Article
Agricultural Engineering
Qian Yang, Ting Yang, Yi Shi, Yu Xin, Liang Zhang, Zhenghua Gu, Youran Li, Zhongyang Ding, Guiyang Shi
Summary: The psychrotrophic bacterium strain Bacillus simplex H-b showed potential for biological nitrogen removal process at low temperatures, demonstrating high removal efficiencies for nitrate-N, nitrite-N, and ammonium-N at 10 degrees C. Additionally, the strain was found to resist low temperature stress through its cellular extreme environment resistant mechanism. This newly isolated strain could be a promising candidate for nitrogen contaminated wastewater treatment, especially in low-temperature conditions.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Medicinal
Huiqin Huang, Shuang Li, Shixiang Bao, Kunlian Mo, Dongmei Sun, Yonghua Hu
Summary: Alg2951 is a PL7 family alginate lyase with exo/endo-type activity, showing maximum activity at 25 degrees C and pH 8.0, and a special preference for poly-guluronic acid (polyG). It can catalyze the hydrolysis of sodium alginate to produce monosaccharides and trisaccharides, displaying good antioxidant activity.
Article
Chemistry, Medicinal
Wenxin Wang, Jianxin Wang, Ruihua Yan, Runying Zeng, Yaqiang Zuo, Dingquan Wang, Wu Qu
Summary: The study discovered that Agarase AgaW1540 expressed from a deep-sea bacterium possesses a wide range of working temperatures and pH values, maintaining good activity at different temperatures. The enzyme generates neoagaro-oligosaccharides during agarose degradation and exhibits high stability at room temperature.
Article
Multidisciplinary Sciences
Lingmin Jiang, Yuxin Peng, Jiyoon Seo, Doeun Jeon, Mi Gyeong Jo, Ju Huck Lee, Jae Cheol Jeong, Cha Young Kim, Hyeong Cheol Park, Jiyoung Lee
Summary: A novel strain of bacteria AK-R2A1-2(T) was isolated from the needle leaves of Abies koreana tree and its genome was sequenced. The results showed that this strain can survive at low temperatures and significantly improve the growth of rice seedlings.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Eva D. Schuiten, Christoffel P. S. Badenhorst, Gottfried J. Palm, Leona Berndt, Michael Lammers, Jan Mican, David Bednar, Jiri Damborsky, Uwe T. Bornscheuer
Summary: The study identified an epoxide hydrolase called CorEH that exhibits dehalogenase activity, suggesting a rare example of a protein with dual enzymatic functions. Despite the much lower dehalogenase activity compared to epoxide hydrolase activity, the presence of multiple activities in one naturally occurring protein demonstrates significant diversity.
Article
Microbiology
Chenchen Guo, Rikuan Zheng, Ruining Cai, Chaomin Sun, Shimei Wu
Summary: The study identified a novel bacterial strain, Pseudomonas marinensis gcc21, isolated from deep-sea cold seep sediment, which exhibited high catalytic activity of cold-active lipases at 4 degrees C. The strain's genome contained two novel encoding genes for cold-active lipases, Lipase 1 and Lipase 2.
Article
Biochemistry & Molecular Biology
Zhongyuan Li, Yan Wang, Zhongqi Liu, Shanzheng Jin, Kungang Pan, Huihui Liu, Tianhui Liu, Xiumei Li, Chaozheng Zhang, Xuegang Luo, Yajian Song, Junqi Zhao, Tongcun Zhang
Summary: The newly discovered FumDSB enzyme effectively degrades fumonisin B1, exhibiting high degrading activity at 30-40 degrees Celsius and within a broad pH range, suitable for animal physiological conditions. This study provides potential for further use of the FumDSB enzyme as a food and feed additive.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Agriculture, Multidisciplinary
Zewei Lu, Hong Jiang, Hamed I. Hamouda, Tao Wang, Yueyang Dong, Xiangzhao Mao
Summary: In this study, a lambda-carrageenase OUC-CglA from Maribacter vaceletii was heterologously expressed, purified, and characterized. The enzyme showed high activity and strict selectivity towards lambda-carrageenan, making it a potential biocatalyst for the preparation of lambda-carrageenan oligosaccharides.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yage Zhang, Wei Lu, Jin Wang, Ming Chen, Wei Zhang, Min Lin, Zhengfu Zhou, Zhu Liu
Summary: A novel cold-adapted family esterase EstDR4 was identified from extremophile Deinococcus radiodurans, showing significant substrate preference towards short and medium chain monoesters and degradation effects on insecticides. EstDR4 displayed high catalytic activity and stability at low temperatures, with optimal activity at 30 degrees C and pH 8. The enzyme's activity was influenced by metal ions and organic solvents, indicating its potential for various biotechnological applications.
