1
|
El-Khamisi EF, Soliman EAM, El-Sayed GM, Nour SA, Abdel-Monem MO, Hassan MG. Optimization, gene cloning, expression, and molecular docking insights for enhanced cellulase enzyme production by Bacillus amyloliquefaciens strain elh1. Microb Cell Fact 2024; 23:191. [PMID: 38956640 PMCID: PMC11218070 DOI: 10.1186/s12934-024-02454-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND In this study, we isolated a cellulase-producing bacterium, Bacillus amyloliquefaciens strain elh, from rice peel. We employed two optimization methods to enhance the yield of cellulase. Firstly, we utilized a one-variable-at-a-time (OVAT) approach to evaluate the impact of individual physical and chemical parameters. Subsequently, we employed response surface methodology (RSM) to investigate the interactions among these factors. We heterologously expressed the cellulase encoding gene using a cloning vectorin E. coli DH5α. Moreover, we conducted in silico molecular docking analysis to analyze the interaction between cellulase and carboxymethyl cellulose as a substrate. RESULTS The bacterial isolate eh1 exhibited an initial cellulase activity of 0.141 ± 0.077 U/ml when cultured in a specific medium, namely Basic Liquid Media (BLM), with rice peel as a substrate. This strain was identified as Bacillus amyloliquefaciens strain elh1 through 16S rRNA sequencing, assigned the accession number OR920278 in GenBank. The optimal incubation time was found to be 72 h of fermentation. Urea was identified as the most suitable nitrogen source, and dextrose as the optimal sugar, resulting in a production increase to 5.04 ± 0.120 U/ml. The peak activity of cellulase reached 14.04 ± 0.42 U/ml utilizing statistical optimization using Response Surface Methodology (RSM). This process comprised an initial screening utilizing the Plackett-Burman design and further refinement employing the BOX -Behnken Design. The gene responsible for cellulase production, egl, was effectively cloned and expressed in E. coli DH5α. The transformed cells exhibited a cellulase activity of 22.3 ± 0.24 U/ml. The egl gene sequence was deposited in GenBank with the accession number PP194445. In silico molecular docking revealed that the two hydroxyl groups of carboxymethyl cellulose bind to the residues of Glu169 inside the binding pocket of the CMCase. This interaction forms two hydrogen bonds, with an affinity score of -5.71. CONCLUSIONS Optimization of cultural conditions significantly enhances the yield of cellulase enzyme when compared to unoptimized culturing conditions. Additionally, heterologous expression of egl gene showed that the recombinant form of the cellulase is active and that a valid expression system can contribute to a better yield of the enzyme.
Collapse
Affiliation(s)
- Elham F El-Khamisi
- Microbial Genetics Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St., (Former El-Tahrir St.) Dokki, P.O. 12622, Giza, Egypt
| | - Effat A M Soliman
- Microbial Genetics Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St., (Former El-Tahrir St.) Dokki, P.O. 12622, Giza, Egypt
| | - Ghada M El-Sayed
- Microbial Genetics Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St., (Former El-Tahrir St.) Dokki, P.O. 12622, Giza, Egypt
| | - Shaimaa A Nour
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, 33 El-Bohouth St., Dokki, P.O. 12622, Giza, Egypt.
| | - Mohamed O Abdel-Monem
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, 13511, Egypt
| | - Mervat G Hassan
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, 13511, Egypt
| |
Collapse
|
2
|
Beech JL, Maurya AK, Rodrigues da Silva R, Akpoto E, Asundi A, Fecko JA, Yennawar NH, Sarangi R, Tassone C, Weiss TM, DuBois JL. Understanding the stability of a plastic-degrading Rieske iron oxidoreductase system. Protein Sci 2024; 33:e4997. [PMID: 38723110 PMCID: PMC11081424 DOI: 10.1002/pro.4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/01/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPADO PDB ID 7Q05) is a structurally characterized heterohexameric α3β3 RO that, with its cognate reductase (TPARED), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPADO/TPARED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPADO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature (Tm) of 39.9°C for the monomeric TPARED, while the independent Tm of TPADO is 50.8°C. Differential scanning calorimetry revealed a two-step thermal decomposition pathway for TPADO with Tm values of 47.6 and 58.0°C (ΔH = 210 and 509 kcal mol-1, respectively) for each step. Temperature-dependent small-angle x-ray scattering and dynamic light scattering both detected heat-induced dissociation of TPADO subunits at 53.8°C, followed by higher-temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β-β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPADO stability, we propose prioritizing the re-engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.
Collapse
Affiliation(s)
- Jessica Lusty Beech
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Anjani K. Maurya
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Emmanuel Akpoto
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Arun Asundi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Julia Ann Fecko
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Neela H. Yennawar
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Christopher Tassone
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Jennifer L. DuBois
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| |
Collapse
|
3
|
Cutroneo S, Prandi B, Pellegrini N, Sforza S, Tedeschi T. Assessment of Protein Quality and Digestibility in Plant-Based Meat Analogues. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8114-8125. [PMID: 38560783 DOI: 10.1021/acs.jafc.3c08956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In this first work, commercial steak-like (n = 3) and cured meat (n = 3) analogues with different legume and cereal formulations were studied and compared to their animal-based (n = 3) counterparts. Plant-based products showed lower protein content than meat controls but a good amino acidic profile even though the sum of essential amino acids of plant-cured meats does not fulfill the requirements set by the Food and Agriculture Organization for children. A comparable release of soluble proteins and peptides in the digestates after in vitro digestion was observed in meat analogues as meat products, whereas the digestibility of proteins was lower in plant-based steaks and higher in plant-based cured meats than their counterparts. The overall protein quality and digestibility of products are related to both the use of good blending of protein sources and processes applied to produce them. An adequate substitution of meat with its analogues depends mostly on the quality of raw materials used, which should be communicated to consumers.
Collapse
Affiliation(s)
- Sara Cutroneo
- Food and Drug Department, University of Parma, Parco Area delle Scienze, 27/A, 43124 Parma, Italy
| | - Barbara Prandi
- Food and Drug Department, University of Parma, Parco Area delle Scienze, 27/A, 43124 Parma, Italy
| | - Nicoletta Pellegrini
- Department of Agricultural, Food, Environmental, and Animal Sciences, University of Udine, 33100 Udine, Italy
| | - Stefano Sforza
- Food and Drug Department, University of Parma, Parco Area delle Scienze, 27/A, 43124 Parma, Italy
| | - Tullia Tedeschi
- Food and Drug Department, University of Parma, Parco Area delle Scienze, 27/A, 43124 Parma, Italy
| |
Collapse
|
4
|
Lhamo P, Mahanty B. Impact of Acetic Acid Supplementation in Polyhydroxyalkanoates Production by Cupriavidus necator Using Mixture-Process Design and Artificial Neural Network. Appl Biochem Biotechnol 2024; 196:1155-1174. [PMID: 37166651 DOI: 10.1007/s12010-023-04567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 05/12/2023]
Abstract
The trend in bioplastic application has increased over the years where polyhydroxyalkanoates (PHAs) have emerged as a potential candidate with the advantage of being bio-origin, biodegradable, and biocompatible. The present study aims to understand the effect of acetic acid concentration (in combination with sucrose) as a mixture variable and its time of addition (process variable) on PHA production by Cupriavidus necator. The addition of acetic acid at a concentration of 1 g l-1 showed a positive influence on biomass and PHA yield; however, the further increase had a reversal effect. The addition of acetic acid at the time of incubation showed a higher PHA yield, whereas maximum biomass was achieved when acetic acid was added after 48 h. Genetic algorithm (GA) optimized artificial neural network (ANN) was used to model PHA concentration from mixture-process design data. Fitness of the GA-ANN model (R2: 0.935) was superior when compared to the polynomial model (R2: 0.301) from mixture design. Optimization of the ANN model projected 2.691 g l-1 PHA from 7.245 g l-1 acetic acid, 12.756 g l-1 sucrose, and the addition of acetic acid at the time of incubation. Sensitivity analysis indicates the inhibitory effect of all the predictors at higher levels. ANN model can be further used to optimize the variables while extending the bioprocess to fed-batch operation.
