1
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Alavi Z, Casanova-Morales N, Quiroga-Roger D, Wilson CAM. Towards the understanding of molecular motors and its relationship with local unfolding. Q Rev Biophys 2024; 57:e7. [PMID: 38715547 DOI: 10.1017/s0033583524000052] [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] [Indexed: 06/14/2024]
Abstract
Molecular motors are machines essential for life since they convert chemical energy into mechanical work. However, the precise mechanism by which nucleotide binding, catalysis, or release of products is coupled to the work performed by the molecular motor is still not entirely clear. This is due, in part, to a lack of understanding of the role of force in the mechanical-structural processes involved in enzyme catalysis. From a mechanical perspective, one promising hypothesis is the Haldane-Pauling hypothesis which considers the idea that part of the enzymatic catalysis is strain-induced. It suggests that enzymes cannot be efficient catalysts if they are fully complementary to the substrates. Instead, they must exert strain on the substrate upon binding, using enzyme-substrate energy interaction (binding energy) to accelerate the reaction rate. A novel idea suggests that during catalysis, significant strain energy is built up, which is then released by a local unfolding/refolding event known as 'cracking'. Recent evidence has also shown that in catalytic reactions involving conformational changes, part of the heat released results in a center-of-mass acceleration of the enzyme, raising the possibility that the heat released by the reaction itself could affect the enzyme's integrity. Thus, it has been suggested that this released heat could promote or be linked to the cracking seen in proteins such as adenylate kinase (AK). We propose that the energy released as a consequence of ligand binding/catalysis is associated with the local unfolding/refolding events (cracking), and that this energy is capable of driving the mechanical work.
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Affiliation(s)
- Zahra Alavi
- Department of Physics, Loyola Marymount University, Los Angeles, CA, USA
| | | | - Diego Quiroga-Roger
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
| | - Christian A M Wilson
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
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2
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Recio M, de la Torre J, Daddaoua A, Udaondo Z, Duque E, Gavira JA, López‐Sánchez C, Ramos JL. Characterization of an extremophile bacterial acid phosphatase derived from metagenomics analysis. Microb Biotechnol 2024; 17:e14404. [PMID: 38588312 PMCID: PMC11001196 DOI: 10.1111/1751-7915.14404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 04/10/2024] Open
Abstract
Acid phosphatases are enzymes that play a crucial role in the hydrolysis of various organophosphorous molecules. A putative acid phosphatase called FS6 was identified using genetic profiles and sequences from different environments. FS6 showed high sequence similarity to type C acid phosphatases and retained more than 30% of consensus residues in its protein sequence. A histidine-tagged recombinant FS6 produced in Escherichia coli exhibited extremophile properties, functioning effectively in a broad pH range between 3.5 and 8.5. The enzyme demonstrated optimal activity at temperatures between 25 and 50°C, with a melting temperature of 51.6°C. Kinetic parameters were determined using various substrates, and the reaction catalysed by FS6 with physiological substrates was at least 100-fold more efficient than with p-nitrophenyl phosphate. Furthermore, FS6 was found to be a decamer in solution, unlike the dimeric forms of crystallized proteins in its family.
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Affiliation(s)
- Maria‐Isabel Recio
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
| | - Jesús de la Torre
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Pharmacy SchoolGranada UniversityGranadaSpain
| | - Zulema Udaondo
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Estrella Duque
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
| | - José Antonio Gavira
- Consejo Superior de Investigaciones Científicas, Instituto de Ciencias de la TierraGranadaSpain
| | - Carmen López‐Sánchez
- Consejo Superior de Investigaciones Científicas, Instituto de Ciencias de la TierraGranadaSpain
| | - Juan L. Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental ProtectionGranadaSpain
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3
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Zhang Y, Barberis M. Exploring cell cycle-mediated regulations of glycolysis in budding yeast. Front Microbiol 2023; 14:1270487. [PMID: 37886071 PMCID: PMC10598772 DOI: 10.3389/fmicb.2023.1270487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Coordination of cell cycle with metabolism exists in all cell types that grow by division. It serves to build a new cell, (i) fueling building blocks for the synthesis of proteins, nucleic acids, and membranes, and (ii) producing energy through glycolysis. Cyclin-dependent kinases (Cdks) play an essential role in this coordination, thereby in the regulation of cell division. Cdks are functional homologs across eukaryotes and are the engines that drive cell cycle events and the clocks that time them. Their function is counteracted by stoichiometric inhibitors; specifically, inhibitors of cyclin-cyclin dependent kinase (cyclin/Cdk) complexes allow for their activity at specific times. Here, we provide a new perspective about the yet unknown cell cycle mechanisms impacting on metabolism. We first investigated the effect of the mitotic cyclin/Cdk1 complex Cyclin B/Cdk1-functional homolog in mammalian cells of the budding yeast Clb2/Cdk1-on yeast metabolic enzymes of, or related to, the glycolysis pathway. Six glycolytic enzymes (Glk1, Hxk2, Pgi1, Fba1, Tdh1, and Pgk1) were subjected to in vitro Cdk-mediated phosphorylation assays. Glucose-6-phosphate dehydrogenase (Zwf1), the first enzyme in the pentose phosphate pathway that is important for NADPH production, and 6-phospho-fructo-2-kinase (Pfk27), which catalyzes fructose-2,6-bisphosphate synthesis, a key regulator of glycolysis, were also included in the study. We found that, among these metabolic enzymes, Fba1 and Pgk1 may be phosphorylated by Cdk1, in addition to the known Cdk1-mediated phosphorylation of Gph1. We then investigated the possible effect of Sic1, stoichiometric inhibitor of mitotic cyclin/Cdk1 complexes in budding yeast, on the activities of three most relevant glycolytic enzymes: Hxk2, Glk1, and Tdh1. We found that Sic1 may have a negative effect on Hxk2. Altogether, we reveal possible new routes, to be further explored, through which cell cycle may regulate cellular metabolism. Because of the functional homology of cyclin/Cdk complexes and their stoichiometric inhibitors across evolution, our findings may be relevant for the regulation of cell division in eukaryotes.
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Affiliation(s)
- Yanfei Zhang
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Matteo Barberis
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom
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4
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Xie T, Chen M, Nielsen J, Xia J. Multi-omics analyses of the transition to the Crabtree effect in S. cerevisiae reveals a key role for the citric acid shuttle. FEMS Yeast Res 2022; 22:6590040. [PMID: 35595470 DOI: 10.1093/femsyr/foac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/30/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022] Open
Abstract
The Crabtree effect in the yeast, Saccharomyces cerevisiae, has been extensively studied, but only few studies have analyzed the dynamic conditions across the critical specific growth rate where the Crabtree effect sets in. Here, we carried out a multi-omics analysis of S. cerevisiae undergoing a specific growth rate transition from 0.2 h-1 to 0.35 h-1. The extracellular metabolome, the transcriptome and the proteome were analyzed in an 8-hour transition period after the specific growth rate shifted from 0.2 h-1 to 0.35 h-1. The changing trends of both the transcriptome and proteome were analyzed using principal component analysis, which showed that the transcriptome clustered together after 60 min, while the proteome reached steady-state much later. Focusing on central carbon metabolism, we analyzed both the changes in the transcriptome and proteome, and observed an interesting changing pattern in the tricarboxylic acid (TCA) pathway, which indicates an important role for citric acid shuttling across the mitochondrial membrane for α-ketoglutarate accumulation during the transition from respiratory to respiro-fermentative metabolism. This was supported by a change in the oxaloacetate and malate shuttle. Together, our findings shed new light into the onset of the Crabtree effect in S. cerevisiae.