APPLIED SCIENCES-BASEL
(2021)
Article
Microbiology
Christopher Riccardi, Marzia Calvanese, Veronica Ghini, Tania Alonso-Vasquez, Elena Perrin, Paola Turano, Giorgio Giurato, Alessandro Weisz, Ermenegilda Parrilli, Maria Luisa Tutino, Marco Fondi
Summary: This study investigates the maintenance of metabolic homeostasis in a cold-adapted marine bacterium during growth at significantly different temperatures. The research shows a strong metabolic stability at the level of the main central metabolites but significant changes in gene expression at the transcriptional level. These findings suggest a transcriptomic buffering of cellular metabolism to produce overlapping metabolic phenotypes despite the temperature gap.
Article
Biotechnology & Applied Microbiology
Lijun Guan, Kunlun Wang, Yang Gao, Jialei Li, Song Yan, Nina Ji, Chuanying Ren, Jiayou Wang, Ye Zhou, Bo Li, Shuwen Lu
Summary: TanA(Lb) is a novel bacterial tannase with optimal activity at neutral pH and higher temperatures, regulated by beneficial metal ions. It shows high affinity and catalytic efficiency towards tannic acid, with structural analysis revealing its interaction with substrates.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Weijun Leng, Xiaoyun Wu, Xianghui Qi, Hongying Liu, Li Yuan, Ruichang Gao
Summary: In this study, the gene encoding serine protease PmSpr288 from cold-adapted bacterium Planococcus maritimus XJ11 was cloned and overexpressed in Escherichia coli BL21 (DE3). Bioinformatics analysis revealed its membership in the serine protease S8 superfamily and the presence of a classical catalytic triad. PmSpr288 exhibited broad alkaline pH and low-moderate temperature activity, wide protein substrate specificity, and the ability to hydrolyze meat proteins. The muscle protein hydrolysates produced by PmSpr288 showed antioxidant activity, suggesting its potential biotechnological applications.
FOOD SCIENCE AND HUMAN WELLNESS
(2023)
Article
Biochemistry & Molecular Biology
Do Young Kim, Jonghoon Kim, Yung Mi Lee, Jong Suk Lee, Dong-Ha Shin, Bon-Hwan Ku, Kwang-Hee Son, Ho-Yong Park
Summary: The study identified and characterized a novel cold-adapted endo-beta-1,4-xylanase, XylR, from Antarctic soil bacterium Duganella sp. PAMC 27433. The enzyme showed the highest activity at pH 5.5 and 40°C, with 12% activity retained even at 4°C. Moreover, rXylR exhibited specific activities towards various xylans and cellobioside.
Article
Food Science & Technology
Yanshang Wei, Ling Jiang, Zhong Yao, Benwei Zhu, Yuguang Du
Summary: In this study, a novel x-carrageenase called CeCgkB was cloned and characterized. CeCgkB exhibited cold-adapted properties and high substrate affinity, and it could degrade x-carrageenan into products of varying DP. The major products of CeCgkB were identified, and its potential application in the efficient preparation of x-carrageenan oligosaccharides was demonstrated.
