1
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Walker EJ, Hamill CJ, Crean R, Connolly MS, Warrender AK, Kraakman KL, Prentice EJ, Steyn-Ross A, Steyn-Ross M, Pudney CR, van der Kamp MW, Schipper LA, Mulholland AJ, Arcus VL. Cooperative Conformational Transitions Underpin the Activation Heat Capacity in the Temperature Dependence of Enzyme Catalysis. ACS Catal 2024; 14:4379-4394. [PMID: 38633402 PMCID: PMC11020164 DOI: 10.1021/acscatal.3c05584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/16/2024] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Many enzymes display non-Arrhenius behavior with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behavior and recently the role of the activation heat capacity (ΔCP⧧) has been widely discussed. If enzyme-catalyzed reactions occur with appreciable negative values of ΔCP⧧ (arising from narrowing of the conformational space along the reaction coordinate), then curved Arrhenius plots are a consequence. To investigate these phenomena in detail, we have collected high precision temperature-rate data over a wide temperature interval for a model glycosidase enzyme MalL, and a series of mutants that change the temperature-dependence of the enzyme-catalyzed rate. We use these data to test a range of models including macromolecular rate theory (MMRT) and an equilibrium model. In addition, we have performed extensive molecular dynamics (MD) simulations to characterize the conformational landscape traversed by MalL in the enzyme-substrate complex and an enzyme-transition state complex. We have crystallized the enzyme in a transition state-like conformation in the absence of a ligand and determined an X-ray crystal structure at very high resolution (1.10 Å). We show (using simulation) that this enzyme-transition state conformation has a more restricted conformational landscape than the wildtype enzyme. We coin the term "transition state-like conformation (TLC)" to apply to this state of the enzyme. Together, these results imply a cooperative conformational transition between an enzyme-substrate conformation (ES) and a transition-state-like conformation (TLC) that precedes the chemical step. We present a two-state model as an extension of MMRT (MMRT-2S) that describes the data along with a convenient approximation with linear temperature dependence of the activation heat capacity (MMRT-1L) that can be used where fewer data points are available. Our model rationalizes disparate behavior seen for MalL and previous results for a thermophilic alcohol dehydrogenase and is consistent with a raft of data for other enzymes. Our model can be used to characterize the conformational changes required for enzyme catalysis and provides insights into the role of cooperative conformational changes in transition state stabilization that are accompanied by changes in heat capacity for the system along the reaction coordinate. TLCs are likely to be of wide importance in understanding the temperature dependence of enzyme activity and other aspects of enzyme catalysis.
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Affiliation(s)
- Emma J. Walker
- Te
Aka Ma̅tuatua School of Science, University
of Waikato, Hamilton 3214, New Zealand
| | - Carlin J. Hamill
- Te
Aka Ma̅tuatua School of Science, University
of Waikato, Hamilton 3214, New Zealand
| | - Rory Crean
- Centre
for Computational Chemistry, School of Chemistry,
University of Bristol, Bristol BS8 1TS, U.K.
| | - Michael S. Connolly
- Centre
for Computational Chemistry, School of Chemistry,
University of Bristol, Bristol BS8 1TS, U.K.
| | - Annmaree K. Warrender
- Te
Aka Ma̅tuatua School of Science, University
of Waikato, Hamilton 3214, New Zealand
| | - Kirsty L. Kraakman
- Te
Aka Ma̅tuatua School of Science, University
of Waikato, Hamilton 3214, New Zealand
| | - Erica J. Prentice
- Te
Aka Ma̅tuatua School of Science, University
of Waikato, Hamilton 3214, New Zealand
| | | | - Moira Steyn-Ross
- School
of Engineering, University of Waikato, Hamilton 3214, New Zealand
| | - Christopher R. Pudney
- Department
of Biology and Biochemistry, Centre for Biosensors, Bioelectronics
and Biodevices, University of Bath, Bath ST16 2TB, U.K.
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Louis A. Schipper
- Te
Aka Ma̅tuatua School of Science, University
of Waikato, Hamilton 3214, New Zealand
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry,
University of Bristol, Bristol BS8 1TS, U.K.
| | - Vickery L. Arcus
- Te
Aka Ma̅tuatua School of Science, University
of Waikato, Hamilton 3214, New Zealand
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2
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Da Lage JL, Fontenelle A, Filée J, Merle M, Béranger JM, Almeida CE, Folly Ramos E, Harry M. Evidence that hematophagous triatomine bugs may eat plants in the wild. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 165:104059. [PMID: 38101706 DOI: 10.1016/j.ibmb.2023.104059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/29/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
Blood feeding is a secondary adaptation in hematophagous bugs. Many proteins are secreted in the saliva that are devoted to coping with the host's defense and to process the blood meal. Digestive enzymes that are no longer required for a blood meal would be expected to be eventually lost. Yet, in many strictly hematophagous arthropods, α-amylase genes, which encode the enzymes that digest starch from plants, are still present and transcribed, including in the kissing bug Rhodnius prolixus (Hemiptera, Reduviidae) and its related species, which transmit the Chagas disease. We hypothesized that retaining α-amylase could be advantageous if the bugs occasionally consume plant tissues. We first checked that the α-amylase protein of Rhodnius robustus retains normal amylolytic activity. Then we surveyed hundreds of gut DNA extracts from the sylvatic R. robustus to detect traces of plants. We found plant DNA in 8% of the samples, mainly identified as Attalea palm trees, where R. robustus are usually found. We suggest that although of secondary importance in the blood-sucking bugs, α-amylase may be needed during occasional plant feeding and thus has been retained.
