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Liow MY, Chan ES, Ng WZ, Song CP. Stabilization of Eversa® Transform 2.0 lipase with sorbitol to enhance the efficiency of ultrasound-assisted biodiesel production. Int J Biol Macromol 2024; 276:133817. [PMID: 39002902 DOI: 10.1016/j.ijbiomac.2024.133817] [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: 05/16/2024] [Revised: 06/26/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Ultrasound technology has emerged as a promising tool for enhancing enzymatic biodiesel production, yet the cavitation effect induced can compromise enzyme stability. This study explored the efficiency of polyols in enhancing lipase stability under ultrasound conditions to further improve biodiesel yield. The incorporation of sorbitol resulted in the highest fatty acid methyl ester (FAME) content in the ultrasound-assisted biodiesel production catalyzed by Eversa® Transform 2.0 among the investigated polyols. Furthermore, sorbitol enhanced the stability of the lipase, allowing it to tolerate up to 100 % ultrasound amplitude, compared to 60 % amplitude in its absence. Enzyme activity assays revealed that sorbitol preserved 99 % of the lipase activity, in contrast to 84 % retention observed without sorbitol under an 80 % ultrasound amplitude. Circular dichroism (CD) and fluorescence spectroscopy analyses confirmed that sorbitol enhanced lipase rigidity and preserved its conformational structure under ultrasound exposure. Furthermore, employing a stepwise methanol addition strategy in ultrasound-assisted reactions with sorbitol achieved an 81.2 wt% FAME content in 8 h with only 0.2 wt% enzyme concentration. This promising result highlights the potential of sorbitol as a stabilizing agent in ultrasound-assisted enzymatic biodiesel production, offering a viable approach for enhancing biodiesel yield and enzyme stability in industrial applications.
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Affiliation(s)
- Min Ying Liow
- Department of Chemical Engineering, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia; Monash-Industry Plant Oils Research Laboratory (MIPO), Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Eng-Seng Chan
- Department of Chemical Engineering, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia; Monash-Industry Plant Oils Research Laboratory (MIPO), Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia.
| | - Wei Zhe Ng
- Department of Chemical Engineering, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia; Monash-Industry Plant Oils Research Laboratory (MIPO), Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Cher Pin Song
- Department of Chemical Engineering, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia; Monash-Industry Plant Oils Research Laboratory (MIPO), Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia.
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2
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Abedi E, Kaveh S, Mohammad Bagher Hashemi S. Structure-based modification of a-amylase by conventional and emerging technologies: Comparative study on the secondary structure, activity, thermal stability and amylolysis efficiency. Food Chem 2024; 437:137903. [PMID: 37931423 DOI: 10.1016/j.foodchem.2023.137903] [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: 07/24/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/08/2023]
Abstract
α-Amylase is an endo-enzyme that catalyzes the hydrolysis of starch into shorter oligosaccharides. α-Amylase plays a crucial role in various industries. Manipulated α-amylases are of particular interest due to their remarkable amylolysis efficiency and thermostability for large-scale biotechnological processes. The retained catalytic activity of enzymes is decreased according to extreme pH, temperature, pressure, and chemical reagents. Broad industrial applications of α-amylases need special properties such as stability against temperature, pH, and chelators, and also attain reusability, desirable enzymatic activity, efficiency, and selectivity. Considering the biotechnological importance of α-amylase, its high stability is the most critical challenge for its economic viability. Therefore, improving its functionality and stability recently gained much interest. To achieve this purpose, various emerging technologies in combination with conventional methods on α-Amylases with different sources have been conducted. The present review is an attempt to summarize the effect of various conventional methods and emerging technologies employed to date on α-amylase secondary structure, thermal stability, and performance.
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Affiliation(s)
- Elahe Abedi
- Department of Food Science and Technology, Faculty of Agriculture, Fasa University, Fasa, Iran
| | - Shima Kaveh
- Department of Food Science and Technology, Faculty of Agriculture, Fasa University, Fasa, Iran.