Collapse
Affiliation(s)
- Pema Lhamo
- Karunya Institute of Technology and Sciences, Coimbatore, India
| | | |
Collapse
|
5
|
Benali J, Ben Atitallah I, Ghariani B, Mechichi T, Hadrich B, Zouari-Mechichi H. Optimized decolorization of two poly azo dyes Sirius Red and Sirius Blue using laccase-mediator system. 3 Biotech 2024; 14:93. [PMID: 38433848 PMCID: PMC10907334 DOI: 10.1007/s13205-024-03937-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/21/2024] [Indexed: 03/05/2024] Open
Abstract
Factors, namely pH, laccase-like activity, dyes concentration as well as 1-Hydroxybenzotriazole (HBT) concentration was examined. The results indicated that the maximum decolorization yield and rate reached 98.30 ± 0.10% and 5.84 ± 0.01%/min, respectively for Sirius Blue, and 99.34 ± 0.47% and 5.85 ± 0.12%/min, respectively for Sirius Red after 4 h. The presence of the redox mediator 1-hydroxybenzotriazole (HBT) greatly improved the decolorization levels. The optimum concentrations of HBT, dyes, and laccase were 0.62 mM, 50 mg/L, and 0.89 U/mL respectively at pH 4.58 for both dyes. Phytotoxicity tests using treated and untreated dyes proved that the applied treatment slightly decreased the toxicity of the by-products. However, the germination index (GI) increased from 14.6 to 36.08% and from 31.6 to 36.96% for Sirius Red and Sirius Blue, respectively. The present study focused on the treatment of two recalcitrant azo dyes, namely: Sirius Blue (Direct Blue 71) and Sirius Red (Direct Red 80). The decolorization was performed using cell-free supernatant from Coriolopsis gallica culture with high laccase activity. Response surface methodology (RSM) and Box-Behnken design were applied to optimize the decolorization of the two tested dyes. The effect of four.
Collapse
Affiliation(s)
- Jihen Benali
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, National School of Engineers of Sfax, University of Sfax, PO box 1173, 3038 Sfax, Tunisia
| | - Imen Ben Atitallah
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, National School of Engineers of Sfax, University of Sfax, PO box 1173, 3038 Sfax, Tunisia
| | - Bouthaina Ghariani
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, National School of Engineers of Sfax, University of Sfax, PO box 1173, 3038 Sfax, Tunisia
| | - Tahar Mechichi
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, National School of Engineers of Sfax, University of Sfax, PO box 1173, 3038 Sfax, Tunisia
| | - Bilel Hadrich
- Department of Chemical Engineering, College of Engineering, Imam Mohammad Ibn Saud Islamic University, IMSIU, 11432 Riyadh, Saudi Arabia
| | - Héla Zouari-Mechichi
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, National School of Engineers of Sfax, University of Sfax, PO box 1173, 3038 Sfax, Tunisia
| |
Collapse
|
6
|
Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
Collapse
Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| |
Collapse
|
7
|
Fouda A, Alshallash KS, Atta HM, El Gamal MS, Bakry MM, Alawam AS, Salem SS. Synthesis, Optimization, and Characterization of Cellulase Enzyme Obtained from Thermotolerant Bacillus subtilis F3: An Insight into Cotton Fabric Polishing Activity. J Microbiol Biotechnol 2024; 34:207-223. [PMID: 37940165 PMCID: PMC10840485 DOI: 10.4014/jmb.2309.09023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 11/10/2023]
Abstract
The efficacy of 40 bacterial isolates obtained from hot spring water samples to produce cellulase enzymes was investigated. As a result, the strain Bacillus subtilis F3, which was identified using traditional and molecular methods, was selected as the most potent for cellulase production. Optimization was carried out using one-factor-at-a-time (OFAT) and BOX-Behnken Design to detect the best conditions for the highest cellulase activity. This was accomplished after an incubation period of 24 h at 45°C and pH 8, with an inoculum size of 1% (v/v), 5 g/l of peptone as nitrogen source, and 7.5 g/l of CMC. Moreover, the best concentration of ammonium sulfate for cellulase enzyme precipitation was 60% followed by purification using a dialysis bag and Sephadex G-100 column chromatography to collect the purified enzyme. The purified cellulase enzyme was characterized by 5.39-fold enrichment, with a specific activity of 54.20 U/mg and a molecular weight of 439 kDa. There were 15 amino acids involved in the purified cellulase, with high concentrations of 160 and 100 mg/l for glycine and proline respectively. The highest stability and activity of the purified cellulase was attained at pH 7 and 50°C in the presence of 150 ppm of CaCl2, NaCl, and ZnO metal ions. Finally, the biopolishing activity of the cellulase enzyme, as indicated by weight loss percentages of the cotton fabric, was dependent on concentration and treatment time. Overall, the thermotolerant B. subtilis F3 strain has the potential to provide highly stable and highly active cellulase enzyme for use in biopolishing of cotton fabrics.
Collapse
Affiliation(s)
- Amr Fouda
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Khalid S. Alshallash
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Hossam M. Atta
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Mamdouh S. El Gamal
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Mohamed M. Bakry
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Abdullah S. Alawam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Salem S. Salem
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| |
Collapse
|
8
|
Masson P, Mukhametgalieva AR. Partial Reversible Inhibition of Enzymes and Its Metabolic and Pharmaco-Toxicological Implications. Int J Mol Sci 2023; 24:12973. [PMID: 37629158 PMCID: PMC10454656 DOI: 10.3390/ijms241612973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Partial reversible inhibition of enzymes, also called hyperbolic inhibition, is an uncommon mechanism of reversible inhibition, resulting from a productive enzyme-inhibitor complex. This type of inhibition can involve competitive, mixed, non-competitive and uncompetitive inhibitors. While full reversible inhibitors show linear plots for reciprocal enzyme initial velocity versus inhibitor concentration, partial inhibitors produce hyperbolic plots. Similarly, dose-response curves show residual fractional activity of enzymes at high doses. This article reviews the theory and methods of analysis and discusses the significance of this type of reversible enzyme inhibition in metabolic processes, and its implications in pharmacology and toxicology.
