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Zhou L, Tao C, Shen X, Sun X, Wang J, Yuan Q. Unlocking the potential of enzyme engineering via rational computational design strategies. Biotechnol Adv 2024; 73:108376. [PMID: 38740355 DOI: 10.1016/j.biotechadv.2024.108376] [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: 12/27/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Enzymes play a pivotal role in various industries by enabling efficient, eco-friendly, and sustainable chemical processes. However, the low turnover rates and poor substrate selectivity of enzymes limit their large-scale applications. Rational computational enzyme design, facilitated by computational algorithms, offers a more targeted and less labor-intensive approach. There has been notable advancement in employing rational computational protein engineering strategies to overcome these issues, it has not been comprehensively reviewed so far. This article reviews recent developments in rational computational enzyme design, categorizing them into three types: structure-based, sequence-based, and data-driven machine learning computational design. Case studies are presented to demonstrate successful enhancements in catalytic activity, stability, and substrate selectivity. Lastly, the article provides a thorough analysis of these approaches, highlights existing challenges and potential solutions, and offers insights into future development directions.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunmeng Tao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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Kalinin EV, Chalenko YM, Kezimana P, Stanishevskyi YM, Ermolaeva SA. Combination of growth conditions and InlB-specific dot-immunoassay for rapid detection of Listeria monocytogenes in raw milk. J Dairy Sci 2023; 106:1638-1649. [PMID: 36710191 DOI: 10.3168/jds.2022-21997] [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: 02/21/2022] [Accepted: 09/03/2022] [Indexed: 01/30/2023]
Abstract
The gram-positive bacterium Listeria monocytogenes is an important foodborne pathogen contaminating dairy products. Closely related to L. monocytogenes saprophytic Listeria spp. are also frequent contaminators of food and, particularly, dairy products. To distinguish L. monocytogenes from nonpathogenic Listeria spp. and other bacteria, a dot-immunoassay was developed. The immunoassay is based on the polyclonal antibody to the secreted form of the surface virulence-associated L. monocytogenes-specific InlB protein. To increase InlB production, bacteria were grown on the brain-heart infusion agar supplemented with 0.2% activated charcoal (BHIC agar). Direct plating of artificially contaminated raw milk samples on the BHIC agar followed by the dot-immunoassay allowed a rapid identification of L. monocytogenes in concentrations as little as 10 cfu/mL. Using the developed approach, preliminary results were obtained within 14 h, and the final results were obtained after 26 h. The dot-immunoassay was tested on L. monocytogenes strains belonging to different clonal complexes and phylogenetic lineages, Listeria spp., and other bacterial species. Results showed the exceptional specificity of the developed dot-immunoassay for the rapid identification of L. monocytogenes.
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Affiliation(s)
- Egor V Kalinin
- Laboratory of Ecology of Pathogenic Bacteria, Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia; Institutue of Biochemical Technology and Nanotechnology, Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia.
| | - Yaroslava M Chalenko
- Laboratory of Ecology of Pathogenic Bacteria, Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia
| | - Parfait Kezimana
- Institutue of Biochemical Technology and Nanotechnology, Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Yaroslav M Stanishevskyi
- Institutue of Biochemical Technology and Nanotechnology, Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Svetlana A Ermolaeva
- Laboratory of Ecology of Pathogenic Bacteria, Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia.
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Yousefi M, Jafari SM, Ahangari H, Ehsani A. Application of Nanoliposomes Containing Nisin and Crocin in Milk. Adv Pharm Bull 2023; 13:134-142. [PMID: 36721817 PMCID: PMC9871285 DOI: 10.34172/apb.2023.014] [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: 04/15/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Purpose: This study aimed to investigate the effects of nanoliposomes containing crocin and nisin in milk samples as a food model. Therefore, three formulations were prepared and compared, including (1) milk samples containing free nisin and crocin, (2) samples with nanoliposomes containing nisin and crocin, and (3) nisin and crocin-loaded nanoliposomes coated with chitosan. Methods: In order to find the optimum amount of both bioactives within nanoliposomes, analyses of size, polydispersity index (PDI), zeta potential, and encapsulation efficiency were accomplished. Then, the best formulated nanoliposome was evaluated and compared with a solution containing free bioactives and nanoliposomes coated with chitosan using other experiments, including antioxidant and antibacterial activities, viscosity, colorimetric and bacterial growth. Results: The best nanoliposomal system based on the factors of size, PDI, zeta potential, and encapsulation efficiency was related for the nanocarrier with 4 mg crocin, 4.5 mg nisin, and 40 mg lecithin. Based on the results obtained, both nanoliposome (a*=5.41) and chitosancoated nanoliposome (a*=5.09) solutions could significantly (P<0.05) reduce the redness of milk induced by free bioactives (a*=12.32). However, viscosity of milk in chitosan-coated nanoliposome solution was found to be higher (3.42 cP) than other formulations (viscosity of samples with free bioactives was 1.65 cP and viscosity of samples containing nanoliposome was 1.71 cP). In addition, chitosan-coated nanoliposomes could inhibit the growth of Listeria monocytogenes stronger than other samples. Conclusion: Encapsulation of nisin and crocin in nanoliposomes showed promising results for preserving food safety and quality.