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Affiliation(s)
- Jean-Luc Da Lage
- Université Paris-Saclay, CNRS, IRD, UMR 9191 Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.
| | - Alice Fontenelle
- Université Paris-Saclay, CNRS, IRD, UMR 9191 Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jonathan Filée
- Université Paris-Saclay, CNRS, IRD, UMR 9191 Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Marie Merle
- Université Paris-Saclay, CNRS, IRD, UMR 9191 Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jean-Michel Béranger
- Département Systématique and Evolution, Muséum National d'Histoire Naturelle, Paris, France; IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Carlos Eduardo Almeida
- Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde, Instituto de Biologia, Departamento de Zoologia, Rio de Janeiro, Brazil
| | - Elaine Folly Ramos
- Departamento de Engenharia e Meio Ambiente - DEMA, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Myriam Harry
- Université Paris-Saclay, CNRS, IRD, UMR 9191 Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
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3
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Wang B, Huang D, Cao C, Gong Y. Insect α-Amylases and Their Application in Pest Management. Molecules 2023; 28:7888. [PMID: 38067617 PMCID: PMC10708458 DOI: 10.3390/molecules28237888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Amylase is an indispensable hydrolase in insect growth and development. Its varied enzymatic parameters cause insects to have strong stress resistance. Amylase gene replication is a very common phenomenon in insects, and different copies of amylase genes enable changes in its location and function. In addition, the classification, structure, and interaction between insect amylase inhibitors and amylases have also invoked the attention of researchers. Some plant-derived amylase inhibitors have inhibitory activities against insect amylases and even mammalian amylases. In recent years, an increasing number of studies have clarified the effects of pesticides on the amylase activity of target and non-target pests, which provides a theoretical basis for exploring safe and efficient pesticides, while the exact lethal mechanisms and safety in field applications remain unclear. Here, we summarize the most recent advances in insect amylase studies, including its sequence and characteristics and the regulation of amylase inhibitors (α-AIs). Importantly, the application of amylases as the nanocide trigger, RNAi, or other kinds of pesticide targets will be discussed. A comprehensive foundation will be provided for applying insect amylases to the development of new-generation insect management tools and improving the specificity, stability, and safety of pesticides.
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Affiliation(s)
| | | | - Chunxia Cao
- National Biopesticide Engineering Research Centre, Hubei Biopesticide Engineering Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (B.W.)
| | - Yan Gong
- National Biopesticide Engineering Research Centre, Hubei Biopesticide Engineering Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (B.W.)
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4
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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5
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Some Clues about Enzymes from Psychrophilic Microorganisms. Microorganisms 2022; 10:microorganisms10061161. [PMID: 35744679 PMCID: PMC9227589 DOI: 10.3390/microorganisms10061161] [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: 04/30/2022] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023] Open
Abstract
Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.
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6
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Sen S, Sarkar M. Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study. J Chem Inf Model 2022; 62:1916-1932. [PMID: 35412825 DOI: 10.1021/acs.jcim.1c01381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rigidity and flexibility of homologous psychrophilic (P), mesophilic (M), and thermophilic (T) proteins have been investigated at the global and local levels in terms of "packing factors" and "atomic fluctuations" obtained from B-factors. For comparison of atomic fluctuations, correction of errors by considering errors in B-factors from all sources in a consolidated manner and conversion of the fluctuations to the same temperature have been suggested and validated. The results indicate no differences in the global values like the average packing factor among the three classes of protein homologues, but at local levels there are differences. A comparison of homologous protein triplets show that the average atomic fluctuations at a given temperature mainly obey the order P > M > T. Packing factors and the atomic fluctuations are anti-correlated, suggesting that altering the rigidity of the active site might be a potential strategy to make tailor-made psychrophilic or thermophilic proteins from their mesophilic homologues. The computer codes developed and used in this work are available at the link https://github.com/Munna-Sarkar/proteins-rigidity-flexibility.git.
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Affiliation(s)
- Srikanta Sen
- Molecular Modeling Section, Biolab, Chembiotek, TCG Lifesciences Limited, Bengal Intelligent Park, Salt Lake Electronic Complex, Sector-V, Kolkata 700091, India
| | - Munna Sarkar
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
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7
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Massad N, Banta SA. NAD(H)-PEG Swing Arms Improve Both the Activities and Stabilities of Modularly-Assembled Transhydrogenases Designed with Predictable Selectivities. Chembiochem 2021; 23:e202100251. [PMID: 34351671 DOI: 10.1002/cbic.202100251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/04/2021] [Indexed: 11/11/2022]
Abstract
Protein engineering has been used to enhance the activities, selectivities, and stabilities of enzymes. Frequently tradeoffs are observed, where improvements in some features can come at the expense of others. Nature uses modular assembly of active sites for complex, multi-step reactions, and natural "swing arm" mechanisms have evolved to transfer intermediates between active sites. Biomimetic polyethylene glycol (PEG) swing arms modified with NAD(H) have been explored to introduce synthetic swing arms into fused oxidoreductases. Here we report that increasing NAD(H)-PEG swing arms can improve the activity of synthetic formate:malate oxidoreductases as well as the thermal and operational stabilities of the biocatalysts. The modular assembly approach enables the K M values of new enzymes to be predictable, based on the parental enzymes. We describe four unique synthetic transhydrogenases that have no native homologs, and this platform could be easily extended for the predictive design of additional synthetic cofactor-independent transhydrogenases.
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Affiliation(s)
- Nadim Massad
- Columbia University, Chemical Engineering, UNITED STATES
| | - Scott A Banta
- Columbia University, Department of Chemical Engineering, 820 Mudd MC4721, 500 West 120th Street, 10027, New York, UNITED STATES
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8
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Romero-Romero S, Costas M, Silva Manzano DA, Kordes S, Rojas-Ortega E, Tapia C, Guerra Y, Shanmugaratnam S, Rodríguez-Romero A, Baker D, Höcker B, Fernández-Velasco DA. The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach. J Mol Biol 2021; 433:167153. [PMID: 34271011 PMCID: PMC8404036 DOI: 10.1016/j.jmb.2021.167153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022]
Abstract
The TIM barrel is a versatile fold to understand structure-stability relationships. A collection of de novo TIM barrels with improved hydrophobic cores was designed. DeNovoTIMs are reversible in chemical and thermal unfolding, which is uncommon in TIM barrels. Epistatic effects play a central role in DeNovoTIMs stabilization. DeNovoTIMs navigate a previously uncharted region of the stability landscape.