Collapse
Affiliation(s)
- Patrick Masson
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, 18 ul. Kremlevskaya, 420008 Kazan, Russia
| | | |
Collapse
|
9
|
Basu S, Pawlowic MC, Hsu FF, Thomas G, Zhang K. Ethanolaminephosphate cytidylyltransferase is essential for survival, lipid homeostasis and stress tolerance in Leishmania major. PLoS Pathog 2023; 19:e1011112. [PMID: 37506172 PMCID: PMC10411802 DOI: 10.1371/journal.ppat.1011112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/09/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Glycerophospholipids including phosphatidylethanolamine (PE) and phosphatidylcholine (PC) are vital components of biological membranes. Trypanosomatid parasites of the genus Leishmania can acquire PE and PC via de novo synthesis and the uptake/remodeling of host lipids. In this study, we investigated the ethanolaminephosphate cytidylyltransferase (EPCT) in Leishmania major, which is the causative agent for cutaneous leishmaniasis. EPCT is a key enzyme in the ethanolamine branch of the Kennedy pathway which is responsible for the de novo synthesis of PE. Our results demonstrate that L. major EPCT is a cytosolic protein capable of catalyzing the formation of CDP-ethanolamine from ethanolamine-phosphate and cytidine triphosphate. Genetic manipulation experiments indicate that EPCT is essential in both the promastigote and amastigote stages of L. major as the chromosomal null mutants cannot survive without the episomal expression of EPCT. This differs from our previous findings on the choline branch of the Kennedy pathway (responsible for PC synthesis) which is required only in promastigotes but not amastigotes. While episomal EPCT expression does not affect promastigote proliferation under normal conditions, it leads to reduced production of ethanolamine plasmalogen or plasmenylethanolamine, the dominant PE subtype in Leishmania. In addition, parasites with episomal EPCT exhibit heightened sensitivity to acidic pH and starvation stress, and significant reduction in virulence. In summary, our investigation demonstrates that proper regulation of EPCT expression is crucial for PE synthesis, stress response, and survival of Leishmania parasites throughout their life cycle.
Collapse
Affiliation(s)
- Somrita Basu
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Mattie C. Pawlowic
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Wellcome Centre for Anti-Infectives Research (WCAIR), Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Geoff Thomas
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Kai Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| |
Collapse
|
10
|
Mukhametgalieva AR, Nemtarev AV, Sykaev VV, Pashirova TN, Masson P. Activation/Inhibition of Cholinesterases by Excess Substrate: Interpretation of the Phenomenological b Factor in Steady-State Rate Equation. Int J Mol Sci 2023; 24:10472. [PMID: 37445649 DOI: 10.3390/ijms241310472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Cholinesterases (ChEs) display a non-michaelian behavior with positively charged substrates. In the steady-state rate equation, the b factor describes this behavior: if b > 1 there is substrate activation, if b < 1 there is substrate inhibition. The mechanistic significance of the b factor was investigated to determine whether this behavior depends on acylation, deacylation or on both steps. Kinetics of human acetyl- (AChE) and butyryl-cholinesterase (BChE) were performed under steady-state conditions and using a time-course of complete substrate hydrolysis. For the hydrolysis of short acyl(thio)esters, where acylation and deacylation are partly rate-limiting, steady-state kinetic analysis could not decide which step determines b. However, the study of the hydrolysis of an arylacylamide, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), where acetylation is rate-limiting, showed that b depends on the acylation step. The magnitude of b and opposite b values between AChE and BChE for the hydrolysis of acetyl(thio)- versus benzoyl-(thio) esters, then indicated that the productive adjustment of substrates in the active center at high concentration depends on motions of both the Ω and the acyl-binding loops. Benzoylcholine was shown to be a poor substrate of AChE, and steady-state kinetics showed a sudden inhibition at high concentration, likely due to the non-dissociation of hydrolysis products. The poor catalytic hydrolysis of this bulky ester by AChE illustrates the importance of the fine adjustment of substrate acyl moiety in the acyl-binding pocket. Molecular modeling and QM/MM simulations should definitively provide evidence for this statement.
Collapse
Affiliation(s)
- Aliya R Mukhametgalieva
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, 18 Ul. Kremlevskaya, 420008 Kazan, Russia
| | - Andrey V Nemtarev
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Ul. Arbuzov, 420088 Kazan, Russia
| | - Viktor V Sykaev
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Ul. Arbuzov, 420088 Kazan, Russia
| | - Tatiana N Pashirova
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Ul. Arbuzov, 420088 Kazan, Russia
| | - Patrick Masson
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, 18 Ul. Kremlevskaya, 420008 Kazan, Russia
| |
Collapse
|
11
|
Lukaszewicz M, Mrozek AF, Bojarska E, Stelmach J, Stepinski J, Darzynkiewicz E. Contribution of Nudt12 enzyme to differentially methylated dinucleotides of 5'RNA cap structure. Biochim Biophys Acta Gen Subj 2023:130400. [PMID: 37301333 DOI: 10.1016/j.bbagen.2023.130400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/17/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
Recent findings have substantially broadened our knowledge about the diversity of modifications of the 5'end of RNAs, an issue generally attributed to mRNA cap structure (m7GpppN). Nudt12 is one of the recently described new enzymatic activities involved in cap metabolism. However, in contrast to its roles in metabolite-cap turnover (e.g., NAD-cap) and NADH/NAD metabolite hydrolysis, little is known regarding its hydrolytic activity towards dinucleotide cap structures. In order to gain further insight into this Nudt12 activity, comprehensive analysis with a spectrum of cap-like dinucleotides was performed with respect to different nucleotide types adjacent to the (m7)G moiety and its methylation status. Among the tested compounds, GpppA, GpppAm, and Gpppm6Am were identified as novel potent Nudt12 substrates, with KM values in the same range as that of NADH. Interestingly, substrate inhibition of Nudt12 catalytic activity was detected in the case of the GpppG dinucleotide, a phenomenon not reported to date. Finally, comparison of Nudt12 with DcpS and Nud16, two other enzymes with known activity on dinucleotide cap structures, revealed their overlapping and more specific substrates. Altogether, these findings provide a basis for clarifying the role of Nudt12 in cap-like dinucleotide turnover.
Collapse
Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Aleksandra-Ferenc Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Stelmach
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| |
Collapse
|
12
|
Vadlamani VMK, Gunasinghe KKJ, Chee XW, Rahman T, Harper MT. Human soluble CD39 displays substrate inhibition in a substrate-specific manner. Sci Rep 2023; 13:8958. [PMID: 37268726 DOI: 10.1038/s41598-023-36257-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/31/2023] [Indexed: 06/04/2023] Open
Abstract
CD39 (ectonucleoside triphosphate diphosphohydrolase-1; ENTPD1) metabolizes extracellular ATP and ADP to AMP. AMP is subsequently metabolized by CD79 to adenosine. CD39 activity is therefore a key regulator of purinergic signalling in cancer, thrombosis, and autoimmune diseases. In this study we demonstrate that soluble, recombinant CD39 shows substrate inhibition with ADP or ATP as the substrate. Although CD39 activity initially increased with increasing substrate concentration, at high concentrations of ATP or ADP, CD39 activity was markedly reduced. Although the reaction product, AMP, inhibits CD39 activity, insufficient AMP was generated under our conditions to account for the substrate inhibition seen. In contrast, inhibition was not seen with UDP or UTP as substrates. 2-methylthio-ADP also showed no substrate inhibition, indicating the nucleotide base is an important determinant of substrate inhibition. Molecular dynamics simulations revealed that ADP can undergo conformational rearrangements within the CD39 active site that were not seen with UDP or 2-methylthio-ADP. Appreciating the existence of substrate inhibition of CD39 will help the interpretation of studies of CD39 activity, including investigations into drugs that modulate CD39 activity.
