1
|
Lio E, Parshin P, D'Oronzo E, Plebani S, Pometun AA, Kleymenov SY, Tishkov VI, Secundo F. Chimeric versus isolated proteins: Biochemical characterization of the NADP +-dependent formate dehydrogenase from Pseudomonas sp. 101 fused with the Baeyer-Villiger monooxygenase from Thermobifida fusca. Int J Biol Macromol 2023; 253:126637. [PMID: 37657580 DOI: 10.1016/j.ijbiomac.2023.126637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/04/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
The expression of multifunctional proteins can facilitate the setup of a biotechnology process that requires multiple functions absolved by different proteins. Herein the functional and conformational characterization of a formate dehydrogenase-monooxygenase chimera enzyme is presented. The fused enzyme (FDH-PAMO) was prepared by linking the C-terminus of the mutant NADP+-dependent formate dehydrogenase from Pseudomonas sp. 101 (FDH) to the N-terminus of the NADPH-dependent monooxygenase from Thermobifida fusca (PAMO) through a peptide linker of 9 amino acids (ASGGGGSGT) generating a chimera protein of 107,056 Da. The catalytic properties (e.g., kinetic parameters kcat and Km), stability, fluorescence and circular dichroism spectra showed that the so-obtained chimera enzyme FDH-PAMO retains the same functional and conformational properties of the two parental enzymes. Furthermore, SEC chromatographic analysis indicated that, in solution (pH 7.4), FDH-PAMO assembles to tetramers (up to 4.2 %) due to the propensity of FDH and PAMO to form dimers, up to 96.6 % and 6.2 %, respectively. This study provides valuable insights into the structural stability of a thermostable protein (e.g., PAMO) after increasing its size through fusion with another similarly sized thermostable protein (e.g., FDH).
Collapse
Affiliation(s)
- Elia Lio
- Istituto di Scienze e Tecnologie Chimiche, CNR, Via Mario Bianco 9, 20131 Milan, Italy
| | - Pavel Parshin
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russian Federation
| | - Erica D'Oronzo
- Istituto di Scienze e Tecnologie Chimiche, CNR, Via Mario Bianco 9, 20131 Milan, Italy
| | - Stefano Plebani
- Istituto di Scienze e Tecnologie Chimiche, CNR, Via Mario Bianco 9, 20131 Milan, Italy
| | - Anastasia A Pometun
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russian Federation; A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, bld. 33-2 Leninsky Ave., Moscow 119071, Russian Federation
| | - S Yu Kleymenov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, bld. 33-2 Leninsky Ave., Moscow 119071, Russian Federation; Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova 26, Moscow 119334, Russian Federation
| | - Vladimir I Tishkov
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russian Federation; A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, bld. 33-2 Leninsky Ave., Moscow 119071, Russian Federation
| | - Francesco Secundo
- Istituto di Scienze e Tecnologie Chimiche, CNR, Via Mario Bianco 9, 20131 Milan, Italy.
| |
Collapse
|
2
|
Microbial Lipases and Their Potential in the Production of Pharmaceutical Building Blocks. Int J Mol Sci 2022; 23:ijms23179933. [PMID: 36077332 PMCID: PMC9456414 DOI: 10.3390/ijms23179933] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Processes involving lipases in obtaining active pharmaceutical ingredients (APIs) are crucial to increase the sustainability of the industry. Despite their lower production cost, microbial lipases are striking for their versatile catalyzing reactions beyond their physiological role. In the context of taking advantage of microbial lipases in reactions for the synthesis of API building blocks, this review focuses on: (i) the structural origins of the catalytic properties of microbial lipases, including the results of techniques such as single particle monitoring (SPT) and the description of its selectivity beyond the Kazlauskas rule as the “Mirror-Image Packing” or the “Key Region(s) rule influencing enantioselectivity” (KRIE); (ii) immobilization methods given the conferred operative advantages in industrial applications and their modulating capacity of lipase properties; and (iii) a comprehensive description of microbial lipases use as a conventional or promiscuous catalyst in key reactions in the organic synthesis (Knoevenagel condensation, Morita–Baylis–Hillman (MBH) reactions, Markovnikov additions, Baeyer–Villiger oxidation, racemization, among others). Finally, this review will also focus on a research perspective necessary to increase microbial lipases application development towards a greener industry.