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3
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Dirak M, Chan J, Kolemen S. Optical imaging probes for selective detection of butyrylcholinesterase. J Mater Chem B 2024; 12:1149-1167. [PMID: 38196348 DOI: 10.1039/d3tb02468g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Butyrylcholinesterase (BChE), a member of the human serine hydrolase family, is an essential enzyme for cholinergic neurotransmission as it catalyzes the hydrolysis of acetylcholine. It also plays central roles in apoptosis, lipid metabolism, and xenobiotic detoxification. On the other side, abnormal levels of BChE are directly associated with the formation of pathogenic states such as neurodegenerative diseases, psychiatric and cardiovascular disorders, liver damage, diabetes, and cancer. Thus, selective and sensitive detection of BChE level in living organisms is highly crucial and is of great importance to further understand the roles of BChE in both physiological and pathological processes. However, it is a very complicated task due to the potential interference of acetylcholinesterase (AChE), the other human cholinesterase, as these two enzymes share a very similar substrate scope. To this end, optical imaging probes have attracted immense attention in recent years as they have modular structures, which can be tuned precisely to satisfy high selectivity toward BChE, and at the same time they offer real time and nondestructive imaging opportunities with a high spatial and temporal resolution. Here, we summarize BChE selective imaging probes by discussing the critical milestones achieved during the development process of these molecular sensors over the years. We put a special emphasis on design principles and biological applications of highly promising new generation activity-based probes. We also give a comprehensive outlook for the future of BChE-responsive probes and highlight the ongoing challenges. This collection marks the first review article on BChE-responsive imaging agents.
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Affiliation(s)
- Musa Dirak
- Department of Chemistry, Koç University, 34450 Istanbul, Turkey.
| | - Jefferson Chan
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Safacan Kolemen
- Department of Chemistry, Koç University, 34450 Istanbul, Turkey.
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4
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Pan F, Li X, Tuersuntuoheti T, Zhao L, Liu M, Fang X, Peng W, Tian W. Self-assembled condensed tannins supramolecular system can adsorb cholesterol micelles to promote cholesterol excretion. Int J Biol Macromol 2023; 253:126549. [PMID: 37659485 DOI: 10.1016/j.ijbiomac.2023.126549] [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: 06/24/2023] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
In this study, the cholesterol (CH)-lowering behavioral mechanisms and drivers of condensed tannins (CTs) were revealed using a molecular aggregation theoretical model combined with in vitro experiments, as well as the CH-lowering effects of CTs validated based on animal experiments. Theoretical model results indicated that CTs can spontaneously aggregate to form supramolecular systems, can break CH micelles and form larger aggregates, a behavior driven by van der Waals forces and hydrogen bonds; DLS and TEM results confirmed that the presence of CH leads to a larger particle size of CTs and the formation of large aggregates; thermodynamic analysis and ITC revealed that the adsorption of CH by CTs is a spontaneous reaction driven by hydrogen bonds and hydrophobic forces; Animal experiments and fecal biochemical parameters further confirmed that the intake of CTs can reduce CH absorption and promotes CH excretion. Overall, this study reveals the CH-lowering behavioral mechanism of CTs from the perspective of molecular aggregation behavior.