Collapse
Affiliation(s)
- Venkat M K Vadlamani
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Xavier W Chee
- Swinburne University of Technology Sarawak, Kuching, Malaysia
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Matthew T Harper
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| |
Collapse
|
13
|
Yip C, Phan JR, Abel-Santos E. Mechanism of germination inhibition of Clostridioides difficile spores by an aniline substituted cholate derivative (CaPA). J Antibiot (Tokyo) 2023; 76:335-345. [PMID: 37016015 PMCID: PMC10406169 DOI: 10.1038/s41429-023-00612-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 04/06/2023]
Abstract
Clostridioides difficile infection (CDI) is the major identifiable cause of antibiotic-associated diarrhea and has been declared an urgent threat by the CDC. C. difficile forms dormant and resistant spores that serve as infectious vehicles for CDI. To cause disease, C. difficile spores recognize taurocholate and glycine to trigger the germination process. In contrast to other sporulating bacteria, C. difficile spores are postulated to use a protease complex, CspABC, to recognize its germinants. Since spore germination is required for infection, we have developed anti-germination approaches for CDI prophylaxis. Previously, the bile salt analog CaPA (an aniline-substituted cholic acid) was shown to block spore germination and protect rodents from CDI caused by multiple C. difficile strains and isolates. In this study, we found that CaPA is an alternative substrate inhibitor of C. difficile spore germination. By competing with taurocholate for binding, CaPA delays C. difficile spore germination and reduces spore viability, thus diminishing the number of outgrowing vegetative bacteria. We hypothesize that the reduction of toxin-producing bacterial burden explains CaPA's protective activity against murine CDI. Previous data combined with our results suggests that CaPA binds tightly to C. difficile spores in a CspC-dependent manner and irreversibly traps spores in an alternative, time-delayed, and low yield germination pathway. Our results are also consistent with kinetic data suggesting the existence of at least two distinct bile salt binding sites in C. difficile spores.
Collapse
Affiliation(s)
- Christopher Yip
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jacqueline R Phan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA.
| |
Collapse
|
14
|
Liao J, Lederer V, Bardhi A, Zou Z, Hoffmann TD, Sun G, Song C, Hoffmann T, Schwab W. Acceptors and Effectors Alter Substrate Inhibition Kinetics of a Plant Glucosyltransferase NbUGT72AY1 and Its Mutants. Int J Mol Sci 2023; 24:ijms24119542. [PMID: 37298492 DOI: 10.3390/ijms24119542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
One of the main obstacles in biocatalysis is the substrate inhibition (SI) of enzymes that play important roles in biosynthesis and metabolic regulation in organisms. The promiscuous glycosyltransferase UGT72AY1 from Nicotiana benthamiana is strongly substrate-inhibited by hydroxycoumarins (inhibitory constant Ki < 20 µM), but only weakly inhibited when monolignols are glucosylated (Ki > 1000 µM). Apocarotenoid effectors reduce the inherent UDP-glucose glucohydrolase activity of the enzyme and attenuate the SI by scopoletin derivatives, which could also be achieved by mutations. Here, we studied the kinetic profiles of different phenols and used the substrate analog vanillin, which has shown atypical Michaelis-Menten kinetics in previous studies, to examine the effects of different ligands and mutations on the SI of NbUGT72AY1. Coumarins had no effect on enzymatic activity, whereas apocarotenoids and fatty acids strongly affected SI kinetics by increasing the inhibition constant Ki. Only the F87I mutant and a chimeric version of the enzyme showed weak SI with the substrate vanillin, but all mutants exhibited mild SI when sinapaldehyde was used as an acceptor. In contrast, stearic acid reduced the transferase activity of the mutants to varying degrees. The results not only confirm the multi-substrate functionality of NbUGT72AY1, but also reveal that the enzymatic activity of this protein can be fine-tuned by external metabolites such as apocarotenoids and fatty acids that affect SI. Since these signals are generated during plant cell destruction, NbUGT72AY1 likely plays an important role in plant defense by participating in the production of lignin in the cell wall and providing direct protection through the formation of toxic phytoalexins.
Collapse
Affiliation(s)
- Jieren Liao
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Veronika Lederer
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Alba Bardhi
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Zhiwei Zou
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Timothy D Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Guangxin Sun
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei 230036, China
| | - Thomas Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| |
Collapse
|
15
|
Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
Collapse
Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| |
Collapse
|
16
|
Moreno CJ, Hernández K, Gittings S, Bolte M, Joglar J, Bujons J, Parella T, Clapés P. Biocatalytic Synthesis of Homochiral 2-Hydroxy-4-butyrolactone Derivatives by Tandem Aldol Addition and Carbonyl Reduction. ACS Catal 2023; 13:5348-5357. [PMID: 37123603 PMCID: PMC10127515 DOI: 10.1021/acscatal.3c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/09/2023] [Indexed: 04/08/2023]
Abstract
Chiral 2-hydroxy acids and 2-hydroxy-4-butyrolactone derivatives are structural motifs often found in fine and commodity chemicals. Here, we report a tandem biocatalytic stereodivergent route for the preparation of these compounds using three stereoselective aldolases and two stereocomplementary ketoreductases using simple and achiral starting materials. The strategy comprises (i) aldol addition reaction of 2-oxoacids to aldehydes using two aldolases from E. coli, 3-methyl-2-oxobutanoate hydroxymethyltransferase (KPHMT Ecoli ), 2-keto-3-deoxy-l-rhamnonate aldolase (YfaU Ecoli ), and trans-o-hydroxybenzylidene pyruvate hydratase-aldolase from Pseudomonas putida (HBPA Pputida ) and (ii) subsequent 2-oxogroup reduction of the aldol adduct by ketopantoate reductase from E. coli (KPR Ecoli ) and a Δ1-piperidine-2-carboxylate/Δ1-pyrroline-2-carboxylate reductase from Pseudomonas syringae pv. tomato DSM 50315 (DpkA Psyrin ) with uncovered promiscuous ketoreductase activity. A total of 29 structurally diverse compounds were prepared: both enantiomers of 2-hydroxy-4-butyrolactone (>99% ee), 21 2-hydroxy-3-substituted-4-butyrolactones with the (2R,3S), (2S,3S), (2R,3R), or (2S,3R) configuration (from 60:40 to 98:2 dr), and 6 2-hydroxy-4-substituted-4-butyrolactones with the (2S,4R) configuration (from 87:13 to 98:2 dr). Conversions of aldol adducts varied from 32 to 98%, while quantitative conversions were achieved by both ketoreductases, with global isolated yields between 20 and 45% for most of the examples. One-pot one-step cascade reactions were successfully conducted achieving isolated yields from 30 to 57%.
Collapse
Affiliation(s)
- Carlos J. Moreno
- Dept. of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Karel Hernández
- Dept. of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Samantha Gittings
- Prozomix Ltd., West End Industrial Estate, Haltwhistle, Northumberland NE49 9HA, United Kingdom
| | - Michael Bolte
- Institut für Anorganische Chemie, J.-W.-Goethe-Universität, Frankfurt/Main, Max-von-Laue-Str. 7, D-60438 Frankfurt/Main, Germany
| | - Jesús Joglar
- Dept. of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jordi Bujons
- Dept. of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear. Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Pere Clapés
- Dept. of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| |
Collapse
|
17
|
Efficient snailase-based production of mogrol from Luo Han Guo extract in an aqueous-organic system. Enzyme Microb Technol 2023; 165:110212. [PMID: 36804180 DOI: 10.1016/j.enzmictec.2023.110212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
To solve the insufficient availability of mogrol, an 11α-hydroxy aglycone of mogrosides in Siraitia grosvenorii, snailase was employed as the enzyme to completely deglycosylate LHG extract containing 50% mogroside V. Other commonly used glycosidases performed less efficiently. Response surface methodology was conducted to optimize the productivity of mogrol, which peaked at 74.7% in an aqueous reaction. In view of the differences in water-solubility between mogrol and LHG extract, we employed an aqueous-organic system for the snailase-catalyzed reaction. Of five tested organic solvents, toluene performed best and was relatively well tolerated by snailase. After optimization, biphasic medium containing 30% toluene (v/v) could produce a high-quality mogrol (98.1% purity) at a 0.5 L scale with a production rate of 93.2% within 20 h. This toluene-aqueous biphasic system would not only provide sufficient mogrol to construct future synthetic biology systems for the preparation of mogrosides, but also facilitate the development of mogrol-based medicines.
