyme stoichiometries of close to 1.0. A dissociation constant of 1.8 microM for the reaction of chicken cystatin with a papain derivative, S-[N-(3-carboxypropyl)succinimidyl]-papain, was also determined by the same technique. These results show the usefulness of the fluorescent papains for the characterization of interactions between cysteine-proteinase inhibitors and their target enzymes.

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