The ability to design stable proteins with custom-made functions is a major goal in biochemistry with practical relevance for our environment and society. Understanding and manipulating protein stability provide crucial information on the molecular determinants that modulate structure and stability, and expand the applications of de novo proteins. Since the (β/⍺)8-barrel or TIM-barrel fold is one of the most common functional scaffolds, in this work we designed a collection of stable de novo TIM barrels (DeNovoTIMs), using a computational fixed-backbone and modular approach based on improved hydrophobic packing of sTIM11, the first validated de novo TIM barrel, and subjected them to a thorough folding analysis. DeNovoTIMs navigate a region of the stability landscape previously uncharted by natural TIM barrels, with variations spanning 60 degrees in melting temperature and 22 kcal per mol in conformational stability throughout the designs. Significant non-additive or epistatic effects were observed when stabilizing mutations from different regions of the barrel were combined. The molecular basis of epistasis in DeNovoTIMs appears to be related to the extension of the hydrophobic cores. This study is an important step towards the fine-tuned modulation of protein stability by design.
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Affiliation(s)
- Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico; Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Daniel-Adriano Silva Manzano
- Department of Biochemistry, University of Washington, 98195 Seattle, USA; Institute for Protein Design, University of Washington, 98195 Seattle, USA
| | - Sina Kordes
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Erendira Rojas-Ortega
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Cinthya Tapia
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Yasel Guerra
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | | | - Adela Rodríguez-Romero
- Instituto de Química, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - David Baker
- Department of Biochemistry, University of Washington, 98195 Seattle, USA; Institute for Protein Design, University of Washington, 98195 Seattle, USA.
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico.
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9
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Miłek J. Determination of Activation Energies and the Optimum Temperatures of Hydrolysis of Starch by α-Amylase from Porcine Pancreas. Molecules 2021; 26:4117. [PMID: 34299392 PMCID: PMC8306296 DOI: 10.3390/molecules26144117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The present paper reports the determination of the activation energies and the optimum temperatures of starch hydrolysis by porcine pancreas α-amylase. The parameters were estimated based on the literature data on the activity curves versus temperature for starch hydrolysis by α-amylase from porcine pancreas. It was assumed that both the hydrolysis reaction process and the deactivation process of α-amylase were first-order reactions by the enzyme concentration. A mathematical model describing the effect of temperature on porcine pancreas α-amylase activity was used. The determine deactivation energies Ea were from 19.82 ± 7.22 kJ/mol to 128.80 ± 9.27 kJ/mol, the obtained optimum temperatures Topt were in the range from 311.06 ± 1.10 K to 326.52 ± 1.75 K. In turn, the values of deactivation energies Ed has been noted in the range from 123.57 ± 14.17 kJ/mol to 209.37 ± 5.17 kJ/mol. The present study is related to the starch hydrolysis by α-amylase. In the industry, the obtained results the values Ea, Ed, Topt can be used to design and optimize starch hydrolysis by α-amylase porcine pancreas. The obtained results might also find application in research on the pharmaceutical preparations used to treat pancreatic insufficiency or prognosis of pancreatic cancer.
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Affiliation(s)
- Justyna Miłek
- Department of Chemical and Biochemical Engineering, Faculty of Chemical Technology and Engineering, University of Science and Technology in Bydgoszcz, Seminaryjna 3, 85-326 Bydgoszcz, Poland
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10
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Habashy MM, Ong ES, Abdeldayem OM, Al-Sakkari EG, Rene ER. Food Waste: A Promising Source of Sustainable Biohydrogen Fuel. Trends Biotechnol 2021; 39:1274-1288. [PMID: 33992456 DOI: 10.1016/j.tibtech.2021.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022]
Abstract
Annually, approximately 1.3 billion tons of food is lost worldwide, accounting for one-third of annual food production. Therefore, turning food waste into energy is of enormous environmental significance because of its sustainable nature. Nutrients and organic acids present in food waste can be used to produce (bio)products such as biohydrogen through biological processes. However, our understanding of the production of biohydrogen from food waste through photofermentation and dark fermentation is still restricted. This comprehensive study aims to review the potential of food waste for biohydrogen production using microbial mediators, including a brief overview of process parameters that affect the (bio)hydrogen production pathway.
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Affiliation(s)
- Mahmoud M Habashy
- Department of Water Supply, Sanitation, and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, The Netherlands.
| | - Ee Shen Ong
- Department of Water Supply, Sanitation, and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, The Netherlands
| | - Omar M Abdeldayem
- Department of Water Supply, Sanitation, and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, The Netherlands
| | - Eslam G Al-Sakkari
- Chemical Engineering Department, Cairo University, Cairo University Road, 12613 Giza, Egypt
| | - Eldon R Rene
- Department of Water Supply, Sanitation, and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX Delft, The Netherlands
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11
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Sakaguchi R, Fujiyoshi S, Wakai S, Yamanaka M, Sambongi Y. Thermal destabilization mechanism of cytochrome c' from psychrophilic Shewanella violacea. Biosci Biotechnol Biochem 2021; 85:1121-1127. [PMID: 33686411 DOI: 10.1093/bbb/zbab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/06/2021] [Indexed: 02/01/2023]
Abstract
Cytochrome c' is a nitric oxide (NO)-binding heme protein found in Gram negative bacteria. The thermal stability of psychrophilic Shewanella violacea cytochrome c' (SVCP) is lower than those of its homologues from other 2 psychrophilic Shewanella species, indicating that thermal destabilization mechanism for low-temperature adaptation accumulates in SVCP. In order to understand this mechanism at the amino acid level, here the stability and function of SVCP variants, modeled using the 2 homologues, were examined. The variants exhibited increased stability, and they bound NO similar to the wild type. The vulnerability as to the SVCP stability could be attributed to less hydrogen bond at the subunit interface, more flexible loop structure, and less salt bridge on the protein surface, which appear to be its destabilization mechanism. This study provides an example for controlling stability without spoiling function in psychrophilic proteins.