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Affiliation(s)
- Fei Pan
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Xiangxin Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
| | - Tuohetisayipu Tuersuntuoheti
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, People's Republic of China
| | - Lei Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, People's Republic of China
| | - Mengyao Liu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Xiaoming Fang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Wenjun Peng
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
| | - Wenli Tian
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
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5
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Mostaraddi S, Pazhang M, Ebadi-Nahari M, Najavand S. The Relationship Between the Cross-Linker on Chitosan-Coated Magnetic Nanoparticles and the Properties of Immobilized Papain. Mol Biotechnol 2023; 65:1809-1823. [PMID: 36795275 DOI: 10.1007/s12033-023-00687-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
The immobilized enzymes' properties can be affected by cross-linkers on the surface of supports. To study how cross-linkers alter enzymes function, chitosan-coated magnetic nanoparticles (CMNPs) with immobilized papain were prepared using glutaraldehyde and or genipin, and then, the properties of the nanoparticles and the immobilized enzymes were assessed. The Scanning Electron Microscope (SEM), Fourier Transform Infrared (FTIR), and X-Ray Diffraction (XRD) results showed that the CMNPs were prepared and papain molecules were immobilized on CMNPs by glutaraldehyde (CMNP-Glu-Papain) or by genipin (CMNP-Gen-Papain). Also, the results associated with enzymes activity indicated that the immobilization by glutaraldehyde and genipin increased the pH optimum of papain from 7 to 7.5 and 9, respectively. The kinetic results indicated that the immobilization by genipin slightly affects the enzyme affinity to the substrate. The stability results showed that CMNP-Gen-Papain has more thermal stability than CMNP-Glu-Papain and papain immobilization on CMNPs by genipin leads to stabilization of the enzyme in the presence of polar solvents, probably due to the more hydroxyl groups on CMNPs activated by genipin. In conclusion, this study suggests that there is a relationship between the types of cross-linker on the surface of supports, and the mechanism of action, kinetic parameters, and the stability of immobilized papain.
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Affiliation(s)
- Samaneh Mostaraddi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Mostafa Ebadi-Nahari
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Saeed Najavand
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
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6
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Cha B, Yea Y, Yun K, Kim T, Kim H, Yoon Y, Kim S, Park CM. Enhanced catalytic oxidation of naproxen via activation of peroxymonosulfate by Fe-based metal-organic framework aerogels functionalized with Ag nanoparticles. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131847. [PMID: 37352778 DOI: 10.1016/j.jhazmat.2023.131847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023]
Abstract
In this study, Ag3PO4 and Fe-based metal-organic frameworks (MOFs)-functionalized three-dimensional (3D) porous gelatin aerogels (Ag/Fe@GMA) were fabricated and used as adsorbents and catalysts for the activation of peroxymonosulfate (PMS) for naproxen (NPX) removal from water. The morphology, crystallinity, surface functional groups, and surface chemical element compositions of the fabricated Ag/Fe@GMA was evaluated using various analytical techniques. Our results showed that as an adsorbent, Ag/Fe@GMA showed a 18.0 % higher NPX adsorption capacity compared with the pristine aerogels. This can be attributed to the well-embedded Ag3PO4 and MOFs, indicating a stronger interaction between functionalized aerogels and NPX. After adsorption, 99.9 % of total NPX removal was achieved within 15 min by activating PMS and effectively generating •OH and •SO4- in water. The PMS/Ag/Fe@GMA aerogel system also showed high removal performance for rhodamine B (99.5 %) and tetracycline (93.7 %). Moreover, the Ag/Fe@GMA aerogels showed excellent reusability to achieve 95.7 % NPX removal efficiency after six times of recycling. This study revealed that the Ag/Fe@GMA aerogels had good potential for PMS activation and NPX removal. In particular, as an alternative to powdery materials, 3D shape of Ag/Fe@GMA with excellent reusability facilitates its application in the treatment of water contaminated with organic contaminants.
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Affiliation(s)
- Byungjun Cha
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, the Republic of Korea
| | - Yeonji Yea
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, the Republic of Korea
| | - Keunyoung Yun
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, the Republic of Korea
| | - Taeyeon Kim
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, the Republic of Korea
| | - Hyeonjeong Kim
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, the Republic of Korea
| | - Yeomin Yoon
- Department of Civil and Environmental Engineering, University of South Carolina, 300 Main Street, Columbia, SC 29208, USA; Department of Environmental Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, the Republic of Korea
| | - Sewoon Kim
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA 52242, USA.
| | - Chang Min Park
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, the Republic of Korea.