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Affiliation(s)
- Tingting Xie
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Min Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE41296, Sweden.,BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen N, Denmark
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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5
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Salminen L, Karjalainen E, Aseyev V, Tenhu H. Phase Separation of Aqueous Poly(diisopropylaminoethyl methacrylate) upon Heating. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5135-5148. [PMID: 34752116 PMCID: PMC9069861 DOI: 10.1021/acs.langmuir.1c02224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Poly(diisopropylaminoethyl methacrylate) (PDPA) is a pH- and thermally responsive water-soluble polymer. This study deepens the understanding of its phase separation behavior upon heating. Phase separation upon heating was investigated in salt solutions of varying pH and ionic strength. The effect of the counterion on the phase transition upon heating is clearly demonstrated for chloride-, phosphate-, and citrate-anions. Phase separation did not occur in pure water. The buffer solutions exhibited similar cloud points, but phase separation occurred in different pH ranges and with different mechanisms. The solution behavior of a block copolymer comprising poly(dimethylaminoethyl methacrylate) (PDMAEMA) and PDPA was investigated. Since the PDMAEMA and PDPA blocks phase separate within different pH- and temperature ranges, the block copolymer forms micelle-like structures at high temperature or pH.
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Affiliation(s)
- Linda Salminen
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtasen aukio
1, FIN-00014 HY Helsinki, Finland
| | - Erno Karjalainen
- VTT
Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Vladimir Aseyev
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtasen aukio
1, FIN-00014 HY Helsinki, Finland
| | - Heikki Tenhu
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtasen aukio
1, FIN-00014 HY Helsinki, Finland
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6
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Wang Y, Mittermaier AK. Characterizing Bi-substrate Enzyme Kinetics at High Resolution by 2D-ITC. Anal Chem 2021; 93:12723-12732. [PMID: 34514786 DOI: 10.1021/acs.analchem.1c02705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
There is growing interest in using isothermal titration calorimetry (ITC) to characterize enzyme kinetics by measuring the heat produced or absorbed by catalysis in real time. Since virtually all chemical reactions are associated with changes in enthalpy, ITC represents a robust and nearly universal experimental approach. Nevertheless, there are technical challenges that limit ITC's applicability. For instance, the full kinetic characterization of enzymes with two substrates (bi-substrate enzymes), which comprise the majority of known examples, requires a series of experiments to be performed as the concentrations of both substrates are varied. This is a time-consuming and expensive process using current ITC methods since many (>5) individual experiments must be performed independently to obtain a sufficient quantity of data. We have developed a new ITC method, which we term 2D-ITC, which maps the reaction velocity as a function of two substrate concentrations in a single, roughly 2 h long experiment. This method provides a level of detail that rivals or exceeds any existing enzyme assay, as a single experiment generates on the order of 7000 catalytic rate measurements. In a proof-of-principle application to rabbit muscle pyruvate kinase (rMPK), the method correctly identified the enzyme's random sequential mechanism and allosteric catalytic suppression by the amino acid phenylalanine (Phe). Unexpectedly, we found that while Phe reduces affinity for the substrate phosphoenolpyruvate, a known phenomenon, it also alleviates inhibition by the reaction product ATP, which had not been reported previously. Given the relative abundance of ATP in the cell, this opposing effect is expected to have a substantial impact on rMPK activity.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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7
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Cao W, Zhao W, Yang B, Wang X, Shen Y, Wei T, Qin W, Li Z, Bao X. Proteomic analysis revealed the roles of YRR1 deletion in enhancing the vanillin resistance of Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:142. [PMID: 34301255 PMCID: PMC8305865 DOI: 10.1186/s12934-021-01633-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/15/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Vanillin is one of the important phenolic inhibitors in Saccharomyces cerevisiae for bioconversion of lignocellulosic materials and has been reported to inhibit the translation process in cells. In our previous studies, it was confirmed that the deletion of the transcription factor gene YRR1 enhanced vanillin resistance by promoting some translation-related processes at the transcription level. In this work, we investigated the effects of proteomic changes upon induction of vanillin stress and deletion of YRR1 to provide unique perspectives from a transcriptome analysis for comprehending the mechanisms of YRR1 deletion in the protective response of yeast to vanillin. RESULTS In wild-type cells, vanillin reduced two dozens of ribosomal proteins contents while upregulated proteins involved in glycolysis, oxidative phosphorylation, and the pentose phosphate pathway in cells. The ratios of NADPH/NADP+ and NADH/NAD+ were increased when cells responded to vanillin stress. The differentially expressed proteins perturbed by YRR1 deletion were much more abundant than and showed no overlaps with transcriptome changes, indicating that Yrr1 affects the synthesis of certain proteins. Forty-eight of 112 upregulated proteins were involved in the stress response, translational and transcriptional regulation. YRR1 deletion increased the expression of HAA1-encoding transcriptional activator, TMA17-encoding proteasome assembly chaperone and MBF1-encoding coactivator at the protein level, as confirmed by ELISA. Cultivation data showed that the overexpression of HAA1 and TMA17 enhanced resistance to vanillin in S. cerevisiae. CONCLUSIONS Cells conserve energy by decreasing the content of ribosomal proteins, producing more energy and NAD(P)H for survival in response to vanillin stress. Yrr1 improved vanillin resistance by increasing the protein quantities of Haa1, Tma17 and Mbf1. These results showed the response of S. cerevisiae to vanillin and how YRR1 deletion increases vanillin resistance at the protein level. These findings may advance our knowledge of how YRR1 deletion protects yeast from vanillin stress and offer novel targets for genetic engineering of designing inhibitor-resistant ethanologenic yeast strains.
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Affiliation(s)
- Wenyan Cao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Weiquan Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Bolun Yang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Xinning Wang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China.
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Tiandi Wei
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Zailu Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
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8
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Zhao Y, Li J, Su R, Liu Y, Wang J, Deng Y. Effect of magnesium ions on glucaric acid production in the engineered Saccharomyces cerevisiae. J Biotechnol 2021; 332:61-71. [PMID: 33812897 DOI: 10.1016/j.jbiotec.2021.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/16/2021] [Accepted: 03/25/2021] [Indexed: 11/27/2022]
Abstract
Glucaric acid has been successfully produced in Escherichia coli and fungus. Here, we first analyzed the effects of different metal ions on glucaric acid production in the engineered Saccharomyces cerevisiae Bga-3 strain harboring the glucaric acid synthesis pathway. We found that magnesium ions could promote the growth rate of yeast cells, and thus, increase the glucaric acid production by elevating the glucose and myo-inositol utilization of Bga-3 strain. RNA-Seq transcriptome analysis results showed that the upregulation of genes involved in the gluconeogenesis pathway, as well as the downregulation of genes associated with the glycolysis pathway and pentose phosphate pathway in response to MgCl2 were all benefit for the enhancement of the glucose-6-phosphate flux, which was the precursor for myo-inositol and glucaric acid. In addition, we found that MgCl2 could also increase the activity of MIOX4, which was also crucial for glucaric acid synthesis. At last, a final glucaric acid titer of 10.6 g/L, the highest reported titer, was achieved in the fed-batch fermentation using a 5-L bioreactor by adding 100 mM MgCl2. Our findings will provide a new way of promoting the production of other chemicals in the engineered yeast cells.