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Affiliation(s)
- Riku Sakaguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - So Fujiyoshi
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Japan
| | - Satoshi Wakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Masaru Yamanaka
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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12
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Molecular strategies to enhance stability and catalysis of extremophile-derived α-amylase using computational biology. Extremophiles 2021; 25:221-233. [PMID: 33754213 DOI: 10.1007/s00792-021-01223-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/10/2021] [Indexed: 12/29/2022]
Abstract
α-Amylase is the most significant glycoside hydrolase having applications in various industries. It cleaves the α,1-4 glucosidic linkages of polysaccharides like starch, glycogen to yield a small polymer of glucose in α-anomeric configuration. α-Amylase is produced by all the three domains of life but microorganisms are preferred sources for industrial-scale production due to several advantages. Enormous studies and research have been done in this field in the past few decades. Still, it is requisite to work on enzyme stability and catalysis, as it loses its functionality in extreme. As the enzyme loses its structural and catalytic property under extreme environmental conditions, it is mandatory to confer some potential strategies for enhancing enzyme behaviour in such conditions. This limitation of an enzyme can be overcome up to some extent by extremophiles. They serve as an excellent source of α-amylase with outstanding features. This review is an attempt to encapsulate some structure-based strategies for improving enzyme behaviour thereby enabling researchers to selectively amend any of the strategies as per requirement during upstream and downstream processing for higher enzyme yield and stability. Thus, it will provide some cutting-edge strategies for tailoring α-amylase producing organism and enzyme with the help of several computational biology tools.
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Rane AS, Joshi RS, Giri AP. Molecular determinant for specificity: Differential interaction of α-amylases with their proteinaceous inhibitors. Biochim Biophys Acta Gen Subj 2020; 1864:129703. [PMID: 32805319 DOI: 10.1016/j.bbagen.2020.129703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND α-Amylase inhibitors (α-AIs) belong to the discrete classes, and exhibited differential specificities against α-amylases from various sources. Several α-amylases and their complexes with inhibitors at the molecular level have been studied in detail. Interestingly, some α-AIs depict specific and selective interactions amid different insect α-amylases. SCOPE OF REVIEW There are studies to understand evolutionary variability and functional differentiation of insect α-amylases and their cognate inhibitors. We have examined sequence, structural, and interaction diversity between various α-amylases and α-AIs. Based on these analyses, we are providing a potential basis for the functional differentiation among certain insect α-amylases concerning mammalian counterparts and their interactions with different proteinaceous α-AIs. MAJOR CONCLUSIONS Insect α-amylases have conserved domain architecture with differences in length, number of disulfide bonds, and secondary structure. Furthermore, few of them exhibit variable characteristics like chloride dependent activity, the presence of N-terminal glutamine residue to protect against proteolytic degradation, and loop variations near the enzyme active site. Conformation of α-AI protein could be an essential factor for their specificity and binding affinities towards target α-amylase(s). Furthermore, variation into the enzyme binding pocket residues might contribute to differential interactions with inhibitors. GENERAL SIGNIFICANCE Molecular insights in the interactions between insect α-amylases and plant α-AI will provide the details of mechanisms assisting the inhibitor specificity. Furthermore, this information will help to design potent and effective α-AIs against specific α-amylase.
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Affiliation(s)
- Ashwini S Rane
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411 008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Rakesh S Joshi
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411 008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| | - Ashok P Giri
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411 008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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14
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Chen Q, Xiao Y, Zhang W, Stressler T, Fischer L, Jiang B, Mu W. Computer-aided search for a cold-active cellobiose 2-epimerase. J Dairy Sci 2020; 103:7730-7741. [PMID: 32684457 DOI: 10.3168/jds.2020-18153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/04/2020] [Indexed: 01/06/2023]
Abstract
Cellobiose 2-epimerase (CE) is a promising industrial enzyme that can catalyze bioconversion of lactose to its high-value derivatives, namely epilactose and lactulose. A need exists in the dairy industry to catalyze lactose bioconversions at low temperatures to avoid microbial growth. We focused on the discovery of cold-active CE in this study. A genome mining method based on computational prediction was used to screen the potential genes encoding cold-active enzymes. The CE-encoding gene from Roseburia intestinalis, with a predicted high structural flexibility, was expressed heterologously in Escherichia coli. The catalytic property of the recombinant enzyme was extensively studied. The optimum temperature and pH of the enzyme were 45°C and 7.0, respectively. The specific activity of this enzyme to catalyze conversion of lactose to epilactose was measured to be 77.3 ± 1.6 U/mg. The kinetic parameters, including turnover number (kcat), Michaelis constant (Km), and catalytic efficiency (kcat/Km) using lactose as a substrate were 117.0 ± 7.7 s-1, 429.9 ± 57.3 mM, and 0.27 mM-1s-1, respectively. In situ production of epilactose was carried out at 8°C: 20.9% of 68.4 g/L lactose was converted into epilactose in 4 h using 0.02 mg/mL (1.5 U/mL, measured at 45°C) of recombinant enzyme. The enzyme discovered by this in silico method is suitable for low-temperature applications.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yaqin Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Timo Stressler
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, 70599 Stuttgart, Germany
| | - Lutz Fischer
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, 70599 Stuttgart, Germany
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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15
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Maffucci I, Laage D, Sterpone F, Stirnemann G. Thermal Adaptation of Enzymes: Impacts of Conformational Shifts on Catalytic Activation Energy and Optimum Temperature. Chemistry 2020; 26:10045-10056. [DOI: 10.1002/chem.202001973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Irene Maffucci
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
- Present address: Centre de recherche Royallieu Université de Technologie de Compiègne, UPJV CNRS, Enzyme and Cell Engineering CS 60319-60203 Compiègne Cedex France
| | - Damien Laage
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
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16
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HAN N, ZHANG ZK, LI YH, WANG W, BIAN LJ. Spectroscopic Analysis of Chloride Ion-induced Structural Change of Bacillus Amyloliquefaciens α-Amylase. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Da Lage JL. The Amylases of Insects. INTERNATIONAL JOURNAL OF INSECT SCIENCE 2018; 10:1179543318804783. [PMID: 30305796 PMCID: PMC6176531 DOI: 10.1177/1179543318804783] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/09/2018] [Indexed: 05/26/2023]
Abstract
Alpha-amylases are major digestive enzymes that act in the first step of maltopolysaccharide digestion. In insects, these enzymes have long been studied for applied as well as purely scientific purposes. In many species, amylases are produced by multiple gene copies. Rare species are devoid of Amy gene. They are predominantly secreted in the midgut but salivary expression is also frequent, with extraoral activity. Enzymological parameters are quite variable among insects, with visible trends according to phylogeny: Coleopteran amylases have acidic optimum activity, whereas dipteran amylases have neutral preference and lepidopteran ones have clear alkaline preference. The enzyme structure shows interesting variations shaped by evolutionary convergences, such as the recurrent loss of a loop involved in substrate handling. Many works have focused on the action of plant amylase inhibitors on pest insect amylases, in the frame of crop protection by transgenesis. It appears that sensitivity or resistance to inhibitors is finely tuned and very specific and that amylases and their inhibitors have coevolved. The multicopy feature of insect amylases appears to allow tissue-specific or stage-specific regulation, but also to broaden enzymological abilities, such as pH range, and to overcome plant inhibitory defenses.
