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Banerjee K, Das B. Elucidating the link between binding statistics and Shannon information in biological networks. J Chem Phys 2024; 161:125102. [PMID: 39319659 DOI: 10.1063/5.0226904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024] Open
Abstract
The response of a biological network to ligand binding is of crucial importance for regulatory control in various cellular biophysical processes that is achieved with information transmission through the different ligand-bound states of such networks. In this work, we address a vital issue regarding the link between the information content of such network states and the experimentally measurable binding statistics. Several fundamental networks of cooperative ligand binding, with the bound states being adjacent in time only and in both space and time, are considered for this purpose using the chemical master equation approach. To express the binding characteristics in the language of information, a quantity denoted as differential information index is employed based on the Shannon information. The index, determined for the whole network, follows a linear relationship with (logarithmic) ligand concentration with a slope equal to the size of the system. On the other hand, the variation of Shannon information associated with the individual network states and the logarithmic sensitivity of its slope are shown to have generic forms related to the average binding number and variance, respectively, the latter yielding the Hill slope, the phenomenological measure of cooperativity. Furthermore, the variation of Shannon information entropy, the average of Shannon information, is also shown to be related to the average binding.
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Affiliation(s)
- Kinshuk Banerjee
- Department of Chemistry, Acharya Jagadish Chandra Bose College, 1/1B A. J. C. Bose Road, Kolkata 700 020, India
| | - Biswajit Das
- School of Artificial Intelligence (AI), Amrita Vishwa Vidyapeetham (Amrita University), Amritanagar, Ettimadai, Coimbatore, Tamil Nadu 641112, India
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Gomez GM, D’Arrigo G, Sanchez CP, Berger F, Wade RC, Lanzer M. PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport. PLoS Pathog 2023; 19:e1011436. [PMID: 37285379 PMCID: PMC10281575 DOI: 10.1371/journal.ppat.1011436] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/20/2023] [Accepted: 05/21/2023] [Indexed: 06/09/2023] Open
Abstract
The chloroquine resistance transporter (PfCRT) confers resistance to a wide range of quinoline and quinoline-like antimalarial drugs in Plasmodium falciparum, with local drug histories driving its evolution and, hence, the drug transport specificities. For example, the change in prescription practice from chloroquine (CQ) to piperaquine (PPQ) in Southeast Asia has resulted in PfCRT variants that carry an additional mutation, leading to PPQ resistance and, concomitantly, to CQ re-sensitization. How this additional amino acid substitution guides such opposing changes in drug susceptibility is largely unclear. Here, we show by detailed kinetic analyses that both the CQ- and the PPQ-resistance conferring PfCRT variants can bind and transport both drugs. Surprisingly, the kinetic profiles revealed subtle yet significant differences, defining a threshold for in vivo CQ and PPQ resistance. Competition kinetics, together with docking and molecular dynamics simulations, show that the PfCRT variant from the Southeast Asian P. falciparum strain Dd2 can accept simultaneously both CQ and PPQ at distinct but allosterically interacting sites. Furthermore, combining existing mutations associated with PPQ resistance created a PfCRT isoform with unprecedented non-Michaelis-Menten kinetics and superior transport efficiency for both CQ and PPQ. Our study provides additional insights into the organization of the substrate binding cavity of PfCRT and, in addition, reveals perspectives for PfCRT variants with equal transport efficiencies for both PPQ and CQ.
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Affiliation(s)
- Guillermo M. Gomez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Giulia D’Arrigo
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg, Heidelberg, Germany
| | - Cecilia P. Sanchez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Fiona Berger
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg, Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld, Heidelberg, Germany
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld, Heidelberg, Germany
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Kühn S, Williams ME, Dercksen M, Sass JO, van der Sluis R. The glycine N-acyltransferases, GLYAT and GLYATL1, contribute to the detoxification of isovaleryl-CoA - an in-silico and in vitro validation. Comput Struct Biotechnol J 2023; 21:1236-1248. [PMID: 36817957 PMCID: PMC9932296 DOI: 10.1016/j.csbj.2023.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/01/2023] Open
Abstract
Isovaleric acidemia (IVA), due to isovaleryl-CoA dehydrogenase (IVD) deficiency, results in the accumulation of isovaleryl-CoA, isovaleric acid and secondary metabolites. The increase in these metabolites decreases mitochondrial energy production and increases oxidative stress. This contributes to the neuropathological features of IVA. A general assumption in the literature exists that glycine N-acyltransferase (GLYAT) plays a role in alleviating the symptoms experienced by IVA patients through the formation of N-isovalerylglycine. GLYAT forms part of the phase II glycine conjugation pathway in the liver and detoxifies excess acyl-CoA's namely benzoyl-CoA. However, very few studies support GLYAT as the enzyme that conjugates isovaleryl-CoA to glycine. Furthermore, GLYATL1, a paralogue of GLYAT, conjugates phenylacetyl-CoA to glutamine. Therefore, GLYATL1 might also be a candidate for the formation of N-isovalerylglycine. Based on the findings from the literature review, we proposed that GLYAT or GLYATL1 can form N-isovalerylglycine in IVA patients. To test this hypothesis, we performed an in-silico analysis to determine which enzyme is more likely to conjugate isovaleryl-CoA with glycine using AutoDock Vina. Thereafter, we performed in vitro validation using purified enzyme preparations. The in-silico and in vitro findings suggested that both enzymes could form N-isovaleryglycine albeit at lower affinities than their preferred substrates. Furthermore, an increase in glycine concentration does not result in an increase in N-isovalerylglycine formation. The results from the critical literature appraisal, in-silico, and in vitro validation, suggest the importance of further investigating the reaction kinetics and binding behaviors between these substrates and enzymes in understanding the pathophysiology of IVA.
