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Omar MN, Rahman RNZRA, Noor NDM, Latip W, Knight VF, Ali MSM. Exploring the Antarctic aminopeptidase P from Pseudomonas sp. strain AMS3 through structural analysis and molecular dynamics simulation. J Biomol Struct Dyn 2024:1-13. [PMID: 38555730 DOI: 10.1080/07391102.2024.2331093] [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: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
Aminopeptidase P (APPro) is a crucial metalloaminopeptidase involved in amino acid cleavage from peptide N-termini, playing essential roles as versatile biocatalysts with applications ranging from pharmaceuticals to industrial processes. Despite acknowledging its potential for catalysis in lower temperatures, detailed molecular basis and biotechnological implications in cold environments are yet to be explored. Therefore, this research aims to investigate the molecular mechanisms underlying the cold-adapted characteristics of APPro from Pseudomonas sp. strain AMS3 (AMS3-APPro) through a detailed analysis of its structure and dynamics. In this study, structure analysis and molecular dynamics (MD) simulation of a predicted model of AMS3-APPro has been performed at different temperatures to assess structural flexibility and thermostability across a temperature range of 0-60 °C over 100 ns. The MD simulation results revealed that the structure were able to remain stable at low temperatures. Increased temperatures present a potential threat to the overall stability of AMS3-APPro by disrupting the intricate hydrogen bond networks crucial for maintaining structural integrity, thereby increasing the likelihood of protein unfolding. While the metal binding site at the catalytic core exhibits resilience at higher temperatures, highlighting its local structural integrity, the overall enzyme structure undergoes fluctuations and potential denaturation. This extensive structural instability surpasses the localized stability observed at the metal binding site. Consequently, these assessments offer in-depth understanding of the cold-adapted characteristics of AMS3-APPro, highlighting its capability to uphold its native conformation and stability in low-temperature environments. In summary, this research provides valuable insights into the cold-adapted features of AMS3-APPro, suggesting its efficient operation in low thermal conditions, particularly relevant for potential biotechnological applications in cold environments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhamad Nadzmi Omar
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Victor Feizal Knight
- Research Centre for Chemical Defence, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Purcarea C, Ruginescu R, Banciu RM, Vasilescu A. Extremozyme-Based Biosensors for Environmental Pollution Monitoring: Recent Developments. BIOSENSORS 2024; 14:143. [PMID: 38534250 DOI: 10.3390/bios14030143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Extremozymes combine high specificity and sensitivity with the ability to withstand extreme operational conditions. This work presents an overview of extremozymes that show potential for environmental monitoring devices and outlines the latest advances in biosensors utilizing these unique molecules. The characteristics of various extremozymes described so far are presented, underlining their stability and operational conditions that make them attractive for biosensing. The biosensor design is discussed based on the detection of photosynthesis-inhibiting herbicides as a case study. Several biosensors for the detection of pesticides, heavy metals, and phenols are presented in more detail to highlight interesting substrate specificity, applications or immobilization methods. Compared to mesophilic enzymes, the integration of extremozymes in biosensors faces additional challenges related to lower availability and high production costs. The use of extremozymes in biosensing does not parallel their success in industrial applications. In recent years, the "collection" of recognition elements was enriched by extremozymes with interesting selectivity and by thermostable chimeras. The perspectives for biosensor development are exciting, considering also the progress in genetic editing for the oriented immobilization of enzymes, efficient folding, and better electron transport. Stability, production costs and immobilization at sensing interfaces must be improved to encourage wider applications of extremozymes in biosensors.
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Affiliation(s)
- Cristina Purcarea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Roberta Maria Banciu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
- Department of Analytical and Physical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Alina Vasilescu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
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Esquirol L, Newman J, Nebl T, Scott C, Vickers C, Sainsbury F, Peat TS. Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii. Acta Crystallogr D Struct Biol 2024; 80:203-215. [PMID: 38411551 PMCID: PMC10910542 DOI: 10.1107/s2059798324001360] [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: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
Mevalonate kinase is central to the isoprenoid biosynthesis pathway. Here, high-resolution X-ray crystal structures of two mevalonate kinases are presented: a eukaryotic protein from Ramazzottius varieornatus and an archaeal protein from Methanococcoides burtonii. Both enzymes possess the highly conserved motifs of the GHMP enzyme superfamily, with notable differences between the two enzymes in the N-terminal part of the structures. Biochemical characterization of the two enzymes revealed major differences in their sensitivity to geranyl pyrophosphate and farnesyl pyrophosphate, and in their thermal stabilities. This work adds to the understanding of the structural basis of enzyme inhibition and thermostability in mevalonate kinases.