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Affiliation(s)
- Jean-Luc Da Lage
- UMR 9191 Évolution, Génomes, Comportement, Écologie,
CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette,
France
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18
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Cruz WO, Sinhori GGC, de Lima CAR, Pontes EG. Biochemical Properties of α-Amylase from Midgut of Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae) Larvae. NEOTROPICAL ENTOMOLOGY 2018; 47:698-708. [PMID: 29484545 DOI: 10.1007/s13744-018-0590-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
The lesser mealworm, Alphitobius diaperinus (Panzer), is the main insect pest in the poultry industry, thus causing serious damage to production. In this work, the properties of midgut α-amylase from larvae of A. diaperinus were characterized, and its in vitro activity to proteinaceous preparations from different cultivars of common bean (Phaseolus vulgaris) was determined, as well as the amylolitic activity of insects reared on different types of poultry diet. In order to establish some assay conditions, time course and enzyme concentration upon the reaction rate were determined. Product proceeded linearly with time, and the activity was directly proportional to the enzyme concentration. Banding patterns in mildly denaturing electrophoresis showed a single band with apparent molecular weight of 42 kDa. α-Amylase reached optimal temperature at 45°C and pH 5.0 as the optimal one. It maintained 34.6% of the activity after being kept at 60°C for 5 min, and 23%, after 60 min. However, at 80°C, only 14 and 6% remained after 5 and 60 min, respectively. The presence of Ca2+ and Na+ ions decreased the enzyme activity at concentrations higher than 2 and 100 mM, respectively. The activity was significantly inhibited by some proteinaceous extracts from common bean cultivars, and it declined with increasing proteinaceous concentration. No significant difference was observed when the amylolytic activity was determined in A. diaperinus reared on different poultry diets, offered to broilers in the starter, grower, finisher, and layer phases.
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Affiliation(s)
- W O Cruz
- Lab de Bioquímica e Biologia Molecular de Artrópodes Depto de Química, Univ Federal Rural do Rio de Janeiro, Br. 465, Km 7, Seropédica, Rio de Janeiro, 23890-000, Brasil.
| | - G G C Sinhori
- Lab de Bioquímica e Biologia Molecular de Artrópodes Depto de Química, Univ Federal Rural do Rio de Janeiro, Br. 465, Km 7, Seropédica, Rio de Janeiro, 23890-000, Brasil
| | - C A R de Lima
- Instituto de Zootecnia, Univ Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - E G Pontes
- Lab de Bioquímica e Biologia Molecular de Artrópodes Depto de Química, Univ Federal Rural do Rio de Janeiro, Br. 465, Km 7, Seropédica, Rio de Janeiro, 23890-000, Brasil
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19
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Feller G. Protein folding at extreme temperatures: Current issues. Semin Cell Dev Biol 2017; 84:129-137. [PMID: 28941878 DOI: 10.1016/j.semcdb.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 08/18/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
The range of temperatures compatible with life is currently estimated from -25°C, as exemplified by metabolically active bacteria between sea ice crystals, and up to 122°C in hydrothermal vents as exemplified by the archaeon Methanopyrus kandleri. In the context of protein folding, as soon as a polypeptide emerges from the ribosome, it is exposed to the effects of environmental temperatures. Recent investigations have shown that the rate of protein folding is not adapted to extreme temperatures and should be very fast at high temperature and low in cold environments. This lack of adaptation is driven by kinetic constraints on protein stability. To counteract the deleterious effects of fast protein folding in hyperthermophiles, chaperones such as the Trigger Factor hold and slow down the rate of folding intermediates. Prolyl isomerization, a rate-limiting step in the folding of many proteins, is strongly temperature-dependent and impairs folding of psychrophilic proteins in the cold. This is compensated by reduction of the proline content in cold-adapted proteins, by an increased number of prolyl isomerases encoded in the genome of psychrophilic microorganisms and by overexpression of prolyl isomerases under low temperature cultivation. After folding, the native state is reached and although extremophilic proteins share the same fold, dramatic differences in stability have been recorded by differential scanning calorimetry.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, Institute of Chemistry B6a, 4000 Liège-Sart Tilman, Belgium.
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20
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Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting. Appl Biochem Biotechnol 2017; 183:636-651. [PMID: 28815469 DOI: 10.1007/s12010-017-2568-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/24/2017] [Indexed: 01/05/2023]
Abstract
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body and ocean water. This review article describes the state-of-the-art techniques and tools in metagenomics and discusses the potential of metagenomic approaches for the bioprospecting of industrial enzymes from various environmental samples. We also describe the unusual novel enzymes discovered via metagenomic approaches and discuss the future prospects for metagenome technologies.