Collapse
|
3
|
Human cytosolic transaminases: side activities and patterns of discrimination towards physiologically available alternative substrates. Cell Mol Life Sci 2022; 79:421. [PMID: 35834009 PMCID: PMC9283133 DOI: 10.1007/s00018-022-04439-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
Abstract
Transaminases play key roles in central metabolism, transferring the amino group from a donor substrate to an acceptor. These enzymes can often act, with low efficiency, on compounds different from the preferred substrates. To understand what might have shaped the substrate specificity of this class of enzymes, we examined the reactivity of six human cytosolic transaminases towards amino acids whose main degradative pathways do not include any transamination. We also tested whether sugars and sugar phosphates could serve as alternative amino group acceptors for these cytosolic enzymes. Each of the six aminotransferases reacted appreciably with at least three of the alternative amino acid substrates in vitro, albeit at usually feeble rates. Reactions with L-Thr, L-Arg, L-Lys and L-Asn were consistently very slow-a bias explained in part by the structural differences between these amino acids and the preferred substrates of the transaminases. On the other hand, L-His and L-Trp reacted more efficiently, particularly with GTK (glutamine transaminase K; also known as KYAT1). This points towards a role of GTK in the salvage of L-Trp (in cooperation with ω-amidase and possibly with the cytosolic malate dehydrogenase, MDH1, which efficiently reduced the product of L-Trp transamination). Finally, the transaminases were extremely ineffective at utilizing sugars and sugar derivatives, with the exception of the glycolytic intermediate dihydroxyacetone phosphate, which was slowly but appreciably transaminated by some of the enzymes to yield serinol phosphate. Evidence for the formation of this compound in a human cell line was also obtained. We discuss the biological and evolutionary implications of our results.
Collapse
|
4
|
Unusual commonality in active site structural features of substrate promiscuous and specialist enzymes. J Struct Biol 2022; 214:107835. [DOI: 10.1016/j.jsb.2022.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/26/2021] [Accepted: 01/23/2022] [Indexed: 11/21/2022]
|
5
|
Fodor I, Schwarz T, Kiss B, Tapodi A, Schmidt J, Cousins ARO, Katsiadaki I, Scott AP, Pirger Z. Studies on a widely-recognized snail model species ( Lymnaea stagnalis) provide further evidence that vertebrate steroids do not have a hormonal role in the reproduction of mollusks. Front Endocrinol (Lausanne) 2022; 13:981564. [PMID: 36157463 PMCID: PMC9493083 DOI: 10.3389/fendo.2022.981564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 11/20/2022] Open
Abstract
Experiments were carried out to determine whether, as with other mollusks that have been studied, the snail, Lymnaea stagnalis, can absorb, esterify and store vertebrate steroids that are present in the water. We also carried out experiments to determine whether neural tissues of the snail could be immunohistochemically stained with an antibody to human aromatase (a key enzyme that catalyzes the conversion of testosterone [T] to 17β-estradiol [E2]); and, if so, to determine the significance of such staining. Previous studies on other mollusks have reported such staining and have proposed this as decisive evidence that mollusks have the same steroid synthesis pathway as vertebrates. We found that snails absorb, esterify and retain esterified T, E2, progesterone and ethinyl-estradiol (albeit with an absorption rate about four times slower, on a weight basis, than the mussel, Mytilus edulis). We also found that not only anti-human aromatase, but also anti-human nuclear progesterone receptor (nPR) and anti-human gonadotropin-releasing hormone antibodies immunohistochemically stained snail neural cells. However, further experiments, involving gel electrophoretic separation, followed by immunostaining, of proteins extracted from the neural tissue, found at least two positively-stained bands for each antibody, none of which had masses matching the human proteins to which the antibodies had been raised. The anti-aromatase antibody even stained the 140 kDA ladder protein used as a molecular weight marker on the gels. Mass spectrometric analysis of the bands did not find any peptide sequences that corresponded to the human proteins. Our findings confirm that the presence of vertebrate-like sex steroids in molluscan tissues is not necessarily evidence of endogenous origin. The results also show that immunohistochemical studies using antibodies against human proteins are grossly non-specific and likely to have little or no value in studying steroid synthesis or activity in mollusks. Our conclusions are consistent with the fact that genes for aromatase and nPR have not been found in the genome of the snail or of any other mollusk. Our overarching conclusion, from this and our previous studies, is that the endocrinology of mollusks is not the same as that of humans or any other vertebrates and that continuing to carry out physiological and ecotoxicological studies on mollusks on the basis of this false assumption, is an unconscionable waste of resources.