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Affiliation(s)
- Stefan Kühn
- Focus Area for Human Metabolomics, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Monray E. Williams
- Focus Area for Human Metabolomics, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Marli Dercksen
- Focus Area for Human Metabolomics, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Jörn Oliver Sass
- Research Group Inborn Errors of Metabolism, Institute for Functional Gene Analytics, Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig-Str. 20, 53359 Rheinbach, Germany
| | - Rencia van der Sluis
- Focus Area for Human Metabolomics, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa,Corresponding author.
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Bartkiene E, Sakiene V, Lele V, Bartkevics V, Rusko J, Wiacek C, Ruzauskas M, Braun PG, Matusevicius P, Zdunczyk Z, Zdunczyk P, Juskiewicz J. Perspectives of lupine wholemeal protein and protein isolates biodegradation. Int J Food Sci Technol 2019. [DOI: 10.1111/ijfs.13901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elena Bartkiene
- Lithuanian University of Health Sciences Tilzes g. 18 LT‐47181 Kaunas Lithuania
| | - Vytaute Sakiene
- Lithuanian University of Health Sciences Tilzes g. 18 LT‐47181 Kaunas Lithuania
| | - Vita Lele
- Lithuanian University of Health Sciences Tilzes g. 18 LT‐47181 Kaunas Lithuania
| | - Vadims Bartkevics
- University of Latvia Jelgavas iela 1 LV‐1004 Riga Latvia
- Institute of Food Safety Animal Health and Environment Lejupes iela 3 LV‐1076 Riga Latvia
| | - Janis Rusko
- Institute of Food Safety Animal Health and Environment Lejupes iela 3 LV‐1076 Riga Latvia
| | - Claudia Wiacek
- Institute of Food Hygiene Universität Leipzig An den Tierkliniken 1 04103 Leipzig Germany
| | - Modestas Ruzauskas
- Lithuanian University of Health Sciences Tilzes g. 18 LT‐47181 Kaunas Lithuania
| | - Peggy G. Braun
- Institute of Food Hygiene Universität Leipzig An den Tierkliniken 1 04103 Leipzig Germany
| | | | - Zenon Zdunczyk
- Department of Biological Analysis of Food Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences 10‐747 Olsztyn Poland
| | - Przemysław Zdunczyk
- Department of Biological Analysis of Food Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences 10‐747 Olsztyn Poland
| | - Jerzy Juskiewicz
- Department of Biological Analysis of Food Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences 10‐747 Olsztyn Poland
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Bartkiene E, Bartkevics V, Ikkere LE, Pugajeva I, Zavistanaviciute P, Lele V, Ruzauskas M, Bernatoniene J, Jakstas V, Klupsaite D, Zadeike D, Viskelis P, Juodeikiene G. The effects of ultrasonication, fermentation with Lactobacillus sp., and dehydration on the chemical composition and microbial contamination of bovine colostrum. J Dairy Sci 2018; 101:6787-6798. [DOI: 10.3168/jds.2018-14692] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/26/2018] [Indexed: 12/17/2022]
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Analysis of volatile compounds and nutritional properties of enzymatic hydrolysate of protein from cod bone. Food Chem 2018; 264:350-357. [PMID: 29853387 DOI: 10.1016/j.foodchem.2018.05.034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 02/04/2023]
Abstract
Hydrolysis of the proteins from cod bone was performed using flavourzyme and trypsin. The nutritional properties of hydrolysates by flavourzyme (HF) and trypsin (HT) were investigated. By comparison, HF exhibits a better degree of hydrolysates (DH) and nitrogen recovery (NR) than HT. The protein content of extract is 97.39% and had a good nutritional value due to the high protein digestibility-corrected amino acid score (PDCAAS) of 0.95 for adults. The content of total amino acids is 942.55 mg/g. The free amino acids content of hydrolysates derived from flavourzyme is 136.82 mg/g after hydrolyzing 3 h, while 17.12 mg/g of such hydrolysates was obtained by using trypsin. The main flavor compounds are alcohols, aldehydes, ketones, acids and alkanes. The molecular weight of predominant peptides ranged from 1000 to 3000 Da in both enzymatic hydrolysates. This study provided a theoretical basis to the preparation of nutritional components with attracting flavor in functional food industry.