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21
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Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H. Extremophiles 2017; 21:919-932. [PMID: 28726126 DOI: 10.1007/s00792-017-0953-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
Abstract
The phrB gene encoding a putative cold-adapted DNA photolyase was cloned from the bacterial genomic DNA of Colwellia psychrerythraea 34H, a psychrophilic bacterium. Recombinant DNA photolyase, rCpPL, was overexpressed and purified from three different vectors. rCpPL binds its DNA substrate by flipping a cyclobutane pyrimidine dimer (CPD) into its active site and repairs CPD-containing DNA in vitro. rCpPL contains one catalytic flavin adenine dinucleotide (FAD) cofactor, but displays promiscuity in cofactor binding, in which either a flavin mononucleotide (FMN) or a methenyltetrahydrofolate (MTHF) molecule is bound as an antenna molecule and found in sub-stoichiometric amounts. The UV/Vis spectrum of oxidized rCpPL shows that the FADOX absorption maximum is the most red-shifted reported for a PL, suggesting a unique cavity electrostatic environment. Modest FAD vibronic structure suggests that the binding pocket is more flexible than warmer PLs, corroborating the hypothesis that psychrophilic proteins must be highly flexible to function at low temperatures. Fluorescence excitation data show that the freshly purified flavin cofactor is in its fully reduced state (FADH¯). A homology analysis of PL protein structures spanning 70 °C in growth temperature supports the data that the structure of CpPL is quite different from its warmer cousins.
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22
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Rahban M, Salehi N, Saboury AA, Hosseinkhani S, Karimi-Jafari MH, Firouzi R, Rezaei-Ghaleh N, Moosavi-Movahedi AA. Histidine substitution in the most flexible fragments of firefly luciferase modifies its thermal stability. Arch Biochem Biophys 2017; 629:8-18. [PMID: 28711358 DOI: 10.1016/j.abb.2017.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 11/26/2022]
Abstract
Molecular dynamics (MD) at two temperatures of 300 and 340 K identified two histidine residues, His461 and His489, in the most flexible regions of firefly luciferase, a light emitting enzyme. We therefore designed four protein mutants H461D, H489K, H489D and H489M to investigate their enzyme kinetic and thermodynamic stability changes. Substitution of His461 by aspartate (H461D) decreased ATP binding affinity, reduced the melting temperature of protein by around 25 °C and shifted its optimum temperature of activity to 10 °C. In line with the common feature of psychrophilic enzymes, the MD data showed that the overall flexibility of H461D was relatively high at low temperature, probably due to a decrease in the number of salt bridges around the mutation site. On the other hand, substitution of His489 by aspartate (H489D) introduced a new salt bridge between the C-terminal and N-terminal domains and increased protein rigidity but only slightly improved its thermal stability. Similar changes were observed for H489K and, to a lesser degree, H489M mutations. Based on our results we conclude that the MD simulation-based rational substitution of histidines by salt-bridge forming residues can modulate conformational dynamics in luciferase and shift its optimal temperature activity.
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Affiliation(s)
- Mahdie Rahban
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Najmeh Salehi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | | | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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23
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Miller SR. An appraisal of the enzyme stability‐activity trade‐off. Evolution 2017; 71:1876-1887. [DOI: 10.1111/evo.13275] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Scott R. Miller
- Division of Biological SciencesThe University of Montana Missoula Montana 59812
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24
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Da Lage JL. An optional C-terminal domain is ancestral in α-amylases of bilaterian animals. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/amylase-2017-0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe modular structure and organization of most proteins is a fascinating aspect of their origin and evolution. α-Amylases are known to be formed of at least three domains. In a number of bacterial α-amylases, one or several additional domains may exist, which are carbohydrate binding modules, interacting with raw substrates. In animal α-amylases, however, no additional domain has been described. Here we report the presence of a C-terminal domain, previously described only in the bacterium Pseudoalteromonas haloplanktis. This domain is widely distributed in invertebrate α-amylases and must be ancestral, although it has been lost in important phyla or groups, such as vertebrates and insects. Its function is still unknown. In a single genome, enzymes with and without the terminal domain may coexist. In a few instances, this domain has been recruited by other proteins in both bacteria and animals through domain shuffling.
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25
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Santiago M, Ramírez-Sarmiento CA, Zamora RA, Parra LP. Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Front Microbiol 2016; 7:1408. [PMID: 27667987 PMCID: PMC5016527 DOI: 10.3389/fmicb.2016.01408] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 08/25/2016] [Indexed: 11/17/2022] Open
Abstract
Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.
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Affiliation(s)
- Margarita Santiago
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Universidad de ChileSantiago, Chile
| | - César A. Ramírez-Sarmiento
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Ricardo A. Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
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26
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Claisse G, Feller G, Bonneau M, Da Lage JL. A single amino-acid substitution toggles chloride dependence of the alpha-amylase paralog amyrel in Drosophila melanogaster and Drosophila virilis species. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 75:70-77. [PMID: 27312592 DOI: 10.1016/j.ibmb.2016.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 06/01/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
In animals, most α-amylases are chloride-dependent enzymes. A chloride ion is required for allosteric activation and is coordinated by one asparagine and two arginine side chains. Whereas the asparagine and one arginine are strictly conserved, the main chloride binding arginine is replaced by a glutamine in some rare instances, resulting in the loss of chloride binding and activation. Amyrel is a distant paralogue of α-amylase in Diptera, which was not characterized biochemically to date. Amyrel shows both substitutions depending on the species. In Drosophila melanogaster, an arginine is present in the sequence but in Drosophila virilis, a glutamine occurs at this position. We have investigated basic enzymological parameters and the dependence to chloride of Amyrel of both species, produced in yeast, and in mutants substituting arginine to glutamine or glutamine to arginine. We found that the amylolytic activity of Amyrel is about thirty times weaker than the classical Drosophila α-amylase, and that the substitution of the arginine by a glutamine in D. melanogaster suppressed the chloride-dependence but was detrimental to activity. In contrast, changing the glutamine into an arginine rendered D. virilis Amyrel chloride-dependent, and interestingly, significantly increased its catalytic efficiency. These results show that the chloride ion is not mandatory for Amyrel but stimulates the reaction rate. The possible phylogenetic origin of the arginine/glutamine substitution is also discussed.
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Affiliation(s)
- Gaëlle Claisse
- UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, F-91198 Gif-sur-Yvette, France; Univ. Paris-Sud, F-91405 Orsay Cedex, France
| | - Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Magalie Bonneau
- UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, F-91198 Gif-sur-Yvette, France; Univ. Paris-Sud, F-91405 Orsay Cedex, France
| | - Jean-Luc Da Lage
- UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, F-91198 Gif-sur-Yvette, France; Univ. Paris-Sud, F-91405 Orsay Cedex, France.