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7
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Jiang M, Gupta A, Zhang X, Chattopadhyay AN, Fedeli S, Huang R, Yang J, Rotello VM. Identification of Proteins Using Supramolecular Gold Nanoparticle-Dye Sensor Arrays. ANALYSIS & SENSING 2023; 3:e202200080. [PMID: 37250385 PMCID: PMC10211330 DOI: 10.1002/anse.202200080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Indexed: 05/31/2023]
Abstract
The rapid detection of proteins is very important in the early diagnosis of diseases. Gold nanoparticles (AuNPs) can be engineered to bind biomolecules efficiently and differentially. Cross-reactive sensor arrays have high sensitivity for sensing proteins using differential interactions between sensor elements and bioanalytes. A new sensor array was fabricated using surface-charged AuNPs with dyes supramolecularly encapsulated into the AuNP monolayer. The fluorescence of dyes is partially quenched by the AuNPs and can be restored or further quenched due to the differential interactions between AuNPs with proteins. This sensing system enables the discrimination of proteins in both buffer and human serum, providing a potential tool for real-world disease diagnostics.
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Affiliation(s)
- Mingdi Jiang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Aarohi Gupta
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Xianzhi Zhang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Aritra Nath Chattopadhyay
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Stefano Fedeli
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Rui Huang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Junwhee Yang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
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8
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Different Effects of Salt Bridges near the Active Site of Cold-Adapted Proteus mirabilis Lipase on Thermal and Organic Solvent Stabilities. Catalysts 2022. [DOI: 10.3390/catal12070761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Organic solvent-tolerant (OST) enzymes have been discovered in psychrophiles. Cold-adapted OST enzymes exhibit increased conformational flexibility in polar organic solvents resulting from their intrinsically flexible structures. Proteus mirabilis lipase (PML), a cold-adapted OST lipase, was used to assess the contribution of salt bridges near the active site involving two arginine residues (R237 and R241) on the helix η1 and an aspartate residue (D248) on the connecting loop to the thermal and organic solvent stabilities of PML. Alanine substitutions for the ion pairs (R237A, R241A, D248A, and R237A/D248A) increased the conformational flexibility of PML mutants compared to that of the wild-type PML in an aqueous buffer. The PML mutants became more susceptible to denaturation after increasing the dimethyl sulfoxide or methanol concentration than after a temperature increase. Methanol was more detrimental to the structural stability of PML compared to dimethyl sulfoxide. These results suggest that direct interactions of dimethyl sulfoxide and methanol with the residues near the active site can have a destructive effect on the structure of PML compared with the global effect of heat on the protein structure. This study provides insight into the conformational changes within an OST enzyme with different effects on its thermal and organic solvent stabilities.
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Mirzaei F, Valizadeh H, Pazhang M. Immobilization of papain on nitrogen-doped graphene quantum dots improves the enzymatic properties and makes it a biosensor for cystatin C. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.04.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Abstract
Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.
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Counterbalance of Stability and Activity Observed for Thermostable Transaminase from Thermobaculum terrenum in the Presence of Organic Solvents. Catalysts 2020. [DOI: 10.3390/catal10091024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pyridoxal-5’-phosphate-dependent transaminases catalyze stereoselective amination of organic compounds and are highly important for industrial applications. Catalysis by transaminases often requires organic solvents to increase the solubility of reactants. However, natural transaminases are prone to inactivation in the presence of water-miscible organic solvents. Here, we present the solvent tolerant thermostable transaminase from Thermobaculum terrenum (TaTT) that catalyzes transamination between L-leucine and alpha-ketoglutarate with an optimum at 75 °C and increases the activity ~1.8-fold upon addition of 15% dimethyl sulfoxide or 15% methanol at high but suboptimal temperature, 50 °C. The enhancement of the activity correlates with a decrease in the thermal denaturation midpoint temperature. The blue-shift of tryptophan fluorescence suggested that solvent molecules penetrate the hydration shell of the enzyme. Analysis of hydrogen bonds in the TaTT dimer revealed a high number of salt bridges and surface hydrogen bonds formed by backbone atoms. The latter are sensitive to the presence of organic solvents; they rearrange, conferring the relaxation of some constraints inherent to a thermostable enzyme at low temperatures. Our data support the idea that the counterbalance of stability and activity is crucial for the catalysis under given conditions; the obtained results may be useful for fine-tuning biocatalyst efficiency.