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Affiliation(s)
- Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jie Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Ruifang Su
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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9
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Vogel K, Greinert T, Reichard M, Held C, Harms H, Maskow T. Thermodynamics and Kinetics of Glycolytic Reactions. Part II: Influence of Cytosolic Conditions on Thermodynamic State Variables and Kinetic Parameters. Int J Mol Sci 2020; 21:ijms21217921. [PMID: 33113841 PMCID: PMC7663428 DOI: 10.3390/ijms21217921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 01/22/2023] Open
Abstract
For systems biology, it is important to describe the kinetic and thermodynamic properties of enzyme-catalyzed reactions and reaction cascades quantitatively under conditions prevailing in the cytoplasm. While in part I kinetic models based on irreversible thermodynamics were tested, here in part II, the influence of the presumably most important cytosolic factors was investigated using two glycolytic reactions (i.e., the phosphoglucose isomerase reaction (PGI) with a uni-uni-mechanism and the enolase reaction with an uni-bi-mechanism) as examples. Crowding by macromolecules was simulated using polyethylene glycol (PEG) and bovine serum albumin (BSA). The reactions were monitored calorimetrically and the equilibrium concentrations were evaluated using the equation of state ePC-SAFT. The pH and the crowding agents had the greatest influence on the reaction enthalpy change. Two kinetic models based on irreversible thermodynamics (i.e., single parameter flux-force and two-parameter Noor model) were applied to investigate the influence of cytosolic conditions. The flux-force model describes the influence of cytosolic conditions on reaction kinetics best. Concentrations of magnesium ions and crowding agents had the greatest influence, while temperature and pH-value had a medium influence on the kinetic parameters. With this contribution, we show that the interplay of thermodynamic modeling and calorimetric process monitoring allows a fast and reliable quantification of the influence of cytosolic conditions on kinetic and thermodynamic parameters.
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Affiliation(s)
- Kristina Vogel
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
- Institute for Drug Development, Leipzig University Medical School, Leipzig University, Bruederstr. 34, 04103 Leipzig, Germany
| | - Thorsten Greinert
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany;
| | - Monique Reichard
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
| | - Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany;
- Correspondence: (C.H.); (T.M.)
| | - Hauke Harms
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
| | - Thomas Maskow
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
- Correspondence: (C.H.); (T.M.)
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10
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Udaondo Z, Duque E, Daddaoua A, Caselles C, Roca A, Pizarro-Tobias P, Ramos JL. Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries. Environ Microbiol 2020; 22:3561-3571. [PMID: 32564477 DOI: 10.1111/1462-2920.15138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022]
Abstract
Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr-B-Phos, Pfr-C-Phos and Pfr-GAP, to describe the three groups of acid phosphatases. These sequence-based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.
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Affiliation(s)
- Zulema Udaondo
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Estrella Duque
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Carlos Caselles
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | | | | | - Juan L Ramos
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
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11
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Wang Y, Guan J, Di Trani JM, Auclair K, Mittermaier AK. Inhibition and Activation of Kinases by Reaction Products: A Reporter-Free Assay. Anal Chem 2019; 91:11803-11811. [PMID: 31426630 DOI: 10.1021/acs.analchem.9b02456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Kinases are widely distributed in nature and are implicated in many human diseases. Thus, an understanding of their activity and regulation is of fundamental importance. Several kinases are known to be inhibited by ADP. However, thorough investigation of this phenomenon is hampered by the lack of a simple and effective assay for studying this inhibition. We now present a quick, general approach for measuring the effects of reaction products on kinase activity. The method, based on isothermal titration calorimetry, is the first universal, reporter-free, continuous assay for probing kinase inhibition or activation by ADP. In applications to an aminoglycoside phosphotransferase [APH(3')-IIIa] and pantothenate kinases from Escherichia coli (EcPanK) and Pseudomonas aeruginosa (PaPanK), we found ADP to be an efficient inhibitor of all three kinases, with inhibition constant (Ki) values similar to or lower than the Michaelis-Menten constant (Km) values of ATP. Interestingly, ADP was an activator at low concentrations and an inhibitor at high concentrations for EcPanK. This unusual effect was quantitatively modeled and attributed to cooperative interactions between the two subunits of the dimeric enzyme. Importantly, our results suggest that, at typical bacterial intracellular concentrations of ATP and ADP (approximately 1.5 mM and 180 μM, respectively), all three kinases are partially inhibited by ADP, allowing enzyme activity to rapidly respond to changes in the levels of both metabolites.
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Affiliation(s)
- Yun Wang
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Jinming Guan
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Justin M Di Trani
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Anthony K Mittermaier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
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12
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Minari K, de Azevedo ÉC, Kiraly VTR, Batista FAH, de Moraes FR, de Melo FA, Nascimento AS, Gava LM, Ramos CHI, Borges JC. Thermodynamic analysis of interactions of the Hsp90 with adenosine nucleotides: A comparative perspective. Int J Biol Macromol 2019; 130:125-138. [PMID: 30797004 DOI: 10.1016/j.ijbiomac.2019.02.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
Hsp90s are key proteins in cellular homeostasis since they interact with many client proteins. Several studies indicated that Hsp90s are potential targets for treating diseases, such as cancer or malaria. It has been shown that Hsp90s from different organisms have peculiarities despite their high sequence identity. Therefore, a detailed comparative analysis of several Hsp90 proteins is relevant to the overall understanding of their activity. Accordingly, the goal of this work was to evaluate the interaction of either ADP or ATP with recombinant Hsp90s from different organisms (human α and β isoforms, Plasmodium falciparum, Leishmania braziliensis, yeast and sugarcane) by isothermal titration calorimetry. The measured thermodynamic signatures of those interactions indicated that despite the high identity among all Hsp90s, they have specific thermodynamic characteristics. Specifically, the interactions with ADP are driven by enthalpy but are opposed by entropy, whereas the interaction with ATP is driven by both enthalpy and entropy. Complimentary structural and molecular dynamics studies suggested that specific interactions with ADP that differ from those with ATP may contribute to the observed enthalpies and entropies. Altogether, the data suggest that selective inhibition may be more easily achieved using analogues of the Hsp90-ADP bound state than those of Hsp90-ATP bound state.
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Affiliation(s)
- Karine Minari
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP 13566-590, Brazil; Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | - Érika Chang de Azevedo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP 13560-970, Brazil
| | | | | | - Fábio Rogério de Moraes
- Biosciences, Languages, and Exact Sciences Institute, Multiuser Center for Biological Innovation (CMIB), São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
| | - Fernando Alves de Melo
- Biosciences, Languages, and Exact Sciences Institute, Multiuser Center for Biological Innovation (CMIB), São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
| | | | - Lisandra Marques Gava
- Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | | | - Júlio César Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP 13566-590, Brazil.
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13
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Quinn CF, Hansen LD. Enzyme Kinetics Determined by Single-Injection Isothermal Titration Calorimetry. Methods Mol Biol 2019; 1964:241-249. [PMID: 30929247 DOI: 10.1007/978-1-4939-9179-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This chapter describes how to collect Michaelis-Menten kinetic data on an enzyme-catalyzed reaction with the isothermal titration calorimetry (ITC) and the single-injection method. ITC measures the heat rate which is directly proportional to the reaction rate. The enthalpy change (ΔrH), Km, kcat, and vmax are determined in a single assay that does not require labeling or immobilization.
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Affiliation(s)
| | - Lee D Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
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14
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Wakai S. Biochemical and thermodynamic analyses of energy conversion in extremophiles. Biosci Biotechnol Biochem 2018; 83:49-64. [PMID: 30381012 DOI: 10.1080/09168451.2018.1538769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the "limits of life". Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase.