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27
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Závodszky P, Hajdú I. Evolution of the concept of conformational dynamics of enzyme functions over half of a century: A personal view. Biopolymers 2016; 99:263-9. [PMID: 23348674 DOI: 10.1002/bip.22159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023]
Abstract
To most physicists, it was always evident that conformational fluctuation is an inherent property of all molecules. Its existence in proteins was mentioned first by Linderström-Lang and Schellman in 1959 based on their hydrogen-deuterium exchange experiments. The "induced fit" mechanism to explain ligand-induced conformational changes was suggested by Koshland in 1958. Straub combined these two concepts in his "fluctuation fit" theory in 1964. The era of protein X-ray crystallography imposed a static view of protein structures. With proteins becoming accessible to NMR analysis, conformational dynamics could be mapped, and a new wave of dynamic interpretation of enzymatic catalysis and molecular recognition appeared. Energy landscapes, energy funnels, conformational selection, conformational distribution shifts are now frequent terms in interpreting biomolecular recognition and enzymatic catalysis. All these interpretations are based on the concept that evolution uses the conformational fluctuations of enzymes to develop efficient and dynamic catalytic machines. In a resurrection of the original "fluctuation fit" concept, it is generally recognized now that spatial and temporal events of catalysis are equally important to describe its mechanism. This special issue, dedicated to the memory of Henryk Eisenberg, prompted us to look back at the last 50 years of development of a concept that-like other important concepts-appeared, evolved and became accepted during the period covered by the scientific lifespan of Henryk.
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Affiliation(s)
- Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1113, Budapest, Hungary.
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Yang J, Li L, Xiao Y, Li J, Long L, Wang F, Zhang S. Identification and thermoadaptation engineering of thermostability conferring residue of deep sea bacterial α-amylase AMY121. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Arcus VL, Prentice EJ, Hobbs JK, Mulholland AJ, Van der Kamp MW, Pudney CR, Parker EJ, Schipper LA. On the Temperature Dependence of Enzyme-Catalyzed Rates. Biochemistry 2016; 55:1681-8. [DOI: 10.1021/acs.biochem.5b01094] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Vickery L. Arcus
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Erica J. Prentice
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Joanne K. Hobbs
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
| | | | | | - Christopher R. Pudney
- Department
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Emily J. Parker
- Biomolecular
Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand
| | - Louis A. Schipper
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
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30
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Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures. J Theor Biol 2015; 383:130-7. [DOI: 10.1016/j.jtbi.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/21/2015] [Accepted: 07/16/2015] [Indexed: 11/21/2022]
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31
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Improving the Thermostability and Activity of a Thermophilic Subtilase by Incorporating Structural Elements of Its Psychrophilic Counterpart. Appl Environ Microbiol 2015; 81:6302-13. [PMID: 26150464 DOI: 10.1128/aem.01478-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/29/2015] [Indexed: 11/20/2022] Open
Abstract
The incorporation of the structural elements of thermostable enzymes into their less stable counterparts is generally used to improve enzyme thermostability. However, the process of engineering enzymes with both high thermostability and high activity remains an important challenge. Here, we report that the thermostability and activity of a thermophilic subtilase were simultaneously improved by incorporating structural elements of a psychrophilic subtilase. There were 64 variable regions/residues (VRs) in the alignment of the thermophilic WF146 protease, mesophilic sphericase, and psychrophilic S41. The WF146 protease was subjected to systematic mutagenesis, in which each of its VRs was replaced with those from S41 and sphericase. After successive rounds of combination and screening, we constructed the variant PBL5X with eight amino acid residues from S41. The half-life of PBL5X at 85°C (57.1 min) was approximately 9-fold longer than that of the wild-type (WT) WF146 protease (6.3 min). The substitutions also led to an increase in the apparent thermal denaturation midpoint temperature (Tm) of the enzyme by 5.5°C, as determined by differential scanning calorimetry. Compared to the WT, PBL5X exhibited high caseinolytic activity (25 to 95°C) and high values of Km and kcat (25 to 80°C). Our study may provide a rational basis for developing highly stable and active enzymes, which are highly desired in industrial applications.
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Chloride Activated Halophilic α-Amylase from Marinobacter sp. EMB8: Production Optimization and Nanoimmobilization for Efficient Starch Hydrolysis. Enzyme Res 2015; 2015:859485. [PMID: 25667773 PMCID: PMC4312637 DOI: 10.1155/2015/859485] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 11/23/2022] Open
Abstract
Halophiles have been perceived as potential source of novel enzymes in recent years. The interest emanates from their ability to catalyze efficiently under high salt and organic solvents. Present work encompasses production optimization and nanoimmobilization of an α-amylase from moderately halophilic Marinobacter sp. EMB8. Media ingredients and culture conditions were optimized by “one-at-a-time approach.” Starch was found to be the best carbon source at 5% (w/v) concentration. Glucose acted as catabolic repressor for amylase production. Salt proved critical for amylase production and maximum production was attained at 5% (w/v) NaCl. Optimization of various culture parameters resulted in 48.0 IU/mL amylase production, a 12-fold increase over that of unoptimized condition (4.0 IU/mL). α-Amylase was immobilized on 3-aminopropyl functionalized silica nanoparticles using glutaraldehyde as cross-linking agent. Optimization of various parameters resulted in 96% immobilization efficiency. Starch hydrolyzing efficiency of immobilized enzyme was comparatively better. Immobilized α-amylase retained 75% of its activity after 5th cycle of repeated use.
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33
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Molecular cloning and biochemical characterization of a novel cold-adapted alpha-amylase with multiple extremozyme characteristics. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Romero-Romero S, Costas M, Rodríguez-Romero A, Fernández-Velasco DA. Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp01599e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The reversible thermal unfolding of oligomeric TIM barrels results from a delicate balance of physicochemical properties related to the sequence, the native and unfolded states and the transition between them.