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Affiliation(s)
- Mohammad Yousefi
- Department of Food Science and Technology, Tabriz University of Medical Sciences. Tabriz, Iran. Food and Beverage Safety Research Center, Urmia University of Medical Sciences
| | - Seid Mahdi Jafari
- Department of Food Materials and Process Design Engineering, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Hossein Ahangari
- Department of Food Science and Technology & Nutrition Research Center, Tabriz University of Medical Sciences. Tabriz, Iran
| | - Ali Ehsani
- Department of Food Science and Technology & Nutrition Research Center, Tabriz University of Medical Sciences. Tabriz, Iran
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Investigation of the efficiency of different biocatalytic systems for the bioconversion of lactose and dairy by-products into lactobionic acid. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Short Communication: Prevalence of Listeria monocytogenes in Raw Milk of Healthy Sheep and Goats. Vet Med Int 2022; 2022:3206172. [PMID: 35646303 PMCID: PMC9135515 DOI: 10.1155/2022/3206172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Listeria monocytogenes, one of the most important bacterial pathogens transmitted through milk, causes listeriosis in humans and animals. This study aimed to investigate the prevalence of L. monocytogenes in raw milk of healthy sheep and goats in the west of Iran (Lorestan Province) by touchdown PCR (TD-PCR). Listeria spp. were found in milk samples taken from 21 sheep (29.16%) and 3 goats (10.71%) whereas L. monocytogenes was isolated from milk samples taken from 4 sheep (5.55%) and 1 goat (3.75%). The results showed that there was a significant difference between sheep and goats in the prevalence of Listeria spp. in their raw milk (p < 0.05), but no significant difference was observed between them in the prevalence of L. monocytogenes. The study findings suggested that the raw milk of healthy sheep and goats was infected with L. monocytogenes and warned of the risk of human infection with listeriosis following consumption of raw and unpasteurized milk.
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Koczoń P, Josefsson H, Michorowska S, Tarnowska K, Kowalska D, Bartyzel BJ, Niemiec T, Lipińska E, Gruczyńska-Sękowska E. The Influence of the Structure of Selected Polymers on Their Properties and Food-Related Applications. Polymers (Basel) 2022; 14:polym14101962. [PMID: 35631843 PMCID: PMC9146511 DOI: 10.3390/polym14101962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022] Open
Abstract
Every application of a substance results from the macroscopic property of the substance that is related to the substance’s microscopic structure. For example, the forged park gate in your city was produced thanks to the malleability and ductility of metals, which are related to the ability of shifting of layers of metal cations, while fire extinguishing powders use the high boiling point of compounds related to their regular ionic and covalent structures. This also applies to polymers. The purpose of this review is to summarise and present information on selected food-related biopolymers, with special attention on their respective structures, related properties, and resultant applications. Moreover, this paper also highlights how the treatment method used affects the structure, properties, and, hence, applications of some polysaccharides. Despite a strong focus on food-related biopolymers, this review is addressed to a broad community of both material engineers and food researchers.
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Affiliation(s)
- Piotr Koczoń
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (P.K.); (K.T.); (D.K.)
| | | | - Sylwia Michorowska
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Katarzyna Tarnowska
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (P.K.); (K.T.); (D.K.)
| | - Dorota Kowalska
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (P.K.); (K.T.); (D.K.)
| | - Bartłomiej J. Bartyzel
- Department of Morphological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-776 Warsaw, Poland;
| | - Tomasz Niemiec
- Animals Nutrition Department, Institute of Animal Sciences, Warsaw University of Life Sciences, 02-786 Warsaw, Poland;
| | - Edyta Lipińska
- Department of Biotechnology, Microbiology and Food Evaluation, Institute of Food Sciences, Warsaw University of Life Sciences, 02-776 Warsaw, Poland;
| | - Eliza Gruczyńska-Sękowska
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 02-776 Warsaw, Poland; (P.K.); (K.T.); (D.K.)
- Correspondence:
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