Collapse
|
18
|
Sánchez-Trasviña C, Galindo-Estrada JD, Tinoco-Valencia R, Serrano-Carreón L, Rito-Palomares M, Willson RC, Mayolo-Deloisa K. Laccase-luminol chemiluminescence system: an investigation of substrate inhibition. LUMINESCENCE 2023; 38:341-349. [PMID: 36760184 DOI: 10.1002/bio.4460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Chemiluminescence (CL) reactions are widely used for the detection and quantification of many types of analytes. Laccase has previously been proposed in CL reactions; however, its light emission behaviour has not been characterized. This study was conducted to characterize the laccase-luminol system, determine its kinetic parameters, and analyze the effects of protein and OH- concentration on the CL signal. Laccase from Coriolopsis gallica was combined with different concentrations of luminol (125 nM to 4 mM), and the enzyme kinetics were evaluated using diverse kinetic models. The laccase-luminol system was able to produce CL without an intermediate molecule, but it exhibited substrate-inhibition behaviour. A two-site random model was used and suggested that when the first luminol molecule was bound to the active site, laccase affinity for the second luminol molecule was increased. This inhibition effect could be avoided using a low luminol concentration. At 5 μM luminol concentration, 1 mg/ml (0.13 U) laccase is needed to achieve nearly 90% of the maximum CL signal, suggesting that the available luminol could not bind to all active sites. Furthermore, the concentration of NaOH negatively affected the CL signal. The laccase-luminol system represents an alternative to existing CL systems, with potential uses in molecular detection and quantification.
Collapse
Affiliation(s)
- Calef Sánchez-Trasviña
- Tecnologico de Monterrey, The Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico
| | - José Daniel Galindo-Estrada
- Universidad Politécnica del Valle de Toluca, Carretera Toluca-Almoloya de Juárez km. 5.6, Almoloya de Juárez, Estado de México, Mexico
| | - Raunel Tinoco-Valencia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Leobardo Serrano-Carreón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Marco Rito-Palomares
- Tecnologico de Monterrey, The Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. Morones Prieto 3000 Pte, Monterrey, NL, Mexico
| | - Richard C Willson
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. Morones Prieto 3000 Pte, Monterrey, NL, Mexico.,Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Karla Mayolo-Deloisa
- Tecnologico de Monterrey, The Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Institute of Materials Science of Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra, Spain
| |
Collapse
|
19
|
Liu HT, Weng CY, Zhou L, Xu HB, Liao ZY, Hong HY, Ye YF, Li SF, Wang YJ, Zheng YG. Coevolving stability and activity of LsCR by a single point mutation and constructing neat substrate bioreaction system. Biotechnol Bioeng 2023; 120:1521-1530. [PMID: 36799475 DOI: 10.1002/bit.28357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/29/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
Carbonyl reductase (CR)-catalyzed bioreduction in the organic phase and the neat substrate reaction system is a lasting challenge, placing higher requirements on the performance of enzymes. Protein engineering is an effective method to enhance the properties of enzymes for industrial applications. In the present work, a single point mutation E145A on our previously constructed CR mutant LsCRM3 , coevolved thermostability, and activity. Compared with LsCRM3 , the catalytic efficiency kcat /KM of LsCRM3 -E145A (LsCRM4 ) was increased from 6.6 to 21.9 s-1 mM-1 . Moreover, E145A prolonged the half-life t1/2 at 40°C from 4.1 to 117 h, T m ${T}_{m}$ was increased by 5°C, T 50 30 ${T}_{50}^{30}$ was increased by 14.6°C, and Topt was increased by 15°C. Only 1 g/L of lyophilized Escherichia coli cells expressing LsCRM4 completely reduced up to 600 g/L 2-chloro-1-(3,4-difluorophenyl)ethanone (CFPO) within 13 h at 45°C, yielding the corresponding (1S)-2-chloro-1-(3,4-difluorophenyl)ethanol ((S)-CFPL) in 99.5% eeP , with a space-time yield of 1.0 kg/L d, the substrate to catalyst ratios (S/C) of 600 g/g. Compared with LsCRM3 , the substrate loading was increased by 50%, with the S/C increased by 14 times. Compared with LsCRWT , the substrate loading was increased by 6.5 times. In contrast, LsCRM4 completely converted 600 g/L CFPO within 12 h in the neat substrate bioreaction system.
Collapse
Affiliation(s)
- Hua-Tao Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Chun-Yue Weng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Hao-Bo Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yu Liao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yuan-Fan Ye
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| |
Collapse
|
20
|
Sun MZ, Lyu LS, Zheng QC. How does multiple substrate binding lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan? A theoretical study. Phys Chem Chem Phys 2023; 25:5164-5173. [PMID: 36723118 DOI: 10.1039/d2cp05634h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CYP2D6 is one of the most important metalloenzymes involved in the biodegradation of many drug molecules in the human body. It has been found that multiple substrate binding can lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan (DM), but the corresponding theoretical mechanism is rarely reported. Therefore, we chose DM as the probe and performed molecular dynamics simulations and quantum mechanical calculations on CYP2D6-DM systems to investigate the mechanism of how the multiple substrate binding leads to the substrate inhibition of CYP2D6 metabolizing substrates. According to our results, three gate residues (Arg221, Val374, and Phe483) for the catalytic pocket are determined. We also found that the multiple substrate binding can lead to substrate inhibition by reducing the stability of CYP2D6 binding DM and increasing the reactive activation energy of the rate-determining step. Our findings would help to understand the substrate inhibition of CYP2D6 metabolizing the DM and enrich the knowledge of the drug-drug interactions for the cytochrome P450 superfamily.
Collapse
Affiliation(s)
- Min-Zhang Sun
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Ling-Shan Lyu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Qing-Chuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130023, China. .,Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| |
Collapse
|
21
|
Wen Y, Xu J, Pan D, Wang C. Removal of substrate inhibition of Acinetobacter baumannii xanthine oxidase by point mutation at Gln-201 enables efficient reduction of purine content in fish sauce. Food Chem X 2023; 17:100593. [PMID: 36845495 PMCID: PMC9944496 DOI: 10.1016/j.fochx.2023.100593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Xanthine oxidase is an oxidase that has a molybdopterin structure with substrate inhibition. Here, we show that a single point mutation (Q201) in the Acinetobacter baumannii xanthine oxidase (AbXOD) obtained mutant Q201E (k cat =799.44 s-1, no inhibition) with high enzyme activity and decrease of substrate inhibition in 5 mmol/L high substrate model, and which cause two loops structure change at active center, characterized by complete loss of substrate inhibition without reduction of enzymatic activity. Molecular docking results showed that the change of flexible loop increased the affinity between substrate and enzyme, and the formation of a π-π bond and two hydrogen bonds made the substrate more stable in the active center. Ultimately, Q201E can still maintain better enzyme activity under high purine content (an approximately 7-fold improvement over the wild-type), indicating a broader application prospect in the manufacture of low-purine food.