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Affiliation(s)
- Satoshi Wakai
- a Graduate School of Science, Technology and Innovation , Kobe University , Kobe , Japan
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15
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Hariharan P, Guan L. Thermodynamic cooperativity of cosubstrate binding and cation selectivity of Salmonella typhimurium MelB. J Gen Physiol 2017; 149:1029-1039. [PMID: 29054867 PMCID: PMC5677108 DOI: 10.1085/jgp.201711788] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 08/17/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
The melibiose symporter MelB couples melibiose transport to that of cations such as Na+. Hariharan and Guan show that the binding of Na+ and melibiose is thermodynamically cooperative and that Na+ coupling is based on ion concentrations and competitive binding, but not ion selectivity. The Na+-coupled melibiose symporter MelB, which can also be coupled to H+ or Li+ transport, is a prototype for the glycoside-pentoside-hexuronide:cation symporter family. Although the 3-D x-ray crystal structure of Salmonella typhimurium MelB (MelBSt) has been determined, the symport mechanisms for the obligatory coupled transport are not well understood. Here, we apply isothermal titration calorimetry to determine the energetics of Na+ and melibiose binding to MelBSt, as well as protonation of this transporter. Studies of the thermodynamic cycle for the formation of the Na+–MelBSt–melibiose ternary complex at pH 7.45 reveal that the binding of Na+ and melibiose is cooperative. The binding affinity for one substrate (Na+ or melibiose) is increased by the presence of the other by about eightfold. The coupling free energies (ΔΔG) of either substrate binding are ∼5 kJ/mol, and binding of both substrates releases a free energy of ∼35 kJ/mol. Measurements of the Na+-binding enthalpy at three different pH values, including the pKa value of MelB, indicate that the binding of one Na+ displaces one H+ per MelBSt molecule. In addition, the absolute dissociation constants for Na+ and H+, determined by competitive binding, show that MelBSt is selective for H+ over Na+ by ∼1,000-fold at a pKa of 6.25. Thus, the Na+ coupling in MelBSt is based not on ion selectivity but on ion concentrations and competitive binding because of a much higher Na+ concentration under physiological conditions. Such a selectivity feature seems to be common for membrane transport proteins that can bind both H+ and Na+ at a common site.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
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16
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Schön A, Clarkson BR, Jaime M, Freire E. Temperature stability of proteins: Analysis of irreversible denaturation using isothermal calorimetry. Proteins 2017; 85:2009-2016. [PMID: 28722205 DOI: 10.1002/prot.25354] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 01/17/2023]
Abstract
The structural stability of proteins has been traditionally studied under conditions in which the folding/unfolding reaction is reversible, since thermodynamic parameters can only be determined under these conditions. Achieving reversibility conditions in temperature stability experiments has often required performing the experiments at acidic pH or other nonphysiological solvent conditions. With the rapid development of protein drugs, the fastest growing segment in the pharmaceutical industry, the need to evaluate protein stability under formulation conditions has acquired renewed urgency. Under formulation conditions and the required high protein concentration (∼100 mg/mL), protein denaturation is irreversible and frequently coupled to aggregation and precipitation. In this article, we examine the thermal denaturation of hen egg white lysozyme (HEWL) under irreversible conditions and concentrations up to 100 mg/mL using several techniques, especially isothermal calorimetry which has been used to measure the enthalpy and kinetics of the unfolding and aggregation/precipitation at 12°C below the transition temperature measured by DSC. At those temperatures the rate of irreversible protein denaturation and aggregation of HEWL is measured to be on the order of 1 day-1 . Isothermal calorimetry appears a suitable technique to identify buffer formulation conditions that maximize the long term stability of protein drugs.
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Affiliation(s)
- Arne Schön
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Benjamin R Clarkson
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Maria Jaime
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Ernesto Freire
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
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17
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DFT-based prediction of reactivity of short-chain alcohol dehydrogenase. J Comput Aided Mol Des 2017; 31:587-602. [PMID: 28550607 PMCID: PMC5487757 DOI: 10.1007/s10822-017-0026-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/20/2017] [Indexed: 01/05/2023]
Abstract
The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, (S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2′ ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R2 = 0.93) and a good prediction of the reaction kinetics (R2 = 0.89). The observed relations were validated in prediction of log Keq obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.
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18
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19
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Qin W, Peng T, Gao Y, Wang F, Hu X, Wang K, Shi J, Li D, Ren J, Fan C. Catalysis-Driven Self-Thermophoresis of Janus Plasmonic Nanomotors. Angew Chem Int Ed Engl 2016; 56:515-518. [DOI: 10.1002/anie.201609121] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/07/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Weiwei Qin
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Tianhuan Peng
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yanjing Gao
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Fei Wang
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xiaocai Hu
- College of Chemistry and Chemical Engineering; Shanghai Jiaotong University; Shanghai 200240 China
| | - Kun Wang
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jiye Shi
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Di Li
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jicun Ren
- College of Chemistry and Chemical Engineering; Shanghai Jiaotong University; Shanghai 200240 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Centre; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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20
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Meurer F, Bobrownik M, Sadowski G, Held C. Standard Gibbs Energy of Metabolic Reactions: I. Hexokinase Reaction. Biochemistry 2016; 55:5665-5674. [DOI: 10.1021/acs.biochem.6b00471] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Meurer
- Laboratory
of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Maria Bobrownik
- Laboratory
of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Gabriele Sadowski
- Laboratory
of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christoph Held
- Laboratory
of Thermodynamics,
Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany
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21
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Frasca V. Using Isothermal Titration Calorimetry Techniques to Quantify Enzyme Kinetics. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1089/ind.2016.29040.vfr] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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23
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Kinetic analysis of gluconate phosphorylation by human gluconokinase using isothermal titration calorimetry. FEBS Lett 2015; 589:3548-55. [PMID: 26505675 DOI: 10.1016/j.febslet.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 11/22/2022]
Abstract
Gluconate is a commonly encountered nutrient, which is degraded by the enzyme gluconokinase to generate 6-phosphogluconate. Here we used isothermal titration calorimetry to study the properties of this reaction. ΔH, KM and kcat are reported along with substrate binding data. We propose that the reaction follows a ternary complex mechanism, with ATP binding first. The reaction is inhibited by gluconate, as it binds to an Enzyme-ADP complex forming a dead-end complex. The study exemplifies that ITC can be used to determine mechanisms of enzyme catalyzed reactions, for which it is currently not commonly applied.
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24
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Bianconi ML. Avoiding Buffer Interference in ITC Experiments: A Case Study from the Analysis of Entropy-Driven Reactions of Glucose-6-Phosphate Dehydrogenase. Methods Enzymol 2015; 567:237-56. [PMID: 26794357 DOI: 10.1016/bs.mie.2015.08.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Isothermal titration calorimetry (ITC) is a label-free technique that allows the direct determination of the heat absorbed or released in a reaction. Frequently used to determining binding parameters in biomolecular interactions, it is very useful to address enzyme-catalyzed reactions as both kinetic and thermodynamic parameters can be obtained. Since calorimetry measures the total heat effects of a reaction, it is important to consider the contribution of the heat of protonation/deprotonation that is possibly taking place. Here, we show a case study of the reaction catalyzed by the glucose-6-phosphate dehydrogenase (G6PD) from Leuconostoc mesenteroides. This enzyme is able to use either NAD(+) or NADP(+) as a cofactor. The reactions were done in five buffers of different enthalpy of protonation. Depending on the buffer used, the observed calorimetric enthalpy (ΔH(cal)) of the reaction varied from -22.93 kJ/mol (Tris) to 19.37 kJ/mol (phosphate) for the NADP(+)-linked reaction, and -11.67 kJ/mol (Tris) to 7.32 kcal/mol or 30.63 kJ/mol (phosphate) for the NAD(+) reaction. We will use this system as an example of how to extract proton-independent reaction enthalpies from kinetic data to ensure that the reported accurately represent the intrinsic heat of reaction.