Collapse
Affiliation(s)
- István Fodor
- Ecophysiological and Environmental Toxicological Research Group, Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Tihany, Hungary
- *Correspondence: István Fodor,
| | - Tamar Schwarz
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth Laboratory, Weymouth, United Kingdom
| | - Bence Kiss
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs, Hungary
| | - Antal Tapodi
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs, Hungary
| | - János Schmidt
- Institute of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs, Hungary
| | - Alex R. O. Cousins
- Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, United Kingdom
| | - Ioanna Katsiadaki
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth Laboratory, Weymouth, United Kingdom
| | - Alexander P. Scott
- Centre for Environment, Fisheries and Aquaculture Research, Weymouth Laboratory, Weymouth, United Kingdom
| | - Zsolt Pirger
- Ecophysiological and Environmental Toxicological Research Group, Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Tihany, Hungary
| |
Collapse
|
6
|
Fodor I, Koene JM, Pirger Z. Neuronal Transcriptome Analysis of a Widely Recognised Molluscan Model Organism Highlights the Absence of Key Proteins Involved in the De Novo Synthesis and Receptor-Mediation of Sex Steroids in Vertebrates. MALACOLOGIA 2021. [DOI: 10.4002/040.064.0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- István Fodor
- NAP Adaptive Neuroethology, Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| | - Joris M. Koene
- Department of Ecological Science, Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - Zsolt Pirger
- NAP Adaptive Neuroethology, Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| |
Collapse
|
7
|
Tokarz J, Schmitt SM, Möller G, Brändli AW, Adamski J. Functional characterization of two 20β-hydroxysteroid dehydrogenase type 2 homeologs from Xenopus laevis reveals multispecificity. J Steroid Biochem Mol Biol 2021; 210:105874. [PMID: 33722706 DOI: 10.1016/j.jsbmb.2021.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 11/23/2022]
Abstract
The African clawed frog, Xenopus laevis, is a versatile model for biomedical research and is largely similar to mammals in terms of organ development, anatomy, physiology, and hormonal signaling mechanisms. Steroid hormones control a variety of processes and their levels are regulated by hydroxysteroid dehydrogenases (HSDs). The subfamily of 20β-HSD type 2 enzymes currently comprises eight members from teleost fish and mammals. Here, we report the identification of three 20β-HSD type 2 genes in X. tropicalis and X. laevis and the functional characterization of the two homeologs from X. laevis. X. laevis Hsd20b2.L and Hsd20b2.S showed high sequence identity with known 20β-HSD type 2 enzymes and mapped to the two subgenomes of the allotetraploid frog genome. Both homeologs are expressed during embryonic development and in adult tissues, with strongest signals in liver, kidney, intestine, and skin. After recombinant expression in human cell lines, both enzymes co-localized with the endoplasmic reticulum and catalyzed the conversion of cortisone to 20β-dihydrocortisone. Both Hsd20b2.L and Hsd20b2.S catalyzed the 20β-reduction of further C21 steroids (17α-hydroxyprogesterone, progesterone, 11-deoxycortisol, 11-deoxycorticosterone), while only Hsd20b2.S was able to convert corticosterone and cortisol to their 20β-reduced metabolites. Estrone was only a poor and androstenedione no substrate for both enzymes. Our results demonstrate multispecificity of 20β-HSD type 2 enzymes from X. laevis similar to other teleost 20β-HSD type 2 enzymes. X. laevis 20β-HSD type 2 enzymes are probably involved in steroid catabolism and in the generation of pheromones for intraspecies communication. A role in oocyte maturation is unlikely.
Collapse
Affiliation(s)
- Janina Tokarz
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany.
| | - Stefan M Schmitt
- Walter Brendel Centre of Experimental Medicine, University Hospital and Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gabriele Möller
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany
| | - André W Brändli
- Walter Brendel Centre of Experimental Medicine, University Hospital and Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jerzy Adamski
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany; German Center for Diabetes Research, Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
8
|
Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
Collapse
|
9
|
Abstract
Drug metabolizing enzymes catalyze the biotransformation of many of drugs and chemicals. The drug metabolizing enzymes are distributed among several evolutionary families and catalyze a range of detoxication reactions, including oxidation/reduction, conjugative, and hydrolytic reactions that serve to detoxify potentially toxic compounds. This detoxication function requires that drug metabolizing enzymes exhibit substrate promiscuity. In addition to their catalytic functions, many drug metabolizing enzymes possess functions unrelated to or in addition to catalysis. Such proteins are termed 'moonlighting proteins' and are defined as proteins with multiple biochemical or biophysical functions that reside in a single protein. This review discusses the diverse moonlighting functions of drug metabolizing enzymes and the roles they play in physiological functions relating to reproduction, vision, cell signaling, cancer, and transport. Further research will likely reveal new examples of moonlighting functions of drug metabolizing enzymes.