Collapse
Affiliation(s)
| | | | | | - Chenghua Wang
- Corresponding author at: College of Light Industry and Food Engineering, 100 Daxue East Road, Nanning 530004, People’s Republic of China.
| |
Collapse
|
22
|
Pardhe BD, Kwon KP, Park JK, Lee JH, Oh TJ. H 2O 2-Driven Hydroxylation of Steroids Catalyzed by Cytochrome P450 CYP105D18: Exploration of the Substrate Access Channel. Appl Environ Microbiol 2023; 89:e0158522. [PMID: 36511686 PMCID: PMC9888293 DOI: 10.1128/aem.01585-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/04/2022] [Indexed: 12/15/2022] Open
Abstract
CYP105D18 supports H2O2 as an oxygen surrogate for catalysis well and shows high H2O2 resistance capacity. We report the hydroxylation of different steroids using H2O2 as a cosubstrate. Testosterone was regiospecifically hydroxylated to 2β-hydroxytestosterone. Based on the experimental data and molecular docking, we predicted that hydroxylation of methyl testosterone and nandrolone would occur at position 2 in the A-ring, while hydroxylation of androstenedione and adrenosterone was predicted to occur in the B-ring. Further, structure-guided rational design of the substrate access channel was performed with the mutagenesis of residues S63, R82, and F184. Among the mutants, S63A showed a marked decrease in product formation, while F184A showed a significant increase in product formation in testosterone, nandrolone, methyl testosterone, androstenedione, and adrenosterone. The catalytic efficiency (kcat/Km) toward testosterone was increased 1.36-fold in the F184A mutant over that in the wild-type enzyme. These findings might facilitate the potential use of CYP105D18 and further engineering to establish the basis of biotechnological applications. IMPORTANCE The structural modification of steroids is a challenging chemical reaction. Modifying the core ring and the side chain improves the biological activity of steroids. In particular, bacterial cytochrome P450s are used as promiscuous enzymes for the activation of nonreactive carbons of steroids. In the present work, we reported the H2O2-mediated hydroxylation of steroids by CYP105D18, which also overcomes the use of expensive cofactors. Further, exploring the substrate access channel and modifying the bulky amino acid F184A increase substrate conversion while modifying the substrate recognizing amino acid S63 markedly decreases product formation. Exploring the substrate access channel and the rational design of CYP105D18 can improve the substrate conversion, which facilitates the engineering of P450s for industrial application.
Collapse
Affiliation(s)
- Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan-si, Chungnam, Republic of Korea
| | - Kyoung Pyo Kwon
- Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asan-si, Chungnam, Republic of Korea
| | - Jong Kook Park
- Department of Biomedical Science and Research Institute for Bioscience & Biotechnology, Hallym University, Chuncheon, Gangwon-do, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan-si, Chungnam, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asan-si, Chungnam, Republic of Korea
- Genome-based BioIT Convergence Institute, Asan-si, Chungnam, Republic of Korea
| |
Collapse
|
23
|
Basu S, Pawlowic M, Hsu FF, Thomas G, Zhang K. Ethanolaminephosphate cytidyltransferase is essential for survival, lipid homeostasis and stress tolerance in Leishmania major. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523530. [PMID: 36712124 PMCID: PMC9882048 DOI: 10.1101/2023.01.10.523530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Glycerophospholipids including phosphatidylethanolamine (PE) and phosphatidylcholine (PC) are vital components of biological membranes. Trypanosomatid parasites of the genus Leishmania can acquire PE and PC via de novo synthesis and the uptake/remodeling of host lipids. In this study, we investigated the ethanolaminephosphate cytidyltransferase (EPCT) in Leishmania major , which is the causative agent for cutaneous leishmaniasis. EPCT is a key enzyme in the ethanolamine branch of the Kennedy pathway which is responsible for the de novo synthesis of PE. Our results demonstrate that L. major EPCT is a cytosolic protein capable of catalyzing the formation of CDP-ethanolamine from ethanolamine-phosphate and cytidine triphosphate. Genetic manipulation experiments indicate that EPCT is essential in both the promastigote and amastigote stages of L. major as the chromosomal null mutants cannot survive without the episomal expression of EPCT. This differs from our previous findings on the choline branch of the Kennedy pathway (responsible for PC synthesis) which is required only in promastigotes but not amastigotes. While episomal EPCT expression does not affect promastigote proliferation under normal conditions, it leads to reduced production of ethanolamine plasmalogen or plasmenylethanolamine, the dominant PE subtype in Leishmania . In addition, parasites with epsiomal EPCT exhibit heightened sensitivity to acidic pH and starvation stress, and significant reduction in virulence. In summary, our investigation demonstrates that proper regulation of EPCT expression is crucial for PE synthesis, stress response, and survival of Leishmania parasites throughout their life cycle. AUTHOR SUMMARY In nature, Leishmania parasites alternate between fast replicating, extracellular promastigotes in sand fly gut and slow growing, intracellular amastigotes in macrophages. Previous studies suggest that promastigotes acquire most of their lipids via de novo synthesis whereas amastigotes rely on the uptake and remodeling of host lipids. Here we investigated the function of ethanolaminephosphate cytidyltransferase (EPCT) which catalyzes a key step in the de novo synthesis of phosphatidylethanolamine (PE) in Leishmania major . Results showed that EPCT is indispensable for both promastigotes and amastigotes, indicating that de novo PE synthesis is still needed at certain capacity for the intracellular form of Leishmania parasites. In addition, elevated EPCT expression alters overall PE synthesis and compromises parasite’s tolerance to adverse conditions and is deleterious to the growth of intracellular amastigotes. These findings provide new insight into how Leishmania acquire essential phospholipids and how disturbance of lipid metabolism can impact parasite fitness.
Collapse
Affiliation(s)
- Somrita Basu
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Mattie Pawlowic
- Wellcome Centre for Anti-Infectives Research (WCAIR), Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, 660S. Euclid Ave., Saint Louis, MO 63110, USA
| | - Geoff Thomas
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Kai Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| |
Collapse
|
24
|
Zabed HM, Akter S, Rupani PF, Akor J, Zhang Y, Zhao M, Zhang C, Ragauskas AJ, Qi X. Biocatalytic gateway to convert glycerol into 3-hydroxypropionic acid in waste-based biorefineries: Fundamentals, limitations, and potential research strategies. Biotechnol Adv 2023; 62:108075. [PMID: 36502965 DOI: 10.1016/j.biotechadv.2022.108075] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Microbial conversion of bioenergy-derived waste glycerol into value-added chemicals has emerged as an important bioprocessing technology due to its eco-friendliness, feasible technoeconomics, and potential to provide sustainability in biodiesel and bioethanol production. Glycerol is an abundant liquid waste from bioenergy plants with a projected volume of 6 million tons by 2025, accounting for about 10% of biodiesel and 2.5% of bioethanol yields. 3-Hydroxypropionic acid (3-HP) is a major product of glycerol bioconversion, which is the third largest biobased platform compound with expected market size and value of 3.6 million tons/year and USD 10 billion/year, respectively. Despite these biorefinery values, 3-HP biosynthesis from glycerol is still at an immature stage of commercial exploitation. The main challenges behind this immaturity are the toxic effects of 3-HPA on cells, the distribution of carbon flux to undesirable pathways, low tolerance of cells to glycerol and 3-HP, co-factor dependence of enzymes, low enzyme activity and stability, and the problems of substrate inhibition and specificity of enzymes. To address these challenges, it is necessary to understand the fundamentals of glycerol bioconversion and 3-HP production in terms of metabolic pathways, related enzymes, cell factories, midstream process configurations, and downstream 3-HP recovery, as discussed in this review critically and comprehensively. It is equally important to know the current challenges and limitations in 3-HP production, which are discussed in detail along with recent research efforts and remaining gaps. Finally, possible research strategies are outlined considering the recent technological advances in microbial biosynthesis, aiming to attract further research efforts to achieve a sustainable and industrially exploitable 3-HP production technology. By discussing the use of advanced tools and strategies to overcome the existing challenges in 3-HP biosynthesis, this review will attract researchers from many other similar biosynthesis technologies and provide a common gateway for their further development.