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Affiliation(s)
- Lygie Esquirol
- Environment, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Janet Newman
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Tom Nebl
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin Scott
- Environment, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Claudia Vickers
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
- Synbio Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
- Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
- Synbio Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Thomas S. Peat
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Chi H, Jiang Q, Feng Y, Zhang G, Wang Y, Zhu P, Lu Z, Lu F. Thermal Stability Enhancement of L-Asparaginase from Corynebacterium glutamicum Based on a Semi-Rational Design and Its Effect on Acrylamide Mitigation Capacity in Biscuits. Foods 2023; 12:4364. [PMID: 38231880 DOI: 10.3390/foods12234364] [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: 09/29/2023] [Revised: 10/19/2023] [Accepted: 11/29/2023] [Indexed: 01/19/2024] Open
Abstract
Acrylamide is present in thermally processed foods, and it possesses toxic and carcinogenic properties. L-asparaginases could effectively regulate the formation of acrylamide at the source. However, current L-asparaginases have drawbacks such as poor thermal stability, low catalytic activity, and poor substrate specificity, thereby restricting their utility in the food industry. To address this issue, this study employed consensus design to predict the crucial residues influencing the thermal stability of Corynebacterium glutamicum L-asparaginase (CgASNase). Subsequently, a combination of site-point saturating mutation and combinatorial mutation techniques was applied to generate the double-mutant enzyme L42T/S213N. Remarkably, L42T/S213N displayed significantly enhanced thermal stability without a substantial impact on its enzymatic activity. Notably, its half-life at 40 °C reached an impressive 13.29 ± 0.91 min, surpassing that of CgASNase (3.24 ± 0.23 min). Moreover, the enhanced thermal stability of L42T/S213N can be attributed to an increased positive surface charge and a more symmetrical positive potential, as revealed by three-dimensional structural simulations and structure comparison analyses. To assess the impact of L42T/S213N on acrylamide removal in biscuits, the optimal treatment conditions for acrylamide removal were determined through a combination of one-way and orthogonal tests, with an enzyme dosage of 300 IU/kg flour, an enzyme reaction temperature of 40 °C, and an enzyme reaction time of 30 min. Under these conditions, compared to the control (464.74 ± 6.68 µg/kg), the acrylamide reduction in double-mutant-enzyme-treated biscuits was 85.31%, while the reduction in wild-type-treated biscuits was 68.78%. These results suggest that L42T/S213N is a promising candidate for industrial applications of L-asparaginase.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingwei Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiqian Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guizheng Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yilian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Dishliyska V, Stoyancheva G, Abrashev R, Miteva-Staleva J, Spasova B, Angelova M, Krumova E. Catalase from the Antarctic Fungus Aspergillus fumigatus I-9-Biosynthesis and Gene Characterization. Indian J Microbiol 2023; 63:541-548. [PMID: 38031622 PMCID: PMC10682308 DOI: 10.1007/s12088-023-01110-8] [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: 07/14/2023] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
Extremely cold habitats are a serious challenge for the existing there organisms. Inhabitants of these conditions are mostly microorganisms and lower mycetae. The mechanisms of microbial adaptation to extreme conditions are still unclear. Low temperatures cause significant physiological and biochemical changes in cells. Recently, there has been increasing interest in the relationship between low-temperature exposure and oxidative stress events, as well as the importance of antioxidant enzymes for survival in such conditions. The catalase is involved in the first line of the cells' antioxidant defense. Published information supports the concept of a key role for catalase in antioxidant defense against cold stress in a wide range of organisms isolated from the Antarctic. Data on representatives of microscopic fungi, however, are rarely found. There is scarce information on the characterization of catalase synthesized by adapted to cold stress organisms. Overall, this study aimed to observe the role of catalase in the survival strategy of filamentous fungi in extremely cold habitats and to identify the gene encoded catalase enzyme. Our results clearly showed that catalase is the main part of antioxidant enzyme defense in fungal cells against oxidative stress caused by low temperature exposure.
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Affiliation(s)
- Vladislava Dishliyska
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Galina Stoyancheva
- Departament of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Radoslav Abrashev
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Jeny Miteva-Staleva
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Boriana Spasova
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Maria Angelova
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Ekaterina Krumova
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
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Lee YCJ, Javdan B. Ice Cores as a Source for Antimicrobials: From Bioprospecting to Biodesign. BIODESIGN RESEARCH 2023; 5:0024. [PMID: 37928441 PMCID: PMC10623340 DOI: 10.34133/bdr.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023] Open
Abstract
The golden age has passed for antibiotic discovery, and while some antibiotics are currently in various phases of clinical trials in the United States, many pharmaceutical companies have abandoned antibiotic research. With the need for antibiotics, we should expand our horizon for therapeutic mining and can look toward understudied sources such as ice cores. Ice cores contain microorganisms and genetic material that have been frozen in time for thousands of years. The antibiotics used by these organisms are encoded in their genomes, which can be unlocked, identified, and characterized with modern advances in molecular biology, genetic sequencing, various computational approaches, and established natural product discovery pipelines. While synthetic biology can be used in natural product discovery approaches, synthetic biology and bioengineering efforts can also be leveraged in the selection and biodesign of increased compound yields, potency, and stability. Here, we provide the perspective that ice cores can be a source of novel antibiotic compounds and that the tools of synthetic biology can be used to design better antimicrobials.
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Affiliation(s)
| | - Bahar Javdan
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
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