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Affiliation(s)
- M Lucia Bianconi
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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25
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Abstract
The real-time power response inherent in an isothermal titration calorimetry (ITC) experiment provides an opportunity to directly analyze association kinetics, which, together with the conventional measurement of thermodynamic quantities, can provide an incredibly rich description of molecular binding in a single experiment. Here, we detail our application of this method, in which interactions occurring with relaxation times ranging from slightly below the instrument response time constant (12.5 s in this case) to as large as 600 s can be fully detailed in terms of both the thermodynamics and kinetics. In a binding titration scenario, in the most general case an injection can reveal an association rate constant (kon). Under more restrictive conditions, the instrument time constant-corrected power decay following each injection is simply an exponential decay described by a composite rate constant (kobs), from which both kon and the dissociation rate constant (koff) can be extracted. The data also support the viability of this exponential approach, for kon only, for a slightly larger set of conditions. Using a bimolecular RNA folding model and a protein-ligand interaction, we demonstrate and have internally validated this approach to experiment design, data processing, and error analysis. An updated guide to thermodynamic and kinetic regimes accessible by ITC is provided.
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26
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Enzyme kinetics determined by single-injection isothermal titration calorimetry. Methods 2015; 76:194-200. [DOI: 10.1016/j.ymeth.2014.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 01/25/2023] Open
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27
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Henao‐Escobar W, Domínguez‐Renedo O, Alonso‐Lomillo MA, Cascalheira JF, Dias‐Cabral AC, Arcos‐Martínez MJ. Characterization of a Disposable Electrochemical Biosensor Based on Putrescine Oxidase from
Micrococcus rubens
for the Determination of Putrescine. ELECTROANAL 2014. [DOI: 10.1002/elan.201400387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- W. Henao‐Escobar
- Department of Chemistry, Faculty of Sciences, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - O. Domínguez‐Renedo
- Department of Chemistry, Faculty of Sciences, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - M. A. Alonso‐Lomillo
- Department of Chemistry, Faculty of Sciences, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - J. F. Cascalheira
- CICS‐UBI – Health Sciences Research Centre, University of Beira Interior, 6200–506 Covilhã, Portugal
- Department of Chemistry, University of Beira Interior, 6200–001 Covilhã, Portugal
| | - A. C. Dias‐Cabral
- CICS‐UBI – Health Sciences Research Centre, University of Beira Interior, 6200–506 Covilhã, Portugal
- Department of Chemistry, University of Beira Interior, 6200–001 Covilhã, Portugal
| | - M. J. Arcos‐Martínez
- Department of Chemistry, Faculty of Sciences, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
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Moreno-García J, García-Martínez T, Moreno J, Mauricio JC. Proteins involved in flor yeast carbon metabolism under biofilm formation conditions. Food Microbiol 2014; 46:25-33. [PMID: 25475262 DOI: 10.1016/j.fm.2014.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
Abstract
A lack of sugars during the production of biologically aged wines after fermentation of grape must causes flor yeasts to metabolize other carbon molecules formed during fermentation (ethanol and glycerol, mainly). In this work, a proteome analysis involving OFFGEL fractionation prior to LC/MS detection was used to elucidate the carbon metabolism of a flor yeast strain under biofilm formation conditions (BFC). The results were compared with those obtained under non-biofilm formation conditions (NBFC). Proteins associated to processes such as non-fermentable carbon uptake, the glyoxylate and TCA cycles, cellular respiration and inositol metabolism were detected at higher concentrations under BFC than under the reference conditions (NBFC). This study constitutes the first attempt at identifying the flor yeast proteins responsible for the peculiar sensory profile of biologically aged wines. A better metabolic knowledge of flor yeasts might facilitate the development of effective strategies for improved production of these special wines.
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Affiliation(s)
- Jaime Moreno-García
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Teresa García-Martínez
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Juan Moreno
- Department of Agricultural Chemistry, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Marie Curie Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain
| | - Juan Carlos Mauricio
- Department of Microbiology, Agrifood Campus of International Excellence ceiA3, University of Cordoba, Severo Ochoa Building, Ctra. N-IV-A km 396, 14014 Cordoba, Spain.
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29
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Siddiqui KS, Ertan H, Charlton T, Poljak A, Daud Khaled A, Yang X, Marshall G, Cavicchioli R. Versatile peroxidase degradation of humic substances: Use of isothermal titration calorimetry to assess kinetics, and applications to industrial wastes. J Biotechnol 2014; 178:1-11. [DOI: 10.1016/j.jbiotec.2014.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/24/2014] [Accepted: 03/03/2014] [Indexed: 01/07/2023]
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30
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Zhao S, Zhao X, Zou H, Fu J, Du G, Zhou J, Chen J. Comparative proteomic analysis of Saccharomyces cerevisiae under different nitrogen sources. J Proteomics 2014; 101:102-12. [PMID: 24530623 DOI: 10.1016/j.jprot.2014.01.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 11/28/2013] [Accepted: 01/24/2014] [Indexed: 11/15/2022]
Abstract
In cultures containing multiple sources of nitrogen, Saccharomyces cerevisiae exhibits a sequential use of nitrogen sources through a mechanism known as nitrogen catabolite repression (NCR). To identify proteins differentially expressed due to NCR, proteomic analysis of S. cerevisiae S288C under different nitrogen source conditions was performed using two-dimensional gel electrophoresis (2-DE), revealing 169 candidate protein spots. Among these 169 protein spots, 121 were identified by matrix assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins were closely associated with four main biological processes through Gene Ontology (GO) categorical analysis. The identification of the potential proteins and cellular processes related to NCR offer a global overview of changes elicited by different nitrogen sources, providing clues into how yeast adapt to different nutritional conditions. Moreover, by comparing our proteomic data with corresponding mRNA data, proteins regulated at the transcriptional and post-transcriptional level could be distinguished. Biological significance In S. cerevisiae, different nitrogen sources provide different growth characteristics and generate different metabolites. The nitrogen catabolite repression (NCR) process plays an important role for S. cerevisiae in the ordinal utilization of different nitrogen sources. NCR process can result in significant shift of global metabolic networks. Previous works on NCR primarily focused on transcriptomic level. The results obtained in this study provided a global atlas of the proteome changes triggered by different nitrogen sources and would facilitate the understanding of mechanisms for how yeast could adapt to different nutritional conditions.