Collapse
Affiliation(s)
- Hossain M Zabed
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Suely Akter
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Parveen Fatemah Rupani
- Department of Chemical Engineering, Ku Luven, Jan De Nayerlaan 5, 2860 Sint-Katelijne-Waver, Belgium
| | - Joseph Akor
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Yufei Zhang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Mei Zhao
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Cunsheng Zhang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, The University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA; UTK-ORNL Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Xianghui Qi
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China; School of Life Sciences, Guangzhou University, Guangzhou 510,006, Guangdong Province, China.
| |
Collapse
|
25
|
Zhang Y, Chen M, Lu J, Li W, Wolynes PG, Wang W. Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis. J Phys Chem B 2022; 126:6792-6801. [PMID: 36044985 PMCID: PMC9483917 DOI: 10.1021/acs.jpcb.2c03832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Substrate inhibition, whereby enzymatic activity decreases
with
excess substrate after reaching a maximum turnover rate, is among
the most elusive phenomena in enzymatic catalysis. Here, based on
a dynamic energy landscape model, we investigate the underlying mechanism
by performing molecular simulations and frustration analysis for a
model enzyme adenylate kinase (AdK), which catalyzes the phosphoryl
transfer reaction ATP + AMP ⇋ ADP + ADP. Intriguingly, these
reveal a kinetic repartitioning mechanism of substrate inhibition,
whereby excess substrate AMP suppresses the population of an energetically
frustrated, but kinetically activated, catalytic pathway going through
a substrate (ATP)-product (ADP) cobound complex with steric incompatibility.
Such a frustrated pathway plays a crucial role in facilitating the
bottleneck product ADP release, and its suppression by excess substrate
AMP leads to a slow down of product release and overall turnover.
The simulation results directly demonstrate that substrate inhibition
arises from the rate-limiting product-release step, instead of the
steps for populating the catalytically competent complex as often
suggested in previous works. Furthermore, there is a tight interplay
between the enzyme conformational equilibrium and the extent of substrate
inhibition. Mutations biasing to more closed conformations tend to
enhance substrate inhibition. We also characterized the key features
of single-molecule enzyme kinetics with substrate inhibition effect.
We propose that the above molecular mechanism of substrate inhibition
may be relevant to other multisubstrate enzymes in which product release
is the bottleneck step.
Collapse
Affiliation(s)
- Yangyang Zhang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Mingchen Chen
- Department of Research and Development, neoX Biotech, Beijing 102206, China.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jiajun Lu
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| |
Collapse
|
26
|
Atypical kinetics of cytochrome P450 enzymes in pharmacology and toxicology. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:131-176. [PMID: 35953154 DOI: 10.1016/bs.apha.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atypical kinetics are observed in metabolic reactions catalyzed by cytochrome P450 enzymes (P450). Yet, this phenomenon is regarded as experimental artifacts in some instances despite increasing evidence challenging the assumptions of typical Michaelis-Menten kinetics. As P450 play a major role in the metabolism of a wide range of substrates including drugs and endogenous compounds, it becomes critical to consider the impact of atypical kinetics on the accuracy of estimated kinetic and inhibitory parameters which could affect extrapolation of pharmacological and toxicological implications. The first half of this book chapter will focus on atypical non-Michaelis-Menten kinetics (e.g. substrate inhibition, biphasic and sigmoidal kinetics) as well as proposed underlying mechanisms supported by recent insights in mechanistic enzymology. In particular, substrate inhibition kinetics in P450 as well as concurrent drug inhibition of P450 in the presence of substrate inhibition will be further discussed. Moreover, mounting evidence has revealed that despite the high degree of sequence homology between CYP3A isoforms (i.e. CYP3A4 and CYP3A5), they have the propensities to exhibit vastly different susceptibilities and potencies of mechanism-based inactivation (MBI) with a common drug inhibitor. These experimental observations pertaining to the presence of these atypical isoform- and probe substrate-specific complexities in CYP3A isoforms by several clinically-relevant drugs will therefore be expounded and elaborated upon in the second half of this book chapter.
Collapse
|
27
|
Bustos D, Hernández-Rodríguez EW, Poblete H, Alzate-Morales J, Challier C, Boetsch C, Vergara-Jaque A, Beassoni P. Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa. J Chem Inf Model 2022; 62:3067-3078. [PMID: 35670773 DOI: 10.1021/acs.jcim.2c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is a highly pathogenic Gram-negative microorganism associated with high mortality levels in burned or immunosuppressed patients or individuals affected by cystic fibrosis. Studies support a colonization mechanism whereby P. aeruginosa can breakdown the host cell membrane phospholipids through the sequential action of two enzymes: (I) hemolytic phospholipase C acting upon phosphatidylcholine or sphingomyelin to produce phosphorylcholine (Pcho) and (II) phosphorylcholine phosphatase (PchP) that hydrolyzes Pcho to generate choline and inorganic phosphate. This coordinated action provides the bacteria with carbon, nitrogen, and inorganic phosphate to support growth. Furthermore, PchP exhibits a distinctive inhibition mechanism by high substrate concentration. Here, we combine kinetic assays and computational approaches such as molecular docking, molecular dynamics, and free-energy calculations to describe the inhibitory site of PchP, which shares specific residues with the enzyme's active site. Our study provides insights into a coupled inhibition mechanism by the substrate, allowing us to postulate that the integrity of the inhibition site is needed to the correct functioning of the active site. Our results allow us to gain a better understanding of PchP function and provide the basis for a rational drug design that might contribute to the treatment of infections caused by this important opportunistic pathogen.