Article
Microbiology
Casper Bojer Rasmussen, Carsten Scavenius, Ida B. Thogersen, Seandean Lykke Harwood, Oivind Larsen, Gro Elin Kjaereng Bjerga, Peter Stougaard, Jan J. Enghild, Mariane Schmidt Thogersen
Summary: In this study, a novel intracellular subtilisin protease (ISP) P355 derived from the genome of Planococcus halocryophilus Or1 was characterized. P355 was found to be one of the most unstable enzymes but had a higher catalytic rate. Compared to other ISPs (T0099, T0034, and SC), P355 and T0034 showed higher catalytic constants, demonstrating the typical stability-activity trade-off observed in cold-adapted proteases.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Oncology
Gaspar P. Pinto, Natalie M. Hendrikse, Jan Stourac, Jiri Damborsky, David Bednar
Summary: This article discusses the use of virtual screening tools to accelerate the development of anticancer drugs based on microbial products. It provides a detailed overview of the principles, workflow, and practical applications, showing the potential to expedite the discovery of novel cancer drugs.
SEMINARS IN CANCER BIOLOGY
(2022)
Review
Pharmacology & Pharmacy
Michal Vasina, Jan Velecky, Joan Planas-Iglesias, Sergio M. Marques, Jana Skarupova, Jiri Damborsky, David Bednar, Stanislav Mazurenko, Zbynek Prokop
Summary: Therapeutic enzymes are valuable biopharmaceuticals that have found successful applications in various biomedical fields. The integration of computational approaches and high-throughput experimental technologies has greatly accelerated the identification and engineering of catalytic therapeutic agents, leading to the discovery of new enzymes and the improvement of their properties.
ADVANCED DRUG DELIVERY REVIEWS
(2022)
Article
Chemistry, Physical
Lea R. Rapp, Sergio M. Marques, Bernd Nebel, Jiri Damborsky, Bernhard Hauer
Summary: The catalytic space of the P450 monooxygenase CYP153A(M.aq) was transformed from a fatty acid hydroxylase to a catalyst capable of omega-hydroxylation of dodecylamine. A rapid screening method called RAPP was established to measure saturation libraries directly from a 96-deepwell plate. Molecular modeling and dynamics simulations revealed significant effects of the mutations on the substrate tunnel architectures.
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Joan Planas-Iglesias, Filip Opaleny, Pavol Ulbrich, Jan Stourac, Zainab Sanusi, Gaspar P. Pinto, Andrea Schenkmayerova, Jan Byska, Jiri Damborsky, Barbora Kozlikova, David Bednar
Summary: The transplantation of loops between structurally related proteins is a method to improve enzyme activity, specificity, and stability. However, there are limited methods for loop-based rational protein design. The unique dynamism and identification of successful excision points are practical challenges. LoopGrafter is a web server that guides users through the loop grafting process, providing step-by-step procedures for loop identification, calculation of geometry, assessment of similarities and dynamics, and selection of loops for transplantation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Antonin Kunka, David Lacko, Jan Stourac, Jiri Damborsky, Zbynek Prokop, Stanislav Mazurenko
Summary: The quantitative description of protein unfolding and aggregation is important for the design of stability and understanding molecular basis of protein misfolding diseases. CalFitter 2.0 incorporates singular value decomposition of multi-wavelength spectral datasets, allowing fitting of different experimental data types and providing spectral fingerprints during unfolding.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Isabel Pardo, David Bednar, Patricia Calero, Daniel C. Volke, Jiri Damborsky, Pablo I. Nikel
Summary: This study discovered a highly efficient nonconventional fluorinase and demonstrated its potential in increasing the production of fluoronucleotides in a bacterial host, paving the way for efficient biohalogenation.
Article
Chemistry, Physical
Ren Wei, Gerlis von Haugwitz, Lara Pfaff, Jan Mican, Christoffel P. S. Badenhorst, Weidong Liu, Gert Weber, Harry P. Austin, David Bednar, Jiri Damborsky, Uwe T. Bornscheuer
Summary: Polyethylene terephthalate (PET) is a widely used synthetic polyester in textile fibers and packaging materials, which contributes significantly to global solid waste and environmental plastic pollution. Enzymatic PET recycling and upcycling have emerged as potential solutions, but there are limitations such as unbalanced enzyme-substrate interactions, limited thermostability, low catalytic efficiency at high temperatures, and inhibition by degradation intermediates. Protein engineering has been successful in addressing these limitations and can be applied to other mass-produced polymer types for biotechnological waste disposal.