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Affiliation(s)
- Shaohui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Huijun Zou
- Zhejiang Guyuelongshan Shaoxing Wine Company, 13 Yangjiang Road, Shaoxing, Zhejiang 312000, China
| | - Jianwei Fu
- Zhejiang Guyuelongshan Shaoxing Wine Company, 13 Yangjiang Road, Shaoxing, Zhejiang 312000, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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31
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Draczkowski P, Matosiuk D, Jozwiak K. Isothermal titration calorimetry in membrane protein research. J Pharm Biomed Anal 2014; 87:313-25. [DOI: 10.1016/j.jpba.2013.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 08/28/2013] [Accepted: 09/03/2013] [Indexed: 01/18/2023]
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32
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Wink PL, Sanchez Quitian ZA, Rosado LA, Rodrigues VDS, Petersen GO, Lorenzini DM, Lipinski-Paes T, Saraiva Macedo Timmers LF, de Souza ON, Basso LA, Santos DS. Biochemical characterization of recombinant nucleoside hydrolase from Mycobacterium tuberculosis H37Rv. Arch Biochem Biophys 2013; 538:80-94. [DOI: 10.1016/j.abb.2013.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/13/2013] [Accepted: 08/17/2013] [Indexed: 11/25/2022]
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33
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Li F, Yu T, Jiang H, Yu S. Effects of activating cations and inhibitor on the allosteric regulation of rabbit muscle pyruvate kinase. Int J Biol Macromol 2013; 60:219-25. [DOI: 10.1016/j.ijbiomac.2013.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 05/23/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
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Wakai S, Kidokoro SI, Masaki K, Nakasone K, Sambongi Y. Constant enthalpy change value during pyrophosphate hydrolysis within the physiological limits of NaCl. J Biol Chem 2013; 288:29247-51. [PMID: 23965994 DOI: 10.1074/jbc.m113.502963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A decrease in water activity was thought to result in smaller enthalpy change values during PPi hydrolysis, indicating the importance of solvation for the reaction. However, the physiological significance of this phenomenon is unknown. Here, we combined biochemistry and calorimetry to solve this problem using NaCl, a physiologically occurring water activity-reducing reagent. The pyrophosphatase activities of extremely halophilic Haloarcula japonica, which can grow at ∼4 M NaCl, and non-halophilic Escherichia coli and Saccharomyces cerevisiae were maximal at 2.0 and 0.1 M NaCl, respectively. Thus, halophilic and non-halophilic pyrophosphatases exhibit distinct maximal activities at different NaCl concentration ranges. Upon calorimetry, the same exothermic enthalpy change of -35 kJ/mol was obtained for the halophile and non-halophiles at 1.5-4.0 and 0.1-2.0 M NaCl, respectively. These results show that solvation changes caused by up to 4.0 M NaCl (water activity of ∼0.84) do not affect the enthalpy change in PPi hydrolysis. It has been postulated that PPi is an ATP analog, having a so-called high energy phosphate bond, and that the hydrolysis of both compounds is enthalpically driven. Therefore, our results indicate that the hydrolysis of high energy phosphate compounds, which are responsible for biological energy conversion, is enthalpically driven within the physiological limits of NaCl.
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Affiliation(s)
- Satoshi Wakai
- From the Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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Roth G, Nunes JES, Rosado LA, Bizarro CV, Volpato G, Nunes CP, Renard G, Basso LA, Santos DS, Chies JM. Recombinant Erwinia carotovora l-asparaginase II production in Escherichia coli fed-batch cultures. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2013. [DOI: 10.1590/s0104-66322013000200003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- G. Roth
- Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Quatro G Pesquisa e Desenvolvimento Ltda., Brazil
| | - J. E. S. Nunes
- Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Quatro G Pesquisa e Desenvolvimento Ltda., Brazil
| | - L. A. Rosado
- Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Pontifícia Universidade Católica do Rio Grande do Sul, Brazil
| | - C. V. Bizarro
- Pontifícia Universidade Católica do Rio Grande do Sul, Brazil
| | - G. Volpato
- Quatro G Pesquisa e Desenvolvimento Ltda., Brazil; Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Brazil
| | - C. P. Nunes
- Quatro G Pesquisa e Desenvolvimento Ltda., Brazil
| | - G. Renard
- Quatro G Pesquisa e Desenvolvimento Ltda., Brazil
| | - L. A. Basso
- Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Quatro G Pesquisa e Desenvolvimento Ltda., Brazil
| | - D. S. Santos
- Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Quatro G Pesquisa e Desenvolvimento Ltda., Brazil
| | - J. M. Chies
- Quatro G Pesquisa e Desenvolvimento Ltda., Brazil
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Jun H, Kieselbach T, Jönsson LJ. Comparative proteome analysis of Saccharomyces cerevisiae: a global overview of in vivo targets of the yeast activator protein 1. BMC Genomics 2012; 13:230. [PMID: 22681880 PMCID: PMC3476450 DOI: 10.1186/1471-2164-13-230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 04/03/2012] [Indexed: 12/16/2022] Open
Abstract
Background The activity of the yeast activator protein 1 (Yap1p) increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a global overview of changes in expression of Yap1p-targeted proteins, we compared a Yap1p-overexpressing transformant with a control transformant by triplicate analysis of the proteome using two-dimensional gel electrophoresis (2-DE). Proteins of interest were identified using MALDI-MS or LC-MS/MS. Results The relative quantities of 55 proteins were elevated significantly upon overexpression of Yap1p, and most of these proteins were found to have a Yap1p-binding site upstream of their coding sequences. Interestingly, the main metabolic enzymes in the glycolysis and pyruvate-ethanol pathways showed a significant increase in the Yap1p-overexpressing transformant. Moreover, a comparison of our proteome data with transcriptome data from the literature suggested which proteins were regulated at the level of the proteome, and which proteins were regulated at the level of the transcriptome. Eight proteins involved in stress response, including seven heat-shock and chaperone proteins, were significantly more abundant in the Yap1p-overexpressing transformant. Conclusions We have investigated the general protein composition in Yap1p-overexpressing S. cerevisiae using proteomic techniques, and quantified the changes in the expression of the potential Yap1p-targeted proteins. Identification of the potential Yap1p targets and analysis of their role in cellular processes not only give a global overview of the ubiquitous cellular changes elicited by Yap1p, but also provide the framework for understanding the mechanisms behind Yap1p-regulated stress response in yeast.
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Affiliation(s)
- He Jun
- Department of Chemistry, Umeå University, Sweden
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Burnouf D, Ennifar E, Guedich S, Puffer B, Hoffmann G, Bec G, Disdier F, Baltzinger M, Dumas P. kinITC: a new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry. J Am Chem Soc 2011; 134:559-65. [PMID: 22126339 DOI: 10.1021/ja209057d] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Isothermal titration calorimetry (ITC) is the method of choice for obtaining thermodynamic data on a great variety of systems. Here we show that modern ITC apparatus and new processing methods allow researchers to obtain a complete kinetic description of systems more diverse than previously thought, ranging from simple ligand binding to complex RNA folding. We illustrate these new features with a simple case (HIV-1 reverse transcriptase/inhibitor interaction) and with the more complex case of the folding of a riboswitch triggered by the binding of its ligand. The originality of the new kinITC method lies in its ability to dissect, both thermodynamically and kinetically, the two components: primary ligand binding and subsequent RNA folding. We are not aware of another single method that can yield, in a simple way, such deep insight into a composite process. Our study also rationalizes common observations from daily ITC use.