Collapse
Affiliation(s)
- Philip G Board
- John Curtin School of Medical Research, ANU College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, NY, USA
| |
Collapse
|
10
|
Fodor I, Urbán P, Scott AP, Pirger Z. A critical evaluation of some of the recent so-called 'evidence' for the involvement of vertebrate-type sex steroids in the reproduction of mollusks. Mol Cell Endocrinol 2020; 516:110949. [PMID: 32687858 DOI: 10.1016/j.mce.2020.110949] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022]
Abstract
Many studies on the control of reproduction in mollusks have focused on hormones (and proteins associated with the production and signaling of those hormones) which were originally discovered in humans, in the belief that if they are also present in mollusks, they must have the same role. However, although human sex steroids can be found in mollusks, they are so readily absorbed that their presence is not necessarily evidence of endogenous synthesis. A homolog of the vertebrate nuclear estrogen receptor has been found in mollusks, but it does not bind to estrogens or indeed to any steroid at all. Antibodies against human aromatase show positive immunostaining in mollusks, yet the aromatase gene has not been found in the genome of any invertebrates (let alone mollusks). This review will deal with these and other examples of contradictory evidence for a role of human hormones in invertebrate reproduction.
Collapse
Affiliation(s)
- István Fodor
- NAP Adaptive Neuroethology, Department of Experimental Zoology, Balaton Limnological Institute, Centre for Ecological Research, 8237, Tihany, Hungary.
| | - Péter Urbán
- Genomics and Bioinformatics Core Facilities, Szentágothai Research Centre, University of Pécs, 7624, Pécs, Hungary
| | - Alexander P Scott
- Centre for Environment, Fisheries and Aquaculture Research (Cefas), Barrack Road, Weymouth, DT4 8UB, UK
| | - Zsolt Pirger
- NAP Adaptive Neuroethology, Department of Experimental Zoology, Balaton Limnological Institute, Centre for Ecological Research, 8237, Tihany, Hungary
| |
Collapse
|
11
|
Flux Enforcement for Fermentative Production of 5-Aminovalerate and Glutarate by Corynebacterium glutamicum. Catalysts 2020. [DOI: 10.3390/catal10091065] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bio-based plastics represent an increasing percentage of the plastics economy. The fermentative production of bioplastic monomer 5-aminovalerate (5AVA), which can be converted to polyamide 5 (PA 5), has been established in Corynebacterium glutamicum via two metabolic pathways. l-lysine can be converted to 5AVA by either oxidative decarboxylation and subsequent oxidative deamination or by decarboxylation to cadaverine followed by transamination and oxidation. Here, a new three-step pathway was established by using the monooxygenase putrescine oxidase (Puo), which catalyzes the oxidative deamination of cadaverine, instead of cadaverine transaminase. When the conversion of 5AVA to glutarate was eliminated and oxygen supply improved, a 5AVA titer of 3.7 ± 0.4 g/L was reached in microcultivation that was lower than when cadaverine transaminase was used. The elongation of the new pathway by 5AVA transamination by GABA/5AVA aminotransferase (GabT) and oxidation by succinate/glutarate semialdehyde dehydrogenase (GabD) allowed for glutarate production. Flux enforcement by the disruption of the l-glutamic acid dehydrogenase-encoding gene gdh rendered a single transaminase (GabT) in glutarate production via the new pathway responsible for nitrogen assimilation, which increased the glutarate titer to 7.7 ± 0.7 g/L, i.e., 40% higher than with two transaminases operating in glutarate biosynthesis. Flux enforcement was more effective with one coupling site, thus highlighting requirements regarding the modularity and stoichiometry of pathway-specific flux enforcement for microbial production.