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Affiliation(s)
- Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas
- Departamento de Bioquímica
- Facultad de Medicina
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica
- Departamento de Fisicoquímica
- Facultad de Química
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
| | - Adela Rodríguez-Romero
- Laboratorio de Química de Biomacromoléculas 3
- Departamento de Química de Biomacromoléculas
- Instituto de Química
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas
- Departamento de Bioquímica
- Facultad de Medicina
- Universidad Nacional Autónoma de México
- 04510 Ciudad de México
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Commin C, Aumont-Nicaise M, Claisse G, Feller G, Da Lage JL. Enzymatic characterization of recombinant α-amylase in the Drosophila melanogaster species subgroup: is there an effect of specialization on digestive enzyme? Genes Genet Syst 2014; 88:251-9. [PMID: 24463528 DOI: 10.1266/ggs.88.251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We performed a comparative study on the enzymological features of purified recombinant α-amylase of three species belonging to the Drosophila melanogaster species subgroup: D. melanogaster, D. erecta and D. sechellia. D. erecta and D. sechellia are specialist species, with host plant Pandanus candelabrum (Pandanaceae) and Morinda citrifolia (Rubiaceae), respectively. The temperature optima were around 57-60℃ for the three species. The pH optima were 7.2 for D. melanogaster, 8.2 for D. erecta and 8.5 for D. sechellia. The kcat and Km were also estimated for each species with different substrates. The specialist species D. erecta and D. sechellia display a higher affinity for starch than D. melanogaster. α-Amylase activity is higher on starch than on glycogen in all species. α-Amylases of D. erecta and D. sechellia have a higher activity on maltooligosaccharides (G6 and G7) than on starch, contrary to D. melanogaster. Such differences in the enzymological features between the species might reflect adaptation to different ecological niches and feeding habits.
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Affiliation(s)
- Céline Commin
- UPR 9034 Evolution, Génomes et Spéciation, CNRS, F-91198 Gif-sur-Yvette, France and Université Paris-Sud
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Hiteshi K, Gupta R. Thermal adaptation of α-amylases: a review. Extremophiles 2014; 18:937-44. [DOI: 10.1007/s00792-014-0674-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 07/06/2014] [Indexed: 11/24/2022]
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Sigtryggsdóttir ÁR, Papaleo E, Thorbjarnardóttir SH, Kristjánsson MM. Flexibility of cold- and heat-adapted subtilisin-like serine proteinases evaluated with fluorescence quenching and molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:705-12. [DOI: 10.1016/j.bbapap.2014.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/04/2014] [Accepted: 02/12/2014] [Indexed: 11/24/2022]
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Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149-70. [PMID: 23807207 PMCID: PMC11114072 DOI: 10.1007/s00018-013-1388-z] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 05/27/2013] [Indexed: 10/26/2022]
Abstract
α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia,
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Roman EA, Faraj SE, Cousido-Siah A, Mitschler A, Podjarny A, Santos J. Frataxin from Psychromonas ingrahamii as a model to study stability modulation within the CyaY protein family. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1168-80. [PMID: 23429177 DOI: 10.1016/j.bbapap.2013.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/26/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
Adaptation of life to low temperatures influences both protein stability and flexibility. Thus, proteins from psychrophilic organisms are excellent models to study relations between these properties. Here we focused on frataxin from Psychromonas ingrahamii (pFXN), an extreme psychrophilic sea ice bacterium that can grow at temperatures as low as -12°C. This α/β protein is highly conserved and plays a key role in iron homeostasis as an iron chaperone. In contrast to other frataxin homologs, chemical and temperature unfolding experiments showed that the thermodynamic stability of pFXN is strongly modulated by pHs: ranging from 5.5±0.9 (pH6.0) to 0.9±0.3kcalmol(-1) (pH8.0). This protein was crystallized and its X-ray structure solved at 1.45Å. Comparison of B-factor profiles between Escherichia coli and P. ingrahamii frataxin variants (51% of identity) suggests that, although both proteins share the same structural features, their flexibility distribution is different. Molecular dynamics simulations showed that protonation of His44 or His67 in pFXN lowers the mobility of regions encompassing residues 20-30 and the C-terminal end, probably through favorable electrostatic interactions with residues Asp27, Glu42 and Glu99. Since the C-terminal end of the protein is critical for the stabilization of the frataxin fold, the predictions presented may be reporting on the microscopic origin of the decrease in global stability produced near neutral pH in the psychrophilic variant. We propose that suboptimal electrostatic interactions may have been an evolutionary strategy for the adaptation of frataxin flexibility and function to cold environments.
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Affiliation(s)
- Ernesto A Roman
- Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
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Puspasari F, Radjasa OK, Noer AS, Nurachman Z, Syah YM, van der Maarel M, Dijkhuizen L, Janeček S, Natalia D. Raw starch-degrading α-amylase from Bacillus aquimaris MKSC 6.2: isolation and expression of the gene, bioinformatics and biochemical characterization of the recombinant enzyme. J Appl Microbiol 2012; 114:108-20. [PMID: 23020612 DOI: 10.1111/jam.12025] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 08/18/2012] [Accepted: 08/29/2012] [Indexed: 11/30/2022]
Abstract
AIMS The aims were to isolate a raw starch-degrading α-amylase gene baqA from Bacillus aquimaris MKSC 6.2, and to characterize the gene product through in silico study and its expression in Escherichia coli. METHODS AND RESULTS A 1539 complete open reading frame of a starch-degrading α-amylase gene baqA from B. aquimaris MKSC 6·2 has been determined by employing PCR and inverse PCR techniques. Bioinformatics analysis revealed that B. aquimaris MKSC 6.2 α-amylase (BaqA) has no starch-binding domain, and together with a few putative α-amylases from bacilli may establish a novel GH13 subfamily most closely related to GH13_1. Two consecutive tryptophans (Trp201 and Trp202, BaqA numbering) were identified as a sequence fingerprint of this novel GH13 subfamily. Escherichia coli cells produced the recombinant BaqA protein as inclusion bodies. The refolded recombinant BaqA protein degraded raw cassava and corn starches, but exhibited no activity with soluble starch. CONCLUSIONS A novel raw starch-degrading B. aquimaris MKSC 6.2 α-amylase BaqA is proposed to be a member of new GH13 subfamily. SIGNIFICANCE AND IMPACT OF THE STUDY This study has contributed to the overall knowledge and understanding of amylolytic enzymes that are able to bind and digest raw starch directly.
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Affiliation(s)
- F Puspasari
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
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