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Affiliation(s)
- Dominique Burnouf
- Architecture et Réactivité de l'ARN, Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15, rue René Descartes, 67084 Strasbourg, France
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Franco TMA, Rostirolla DC, Ducati RG, Lorenzini DM, Basso LA, Santos DS. Biochemical characterization of recombinant guaA-encoded guanosine monophosphate synthetase (EC 6.3.5.2) from Mycobacterium tuberculosis H37Rv strain. Arch Biochem Biophys 2011; 517:1-11. [PMID: 22119138 DOI: 10.1016/j.abb.2011.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/29/2022]
Abstract
Administration of the current tuberculosis (TB) vaccine to newborns is not a reliable route for preventing TB in adults. The conversion of XMP to GMP is catalyzed by guaA-encoded GMP synthetase (GMPS), and deletions in the Shiguella flexneri guaBA operon led to an attenuated auxotrophic strain. Here we present the cloning, expression, and purification of recombinant guaA-encoded GMPS from Mycobacterium tuberculosis (MtGMPS). Mass spectrometry data, oligomeric state determination, steady-state kinetics, isothermal titration calorimetry (ITC), and multiple sequence alignment are also presented. The homodimeric MtGMPS catalyzes the conversion of XMP, MgATP, and glutamine into GMP, ADP, PP(i), and glutamate. XMP, NH(4)(+), and Mg(2+) displayed positive homotropic cooperativity, whereas ATP and glutamine displayed hyperbolic saturation curves. The activity of ATP pyrophosphatase domain is independent of glutamine amidotransferase domain, whereas the latter cannot catalyze hydrolysis of glutamine to NH(3) and glutamate in the absence of substrates. ITC data suggest random order of binding of substrates, and PP(i) is the last product released. Sequence comparison analysis showed conservation of both Cys-His-Glu catalytic triad of N-terminal Class I amidotransferase and of amino acid residues of the P-loop of the N-type ATP pyrophosphatase family.
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Affiliation(s)
- Tathyana Mar A Franco
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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Abstract
Almost any process in life is accompanied by heat changes which can be monitored by isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC). Both techniques are now established tools in fundamental research but over the last decade a clear tendency towards more problem-driven applications is noted. This review aims at summarizing these problem-oriented applications of microcalorimetry and the solutions both techniques can provide to problems in biotechnology. The biotechnological issues to which microcalorimetry has been successfully applied are as diverse as rational drug design, overcoming drug resistance, optimization of long-term stability of proteins, estimation of the bioavailability of drugs, control of complex pharmaceutical products or the optimization of gene delivery efficiency. The main limitation of microcalorimetry, which is the relatively large amounts of sample necessary for analysis, is less important in the biotechnology sector which frequently uses large-scale produced bulk products for analysis. The recently developed high-throughput DSC and ITC microcalorimeters will additionally reduce the labour intensity of these techniques. Due to the precision of microcalorimetric analyses and the versatility of processes which can be studied, it is expected that ITC and DSC will soon be key technologies in biotechnological research.
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Affiliation(s)
- Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008 Granada, Spain.
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40
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Wang S, Spor A, Nidelet T, Montalent P, Dillmann C, de Vienne D, Sicard D. Switch between life history strategies due to changes in glycolytic enzyme gene dosage in Saccharomyces cerevisiae. Appl Environ Microbiol 2011; 77:452-9. [PMID: 21075872 PMCID: PMC3020566 DOI: 10.1128/aem.00808-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 10/26/2010] [Indexed: 12/24/2022] Open
Abstract
Adaptation is the process whereby a population or species becomes better fitted to its habitat through modifications of various life history traits which can be positively or negatively correlated. The molecular factors underlying these covariations remain to be elucidated. Using Saccharomyces cerevisiae as a model system, we have investigated the effects on life history traits of varying the dosage of genes involved in the transformation of resources into energy. Changing gene dosage for each of three glycolytic enzyme genes (hexokinase 2, phosphoglucose isomerase, and fructose-1,6-bisphosphate aldolase) resulted in variation in enzyme activities, glucose consumption rate, and life history traits (growth rate, carrying capacity, and cell size). However, the range of effects depended on which enzyme was expressed differently. Most interestingly, these changes revealed a genetic trade-off between carrying capacity and cell size, supporting the discovery of two extreme life history strategies already described in yeast populations: the "ants," which have lower glycolytic gene dosage, take up glucose slowly, and have a small cell size but reach a high carrying capacity, and the "grasshoppers," which have higher glycolytic gene dosage, consume glucose more rapidly, and allocate it to a larger cell size but reach a lower carrying capacity. These results demonstrate antagonist pleiotropy for glycolytic genes and show that altered dosage of a single gene drives a switch between two life history strategies in yeast.
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Affiliation(s)
- Shaoxiao Wang
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Aymé Spor
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Thibault Nidelet
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Pierre Montalent
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Christine Dillmann
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Dominique de Vienne
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Delphine Sicard
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France, INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
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41
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Thierfelder S, Ostermann K, Göbel A, Rödel G. Vectors for glucose-dependent protein expression in Saccharomyces cerevisiae. Appl Biochem Biotechnol 2010; 163:954-64. [PMID: 20949330 DOI: 10.1007/s12010-010-9099-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 09/28/2010] [Indexed: 11/25/2022]
Abstract
Based on the p426 series of expression vectors developed by Mumberg et al. (Gene 156, 119-122, 1995), we have generated a set of plasmids that allow the glucose-dependent expression of target genes in the yeast, Saccharomyces cerevisiae. The ADH1 promoter in plasmid p426-ADH1 was replaced by the 1-kb 5'-region from either of the following genes: HXK1, YGR243, HXT4 and HXT7. Expression mediated by the respective 5'-regions was monitored with EGFP, yEGFP3-CLN2pest and TurboGFP as marker genes. Fluorescence is induced 2.7-fold using the HXK1, 2.3-fold using the YGR243-, 5-fold using the HXT7- and 12.6-fold using the HXT4 5'-regions upon depletion of glucose to a concentration of <0.5 g/l.
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Affiliation(s)
- Simone Thierfelder
- Institut für Genetik, Technische Universität Dresden, 01062 Dresden, Germany.
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42
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Tung YT, Hsu CA, Chen CS, Yang SC, Huang CC, Chang ST. Phytochemicals from Acacia confusa heartwood extracts reduce serum uric acid levels in oxonate-induced mice: their potential use as xanthine oxidase inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:9936-9941. [PMID: 20806936 DOI: 10.1021/jf102689k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this study, the antihyperuricemic effect of Acacia confusa heartwood extracts and their phytochemicals on potassium oxonate (PO)-induced acute hyperuricemia was investigated for the first time. All treatments at the same dosage (100 mmol/kg) were administered to the abdominal cavity of PO-induced hyperuricemic mice, and serum uric acid level was measured at 3 h after administration. In experimental mice, serum uric acid level was significantly suppressed by the administration of A. confusa heartwood extracts and their major phytochemicals, (-)-2,3-cis-3,4-cis-3,3',4,4',7,8-hexahydroxyflavan, (-)-2,3-cis-3,4-cis-4'-methoxy-3,3',4,7,8-pentahydroxyflavan, melanoxetin, transilitin, and okanin, relative to the PO group. The direct inhibitory effect of these five compounds on xanthine oxidase (XOD) activity was examined using isothermal titration calorimetry (ITC). Among them, melanoxetin showed a more remarkable inhibitory effect on XOD activity than allopurinol, a clinical drug used for XOD inhibitor. To further understand the stereochemistry between XOD and melanoxetin (or allopurinol), structure-based molecular modeling was performed. Melanoxetin undergoes extended interactions in the hydrophobic region via the 3',4'-dihydroxyphenyl moiety, thus accounting for its higher binding affinity to XOD than allopurinol. These results indicate that A. confusa heartwood extracts and their major phytochemicals exhibit strong XOD inhibitory effects, which reduce serum uric acid levels while inhibiting uric acid generation in purine metabolism.