Article
Chemistry, Physical
Martin Toul, Dmitri Nikitin, Martin Marek, Jiri Damborsky, Zbynek Prokop
Summary: This study provides a detailed understanding of the biochemical mechanism and limiting steps of the plasminogen activator staphylokinase, and determines its high catalytic activity. This knowledge is crucial for fully understanding its catalytic functionality and designing rational engineering strategies.
Article
Chemistry, Physical
Kridsadakorn Prakinee, Aisaraphon Phintha, Surawit Visitsatthawong, Narin Lawan, Jeerus Sucharitakul, Chadaporn Kantiwiriyawanitch, Jiri Damborsky, Penchit Chitnumsub, Karl-Heinz Van Pee, Pimchai Chaiyen
Summary: By employing a mechanism-guided semi-rational approach, we have successfully improved the performance of flavin-dependent halogenases by modifying the structure of the intermediate transfer tunnel. This improvement leads to faster halogenation, broader substrate utilization, and greater stability and pH tolerance. Our findings highlight the value of understanding reaction mechanisms for enhancing the efficiency of flavin-dependent halogenases.
Article
Chemistry, Physical
Petr Kouba, Pavel Kohout, Faraneh Haddadi, Anton Bushuiev, Raman Samusevich, Jiri Sedlar, Jiri Damborsky, Tomas Pluskal, Josef Sivic, Stanislav Mazurenko
Summary: Recent progress has been made in engineering biocatalysts using machine learning methods. These methods utilize experimental and simulation data to discover and annotate enzymes, as well as suggest beneficial mutations. The field is expanding to cover various aspects of protein engineering, but there are still challenges to overcome. This Perspective provides an overview of ongoing trends, highlights case studies, and discusses limitations of machine learning-based methods.
Article
Biochemical Research Methods
Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar
Summary: Access pathways are critical for substrate and product transport in enzymes. A Python3 API called pyCaverDock is introduced to enhance the user experience and facilitate ligand transport analysis. This API simplifies the steps needed to use CaverDock and allows for automation of setup processes.
Article
Chemistry, Physical
Jan Mican, Da 'san M. M. Jaradat, Weidong Liu, Gert Weber, Stanislav Mazurenko, Uwe T. Bornscheuer, Jiri Damborsky, Ren Wei, David Bednar
Summary: Enzymatic PET recycling is a promising alternative to conventional methods, but requires optimization of PET hydrolases through engineering. A workflow integrating various methods can accelerate the discovery of PET-degrading enzymes, leading to the development of innovative plastic recycling techniques.
APPLIED CATALYSIS B-ENVIRONMENT AND ENERGY
(2024)
Article
Biochemistry & Molecular Biology
Anna Spackova, Ondrej Vavra, Tomas Racek, Vaclav Bazgier, David Sehnal, Jiri Damborsky, Radka Svobodova, David Bednar, Karel Berka
Summary: ChannelsDB 2.0 is an updated database that provides structural information about the position, geometry, and physicochemical properties of protein channels and pores. It incorporates data calculated by CAVER and MOLE tools, as well as additional information from AlphaFill database, resulting in significantly expanded channel annotations. The database stores information such as geometrical features and physico-chemical properties based on channel-lining amino acids, and is interlinked with UniProt mutation annotation data. ChannelsDB 2.0 serves as an important resource for in-depth analysis of the role of biomacromolecular tunnels and pores.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Dmitri Nikitin, Jan Mican, Martin Toul, David Bednar, Michaela Peskova, Patricia Kittova, Sandra Thalerova, Jan Vitecek, Jiri Damborsky, Robert Mikulik, Sarel J. Fleishman, Zbynek Prokop, Martin Marek
Summary: Cardio- and cerebrovascular diseases are major causes of death and disability, but the discovery of bacterial and human plasminogen activators has revolutionized their treatment. This study redesigned the molecular surface of staphylokinase (SAK) computationally to increase its affinity for plasmin. The engineered SAK mutant showed significantly enhanced affinity, selectivity, and efficiency in generating plasmin, providing a framework for the development of next-generation thrombolytic drugs.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