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Supo-Escalante RR, Médico A, Gushiken E, Olivos-Ramírez GE, Quispe Y, Torres F, Zamudio M, Antiparra R, Amzel LM, Gilman RH, Sheen P, Zimic M. Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors. PLoS One 2020; 15:e0235643. [PMID: 32735615 PMCID: PMC7394417 DOI: 10.1371/journal.pone.0235643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/19/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pyrazinamide is an important drug against the latent stage of tuberculosis and is used in both first- and second-line treatment regimens. Pyrazinamide-susceptibility test usually takes a week to have a diagnosis to guide initial therapy, implying a delay in receiving appropriate therapy. The continued increase in multi-drug resistant tuberculosis and the prevalence of pyrazinamide resistance in several countries makes the development of assays for prompt identification of resistance necessary. The main cause of pyrazinamide resistance is the impairment of pyrazinamidase function attributed to mutations in the promoter and/or pncA coding gene. However, not all pncA mutations necessarily affect the pyrazinamidase function. OBJECTIVE To develop a methodology to predict pyrazinamidase function from detected mutations in the pncA gene. METHODS We measured the catalytic constant (kcat), KM, enzymatic efficiency, and enzymatic activity of 35 recombinant mutated pyrazinamidase and the wild type (Protein Data Bank ID = 3pl1). From all the 3D modeled structures, we extracted several predictors based on three categories: structural stability (estimated by normal mode analysis and molecular dynamics), physicochemical, and geometrical characteristics. We used a stepwise Akaike's information criterion forward multiple log-linear regression to model each kinetic parameter with each category of predictors. We also developed weighted models combining the three categories of predictive models for each kinetic parameter. We tested the robustness of the predictive ability of each model by 6-fold cross-validation against random models. RESULTS The stability, physicochemical, and geometrical descriptors explained most of the variability (R2) of the kinetic parameters. Our models are best suited to predict kcat, efficiency, and activity based on the root-mean-square error of prediction of the 6-fold cross-validation. CONCLUSIONS This study shows a quick approach to predict the pyrazinamidase function only from the pncA sequence when point mutations are present. This can be an important tool to detect pyrazinamide resistance.