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Affiliation(s)
- Yu-Tang Tung
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 106, Taiwan
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43
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Rezaei Behbehani G, Saboury AA, Zarean O, Barzegar L, Ghamamy S. Thermodynamic Study of Myelin Basic Protein upon Interaction with [Hg2+] Using Extension Solvation Model. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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44
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Kinetic mechanism and catalysis of Trypanosoma cruzi dihydroorotate dehydrogenase enzyme evaluated by isothermal titration calorimetry. Anal Biochem 2010; 399:13-22. [DOI: 10.1016/j.ab.2009.11.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 11/14/2009] [Accepted: 11/15/2009] [Indexed: 11/20/2022]
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45
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Huang YT, Lyu SY, Chuang PH, Hsu NS, Li YS, Chan HC, Huang CJ, Liu YC, Wu CJ, Yang WB, Li TL. In vitro Characterization of Enzymes Involved in the Synthesis of Nonproteinogenic Residue (2S,3S)-β-Methylphenylalanine in Glycopeptide Antibiotic Mannopeptimycin. Chembiochem 2009; 10:2480-7. [DOI: 10.1002/cbic.200900351] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Shukla S, Sastry M. Probing differential Ag+-nucleobase interactions with isothermal titration calorimetry (ITC): Towards patterned DNA metallization. NANOSCALE 2009; 1:122-7. [PMID: 20644870 DOI: 10.1039/b9nr00004f] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
DNA has been successfully used as a scaffold for the fabrication of metallic nanowires, primarily based on the electrostatic complexation and reduction of the metal cations on the negatively charged sugar-phosphate backbone. Here, we probe the differential binding affinities of nucleobases for silver ions using sensitive isothermal titration calorimetry (ITC) measurements of the reaction enthalpies, which go in order: C > G > A > or = T. Using the disparity between the interaction of cytosine (strong binding) and thymine (weak binding) with silver ions, we have successfully generated silver nanoparticle doublets and triplets on custom-made oligonucleotides, C(30)-T(40)-C(30) and C(20)-T(20)-C(20)-T(20)-C(20), respectively. Thus, a new and simple method of generating metallized DNA wires is presented, based entirely on the nucleotide sequence of DNA. The concept could be extended to other cations and complex DNA sequences in order to achieve intricately patterned DNA constructs.
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Affiliation(s)
- Sourabh Shukla
- Nanoscience Group, Physical and Materials Chemistry Division, National Chemical Laboratory, Pune, 411 008, India
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47
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Recht MI, Torres FE, De Bruyker D, Bell AG, Klumpp M, Bruce RH. Measurement of enzyme kinetics and inhibitor constants using enthalpy arrays. Anal Biochem 2009; 388:204-12. [PMID: 19250916 DOI: 10.1016/j.ab.2009.02.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 02/10/2009] [Accepted: 02/20/2009] [Indexed: 11/24/2022]
Abstract
Enthalpy arrays enable label-free, solution-based calorimetric detection of molecular interactions in a 96-detector array format. Compared with conventional calorimetry, enthalpy arrays achieve a significant reduction of sample volume and measurement time through the combination of the small size of the detectors and ability to perform measurements in parallel. The current capabilities of the technology for studying enzyme-catalyzed reactions are demonstrated by determining the kinetic parameters for reactions with three model enzymes. In addition, the technology has been used with two classes of enzymes to determine accurate inhibitor constants for competitive inhibitors from measurements at a single inhibitor concentration.
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48
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Kjelstrup S, de Meis L, Bedeaux D, Simon JM. Is the Ca2+-ATPase from sarcoplasmic reticulum also a heat pump? EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:59-67. [PMID: 18679670 DOI: 10.1007/s00249-008-0358-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 06/27/2008] [Accepted: 07/03/2008] [Indexed: 10/21/2022]
Abstract
We calculate, using the first law of thermodynamics, the membrane heat fluxes during active transport of Ca(2+) in the Ca(2+)-ATPase in leaky and intact vesicles, during ATP hydrolysis or synthesis conditions. The results show that the vesicle interior may cool down during hydrolysis and Ca(2+)-uptake, and heat up during ATP synthesis and Ca(2+)-efflux. The heat flux varies with the SERCA isoform. Electroneutral processes and rapid equilibration of water were assumed. The results are consistent with the second law of thermodynamics for the overall processes. The expression for the heat flux and experimental data, show that important contributions come from the enthalpy of hydrolysis for the medium in question, and from proton transport between the vesicle interior and exterior. The analysis give quantitative support to earlier proposals that certain, but not all, Ca(2+)-ATPases, not only act as Ca(2+)-pumps, but also as heat pumps. It can thus help explain why SERCA 1 type enzymes dominate in tissues where thermal regulation is important, while SERCA 2 type enzymes, with their lower activity and better ability to use the energy from the reaction to pump ions, dominate in tissues where this is not an issue.
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Affiliation(s)
- Signe Kjelstrup
- Centre of Advanced Study, Norwegian Academy of Science and Letters, Drammensveien 78, Oslo, Norway.
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49
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Enzymatic activity of immobilized enzyme determined by isothermal titration calorimetry. Anal Biochem 2008; 378:184-9. [DOI: 10.1016/j.ab.2008.04.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 04/03/2008] [Accepted: 04/05/2008] [Indexed: 11/19/2022]
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50
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Quesada-Soriano I, Leal I, Casas-Solvas JM, Vargas-Berenguel A, Barón C, Ruiz-Pérez LM, González-Pacanowska D, García-Fuentes L. Kinetic and thermodynamic characterization of dUTP hydrolysis by Plasmodium falciparum dUTPase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1347-55. [PMID: 18586121 DOI: 10.1016/j.bbapap.2008.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 11/27/2022]
Abstract
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate and plays an important role in nucleotide metabolism and DNA replication controlling relative cellular levels of dTTP/dUTP, both of which can be incorporated into DNA. Isothermal titration calorimetry has been applied to the determination of the kinetic and thermodynamic parameters of the trimeric Plasmodium falciparum dUTPase, a potential drug target against malaria. The role of divalent ions in binding, and inhibition by different uridine derivatives has been assessed. When dUTP hydrolysis in the presence of EDTA was evaluated, a 105-fold decrease and a 12-fold increase of the k(cat) and Km values, respectively, were observed when compared with the dUTP.Mg2+ complex. Calculation of the activation energy, E(a), and the thermodynamic activation parameters showed that the energetic barrier was approximately 4-fold higher when Mg2+ was depleted. Other divalent ions such as Co2+ or Mn2+ can substitute the physiological cofactor, however the k(cat) was significantly reduced compared to dUTP.Mg2+. Binding and inhibition by dU, dUMP, dUDP, and alpha,beta-imido-dUTP were analysed by ITC and compared with data obtained by spectrophotometric methods and binding equilibrium studies. Product inhibition (Kip dUMP: 99.34 microM) was insignificant yet Ki values for dUDP and alpha,beta-imido-dUTP were in the low micromolar range. The effect of ionic strength on protein stability was also monitored. DSC analysis evidenced a slight increase in the unfolding temperature, Tm, with increasing salt concentrations. Moreover, the thermal unfolding pathway in the presence of salt fits adequately to an irreversible two-state model (N3-->3D).
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Affiliation(s)
- Indalecio Quesada-Soriano
- Area de Química Física, Facultad de Ciencias Experimentales, Universidad de Almería, La Cañada de San Urbano, 04120 Almería, Spain
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