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Ali A, Wathes DC, Swali A, Burns H, Burns S. A novel mammalian glucokinase exhibiting exclusive inorganic polyphosphate dependence in the cell nucleus. Biochem Biophys Rep 2017; 12:151-157. [PMID: 29090276 PMCID: PMC5645163 DOI: 10.1016/j.bbrep.2017.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
Background Hexokinase and glucokinase enzymes are ubiquitously expressed and use ATP and ADP as substrates in mammalian systems and a variety of polyphosphate substrates and/or ATP in some eukaryotic and microbial systems. Polyphosphate synthesising or utilizing enzymes are widely expressed in microbial systems but have not been reported in mammalian systems, despite the presence of polyphosphate in mammalian cells. Only two micro-organisms have previously been shown to express an enzyme that uses polyphosphate exclusively. Methods A variety of experimental approaches, including NMR and NAD-linked assay systems were used to conduct a biochemical investigation of polyphosphate dependent glucokinase activity in mammalian tissues. Results A novel mammalian glucokinase, highly responsive to hexametaphosphate (HMP) but not ATP or ADP as a phosphoryl donor is present in the nuclei of mammalian hepatocytes. The liver enzyme exhibited sigmoidal kinetics with respect to glucose with a S0.5 of 12 mM, similar to the known kinetics of mammalian ATP-glucokinase. The Km for HMP (0.5 mM) was also similar to that of phosphoryl donors for mammalian ATP-glucokinases. The new enzyme was inhibited by several nucleotide phosphates. Conclusions We report the discovery of a polyphosphate-dependent enzyme system in mammalian cells with kinetics similar to established ATP-dependent glucokinase, also known to have a nuclear location. The kinetics suggest possible regulatory or redox protective roles. General significance The role of polyphosphate in mammalian systems has remained an enigma for decades, and the present report describes progress on the significance of this compound in intracellular metabolism in mammals. The first mammalian enzyme activity using polyphosphate as a phosphorylation substrate. A polyphosphate dependent glucokinase with kinetics similar to human glucokinase. Further evidence of discreet substrate specificity of hexokinases. A possible evolutionary link between polyphosphate and ATP utilization.
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Affiliation(s)
- Antasar Ali
- Biological Sciences, University of Huddersfield, Huddersfield UK HD1 3DH, United Kingdom
| | - D. Claire Wathes
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London UK NW1 0TU, United Kingdom
| | - Angelina Swali
- School of Biosciences, University of Nottingham, Nottingham UK LE12 5RD, United Kingdom
| | - Helena Burns
- Biological Sciences, University of Huddersfield, Huddersfield UK HD1 3DH, United Kingdom
| | - Shamus Burns
- Biological Sciences, University of Huddersfield, Huddersfield UK HD1 3DH, United Kingdom
- Corresponding author.
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Bartkiene E, Bartkevics V, Rusko J, Starkute V, Zadeike D, Juodeikiene G. Changes in the free amino acids and the biogenic amine contents during lactic acid fermentation of different lupin species. Int J Food Sci Technol 2016. [DOI: 10.1111/ijfs.13177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elena Bartkiene
- Lithuanian University of Health Sciences; Tilzes g. 18 47181 Kaunas Lithuania
| | - Vadims Bartkevics
- University of Latvia; Jelgavas iela 1 1004 Riga Latvia
- Institute of Food Safety, Animal Health and Environment; Lejupes iela 3 1076 Riga Latvia
| | - Janis Rusko
- Institute of Food Safety, Animal Health and Environment; Lejupes iela 3 1076 Riga Latvia
| | - Vytaute Starkute
- Lithuanian University of Health Sciences; Tilzes g. 18 47181 Kaunas Lithuania
| | - Daiva Zadeike
- Kaunas University of Technology; Radvilenu pl. 19 50254 Kaunas Lithuania
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Cappiello M, Balestri F, Moschini R, Del-Corso A, Mura U. Apparent cooperativity and apparent hyperbolic behavior of enzyme mixtures acting on the same substrate. J Enzyme Inhib Med Chem 2016; 31:1556-9. [PMID: 27072427 DOI: 10.3109/14756366.2016.1158169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
It is well known that a negative cooperative behavior displayed by a monomeric enzyme may be associated with the simultaneous presence of two enzymes acting on the same substrate. In this paper, emphasis is given to the effect exerted by a rapid equilibrium between the enzyme forms in leading to a hyperbolic behavior, thus masking the presence of multiple enzyme forms.
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Affiliation(s)
- Mario Cappiello
- a Department of Biology-Biochemistry Unit , University of Pisa , Pisa , Italy
| | - Francesco Balestri
- a Department of Biology-Biochemistry Unit , University of Pisa , Pisa , Italy
| | - Roberta Moschini
- a Department of Biology-Biochemistry Unit , University of Pisa , Pisa , Italy
| | - Antonella Del-Corso
- a Department of Biology-Biochemistry Unit , University of Pisa , Pisa , Italy
| | - Umberto Mura
- a Department of Biology-Biochemistry Unit , University of Pisa , Pisa , Italy
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