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Affiliation(s)
- Rydberg Roman Supo-Escalante
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Aldhair Médico
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gustavo E. Olivos-Ramírez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Yaneth Quispe
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Fiorella Torres
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Zamudio
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert H. Gilman
- International Health Department, Johns Hopkins School of Public Health, Baltimore, MD, United States of America
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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Mirzaeinia S, Pazhang M, Imani M, Chaparzadeh N, Amani-Ghadim AR. Improving the stability of uricase from Aspergillus flavus by osmolytes: Use of response surface methodology for optimization of the enzyme stability. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.04.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Liu C, Li R, Peng J, Qu D, Huang M, Chen Y. Enhanced hydrolysis and antitumor efficacy of Epimedium flavonoids mediated by immobilized snailase on silica. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.06.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Srivastava G, Darokar MP, Sharma A. Molecular investigation against the resistant mechanism of PncA mutated pyrazinamide resistance and insight into the role of pH environment for pyrazinamide activation. J Biomol Struct Dyn 2019; 38:3411-3431. [PMID: 31448694 DOI: 10.1080/07391102.2019.1659854] [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: 10/26/2022]
Abstract
Pyrazinamide (PZA), a crucial component of anti-TB therapy, is a prodrug. PZA interacts with PncA protein to be converted into its functional form i.e. pyrazinoic acid (POA). It has unique feature to kill dormant tubercle bacilli of acidic environment. Although significance of pH environment in PZA activation has been investigated in several of previous studies, insight into the significant atomistic variations in the interaction pattern of PZA with PncA, at different pH environments, are still required to be explored. On the other hand, continuously emerging PncA mutants, associated with PZA resistance, have also become a serious threat for global TB control program. Therefore, the current study was designed to understand the role of pH environment in the PZA activation and to explore the PZA resistance mechanism in various PncA mutants. The study included various in silico experiments like molecular docking, MD simulation, binding free energy estimation, PCA and FEL. In our study, we have found pH-3 and pH-5 environment as a highly significant environment for PZA activation. It was found that protonation or deprotonation of PZA activation site (PAS) residues, majorly K48, D56, K96 and E107, resulted in rearrangement of the PAS according to the pH conditions. It has also been observed that positioning of PZA binding near to Fe2+ and residues of catalytic triad (i.e. D8, K96 and C138) also play a very crucial role in the activation of PZA. The overall insight from the current study may help to develop new therapeutics against PncA mutated PZA resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M P Darokar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Immobilization of endoglucanase Cel9A on chitosan nanoparticles leads to its stabilization against organic solvents: the use of polyols to improve the stability. 3 Biotech 2019; 9:269. [PMID: 31218180 DOI: 10.1007/s13205-019-1794-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/03/2019] [Indexed: 12/21/2022] Open
Abstract
The immobilization of enzymes improves their stability in non-conventional media such as organic solvents. In this work, the effects of solvents (DMSO, methanol, ethanol, and n-propanol) on the endoglucanase Cel9A activity and stability were studied. Then, the enzymes were stabilized by its immobilization on chitosan nanoparticles and also using polyols (sorbitol and glycerol) against organic solvents. The SEM results illustrated that the chitosan nanoparticles had about 40 nm diameter. The results indicated that the organic solvents, especially n-propanol, decreased the activity of the free and immobilized enzymes. The reduced activity of the immobilized enzyme was less than that of the free enzyme. Our studies about the enzymes' stability showed that the free and immobilized enzymes in hydrophobic solvents (with high log P) had the lowest stability compared to other solvents as we observed the half-life of the free enzyme in n-propanol solvent was 2.84 min, and the half-life of the immobilized enzyme was 4.98 min in n-propanol and ethanol solvents 4.50 min. Analysis of the combinatory effects of polyols (sorbitol and glycerol) and the solvents on the stability revealed that sorbitol and glycerol had the most stabilizing effect on the free enzyme in hydrophilic (DMSO) and hydrophobic (n-propanol) solvents, respectively. However, the stabilizing effects of polyols in the immobilized enzyme were independent of the solvents' hydrophobicity (or log P) due to the hydrophilic properties of chitosan nanoparticles. Therefore, one can conclude that the physiochemical properties of nanoparticles (such as hydrophilicity) influence the stabilizing effects of polyols on immobilized enzyme.
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Calcium and sodium ions synergistically enhance the thermostability of a maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04. Food Chem 2019; 283:170-176. [DOI: 10.1016/j.foodchem.2019.01.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 11/27/2018] [Accepted: 01/03/2019] [Indexed: 01/27/2023]
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Di X, Zhang Y, Fu J, Yu Q, Wang Z, Yuan Z. Biocatalytic upgrading of levulinic acid to methyl levulinate in green solvents. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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A novel strategy to improve the thermostability of Penicillium camembertii mono- and di-acylglycerol lipase. Biochem Biophys Res Commun 2018; 500:639-644. [DOI: 10.1016/j.bbrc.2018.04.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 04/14/2018] [Indexed: 01/24/2023]
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