Collapse
Affiliation(s)
- Daniel Bustos
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3460000, Chile.,Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
| | - Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile.,Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile
| | - Horacio Poblete
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, 1 Poniente 1141, Talca 3465548, Chile.,Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Talca, Talca 3465548, Chile
| | - Jans Alzate-Morales
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, 1 Poniente 1141, Talca 3465548, Chile
| | - Cecilia Challier
- Instituto para el Desarrollo Agroindustrial y de la Salud (IDAS), CONICET, Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto (UNRC), Río Cuarto X5804BYA, Córdoba, Argentina
| | - Cristhian Boetsch
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CONICET, Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto (UNRC), Río Cuarto X5804BYA, Córdoba, Argentina
| | - Ariela Vergara-Jaque
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, 1 Poniente 1141, Talca 3465548, Chile.,Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Talca, Talca 3465548, Chile
| | - Paola Beassoni
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CONICET, Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto (UNRC), Río Cuarto X5804BYA, Córdoba, Argentina
| |
Collapse
|
28
|
Tao J, Ai H. Metabolism of gartanin in liver microsomes and its modulating effects on cytochrome P450s. Xenobiotica 2022; 52:335-345. [PMID: 35607983 DOI: 10.1080/00498254.2022.2076631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Gartanin, a compound found in mangosteen, has various pharmacological activities, including anticancer, anti-inflammation, and antioxidation.In the present study, we reported differences of gartanin metabolism among species and the effect of gartanin on cytochrome P450 (CYP) activities and protein expression.We found significant difference in gartanin metabolism among species, where rabbits and humans had similar metabolic characteristics. Five CYP-catalysed metabolites and three glucuronosyltransferase (UGT)-catalysed metabolites were identified by LC-MS/MS. Hydroxylation was the major metabolic pathway. Gartanin exhibited mixed inhibition on CYP1A2 activity with IC50 and Ki values of 1.48 and 3.71 μM, respectively. In addition, gartanin down-regulated the protein expressions of CYP2C9 and CYP2D6 and up-regulated the protein expression of CYP2D6. The present study supports the pharmacological and toxicological research of gartanin.
Collapse
Affiliation(s)
- Jia Tao
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, China
| | - Hao Ai
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, China
| |
Collapse
|
29
|
Shimozawa Y, Matsuhisa H, Nakamura T, Himiyama T, Nishiya Y. Reducing substrate inhibition of malate dehydrogenase from Geobacillus stearothermophilus by C-terminal truncation. Protein Eng Des Sel 2022; 35:6753781. [DOI: 10.1093/protein/gzac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022] Open
Abstract
Abstract
Malate dehydrogenase (MDH) catalyzes the reduction of oxaloacetate to L-malate. Geobacillus stearothermophilus MDH (gs-MDH) is used as a diagnostic reagent; however, gs-MDH is robustly inhibited at high substrate concentrations, which limits its reaction rate. Here, we reduced substrate inhibition of gs-MDH by deleting its C-terminal residues. Computational analysis showed that C-terminal residues regulate the position of the active site loop. C-terminal deletions of gs-MDH successfully increased Ki values by 5- to 8-fold with maintained thermal stability (>90% of the wild-type enzyme), although kcat/Km values were decreased by <2-fold. The structure of the mutant showed a shift in the location of the active site loop and a decrease in its volume, suggesting that substrate inhibition was reduced by eliminating the putative substrate binding site causing inhibition. Our results provide an effective method to reduce substrate inhibition of the enzyme without loss of other parameters, including binding and stability constants.
Collapse
Affiliation(s)
- Yuya Shimozawa
- Graduate School of Science and Engineering, Setsunan University Division of Life Science, , Osaka 572-8508, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology , Osaka 563-8577, Japan
| | - Hinano Matsuhisa
- Setsunan University Department of Life Science, Faculty of Science and Engineering, , Osaka 572-8508, Japan
| | - Tsutomu Nakamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology , Osaka 563-8577, Japan
| | - Tomoki Himiyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology , Osaka 563-8577, Japan
| | - Yoshiaki Nishiya
- Graduate School of Science and Engineering, Setsunan University Division of Life Science, , Osaka 572-8508, Japan
| |
Collapse
|
30
|
Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
|
31
|
Rapp LR, Marques SM, Nebel B, Damborsky J, Hauer B. Engineering CYP153A
M.aq
to Oxyfunctionalize its Inhibitor Dodecylamine Using a LC/MS Based Rapid Flow Analysis Screening. ChemCatChem 2022. [DOI: 10.1002/cctc.202101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lea R. Rapp
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry University of Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Sérgio M. Marques
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of Science Masaryk University Kamenice 5/A13 625 00 Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Bernd Nebel
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry University of Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Jiri Damborsky
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of Science Masaryk University Kamenice 5/A13 625 00 Brno Czech Republic
- International Clinical Research Center St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry University of Stuttgart Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
32
|
Ahmad S, Strunk CH, Schott-Verdugo SN, Jaeger KE, Kovacic F, Gohlke H. Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. J Chem Inf Model 2021; 61:5626-5643. [PMID: 34748335 DOI: 10.1021/acs.jcim.1c00973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates have remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free-energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid (FA) products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by FA-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
Collapse
Affiliation(s)
- Sabahuddin Ahmad
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan N Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering, University of Talca, 3460000 Talca, Chile.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| |
Collapse
|
33
|
Korasick DA, Christgen SL, Qureshi IA, Becker DF, Tanner JJ. Probing the function of a ligand-modulated dynamic tunnel in bifunctional proline utilization A (PutA). Arch Biochem Biophys 2021; 712:109025. [PMID: 34506758 DOI: 10.1016/j.abb.2021.109025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022]
Abstract
In many bacteria, the reactions of proline catabolism are catalyzed by the bifunctional enzyme known as proline utilization A (PutA). PutA catalyzes the two-step oxidation of l-proline to l-glutamate using distinct proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH) active sites, which are separated by over 40 Å and connected by a complex tunnel system. The tunnel system consists of a main tunnel that connects the two active sites and functions in substrate channeling, plus six ancillary tunnels whose functions are unknown. Here we used tunnel-blocking mutagenesis to probe the role of a dynamic ancillary tunnel (tunnel 2a) whose shape is modulated by ligand binding to the PRODH active site. The 1.90 Å resolution crystal structure of Geobacter sulfurreducens PutA variant A206W verified that the side chain of Trp206 cleanly blocks tunnel 2a without perturbing the surrounding structure. Steady-state kinetic measurements indicate the mutation impaired PRODH activity without affecting the GSALDH activity. Single-turnover experiments corroborated a severe impairment of PRODH activity with flavin reduction decreased by nearly 600-fold in A206W relative to wild-type. Substrate channeling is also significantly impacted as A206W exhibited a 3000-fold lower catalytic efficiency in coupled PRODH-GSALDH activity assays, which measure NADH formation as a function of proline. The structure suggests that Trp206 inhibits binding of the substrate l-proline by preventing the formation of a conserved glutamate-arginine ion pair and closure of the PRODH active site. Our data are consistent with tunnel 2a serving as an open space through which the glutamate of the ion pair travels during the opening and closing of the active site in response to binding l-proline. These results confirm the essentiality of the conserved ion pair in binding l-proline and support the hypothesis that the ion pair functions as a gate that controls access to the PRODH active site.
Collapse
Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Shelbi L Christgen
- Department Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - Insaf A Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Donald F Becker
- Department Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
| |
Collapse
|
34
|
Seo E, Kim M, Park S, Park S, Oh D, Bornscheuer U, Park J. Enzyme Access Tunnel Engineering in Baeyer‐Villiger Monooxygenases to Improve Oxidative Stability and Biocatalyst Performance. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eun‐Ji Seo
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Myeong‐Ju Kim
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - So‐Yeon Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Seongsoon Park
- Department of Chemistry, Center for NanoBio Applied Technology Sungshin Women's University Seoul 01133 Republic of Korea
| | - Deok‐Kun Oh
- Department of Bioscience and Biotechnology Konkuk University Seoul 05029 Republic of Korea
| | - Uwe Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis Greifswald University Greifswald 17487 Germany
| | - Jin‐Byung Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| |
Collapse
|
35
|
Ott F, Rabe KS, Niemeyer CM, Gygli G. Toward Reproducible Enzyme Modeling with Isothermal Titration Calorimetry. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Felix Ott
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| |
Collapse
|