Collapse
|
12
|
Stockinger P, Roth S, Müller M, Pleiss J. Systematic Evaluation of Imine-Reducing Enzymes: Common Principles in Imine Reductases, β-Hydroxy Acid Dehydrogenases, and Short-Chain Dehydrogenases/ Reductases. Chembiochem 2020; 21:2689-2695. [PMID: 32311225 PMCID: PMC7540600 DOI: 10.1002/cbic.202000213] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/16/2020] [Indexed: 12/26/2022]
Abstract
The enzymatic, asymmetric reduction of imines is catalyzed by imine reductases (IREDs), members of the short-chain dehydrogenase/reductase (SDR) family, and β-hydroxy acid dehydrogenase (βHAD) variants. Systematic evaluation of the structures and substrate-binding sites of the three enzyme families has revealed four common principles for imine reduction: structurally conserved cofactor-binding domains; tyrosine, aspartate, or glutamate as proton donor; at least four characteristic flanking residues that adapt the donor's pKa and polarize the substrate; and a negative electrostatic potential in the substrate-binding site to stabilize the transition state. As additional catalytically relevant positions, we propose alternative proton donors in IREDs and βHADs as well as proton relays in IREDs, βHADs, and SDRs. The functional role of flanking residues was experimentally confirmed by alanine scanning of the imine-reducing SDR from Zephyranthes treatiae. Mutating the "gatekeeping" phenylalanine at standard position 200 resulted in a tenfold increase in imine-reducing activity.
Collapse
Affiliation(s)
- Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Sebastian Roth
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Michael Müller
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| |
Collapse
|
13
|
Gupta MN, Roy I. Drugs, host proteins and viral proteins: how their promiscuities shape antiviral design. Biol Rev Camb Philos Soc 2020; 96:205-222. [PMID: 32918378 DOI: 10.1111/brv.12652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
The reciprocal nature of drug specificity and target specificity implies that the same is true for their respective promiscuities. Protein promiscuity has two broadly different types of footprint in drug design. The first is relaxed specificity of binding sites for substrates, inhibitors, effectors or cofactors. The second involves protein-protein interactions of regulatory processes such as signal transduction and transcription, and here protein intrinsic disorder plays an important role. Both viruses and host cells exploit intrinsic disorder for their survival, as do the design and discovery programs for antivirals. Drug action, strictly speaking, always relies upon promiscuous activity, with drug promiscuity enlarging its scope. Drug repurposing searches for additional promiscuity on the part of both the drug and the target in the host. Understanding the subtle nuances of these promiscuities is critical in the design of novel and more effective antivirals.
Collapse
Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160062, India
| |
Collapse
|
14
|
Tokarz J, Lintelmann J, Möller G, Adamski J. Substrate multispecificity among 20β-hydroxysteroid dehydrogenase type 2 members. Mol Cell Endocrinol 2020; 510:110822. [PMID: 32315721 DOI: 10.1016/j.mce.2020.110822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 10/24/2022]
Abstract
Steroids regulate many physiological processes. Hydroxysteroid dehydrogenases (HSDs) modulate the levels of steroids in pre- and post-receptor metabolism. The subfamily of 20β-HSD type 2 currently comprises six members from six different species. The zebrafish ortholog converts cortisone to 20β-dihydrocortisone and is involved in the catabolism of the stress hormone cortisol. Here, we elucidated the substrate preferences of all 20β-HSD type 2 enzymes towards a selected panel of steroids. For quantification of the substrates and their respective 20β-reduced products, we first developed and validated a liquid chromatography-mass spectrometry based method. Applying this method to activity assays with recombinantly expressed enzymes, our findings indicate that the 20β-HSD type 2 enzymes catalyze the 20β-reduction of a plethora of steroids of the glucocorticoid biosynthesis pathway. The observed multispecificity among the homologous 20β-HSD type 2 enzymes implies different physiological roles in different species.
Collapse
Affiliation(s)
- Janina Tokarz
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany.
| | - Jutta Lintelmann
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany
| | - Gabriele Möller
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany
| | - Jerzy Adamski
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany; German Center for Diabetes Research, Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
15
|
Gupta MN, Alam A, Hasnain SE. Protein promiscuity in drug discovery, drug-repurposing and antibiotic resistance. Biochimie 2020; 175:50-57. [PMID: 32416199 DOI: 10.1016/j.biochi.2020.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/01/2022]
Abstract
Proteins are supposed to bind to their substrates/ligands in a specific manner via their pre-formed binding sites, according to classical biochemistry. In recent years, several types of deviations from this norm have been observed and called promiscuous behavior. Enzymatic promiscuities allow several biochemical functions to be carried out by the same enzyme. The promiscuous activity can also be the origin of "new proteins" via gene duplication. In more recent years, proteins from prokaryotes, eukaryotes and viruses have been found to have intrinsic disorder and lack a preformed binding site. Intrinsic disorder is exploited in regulatory proteins such as those that are involved in transcription and signal transduction. Such proteins function by folding locally while binding to their ligands or interacting with other proteins. These phenomena have also been classified as examples of protein promiscuity and encompass diverse kinds of ligands that can bind to a protein. Given the significant extent of structural homology in many protein families, it is not surprising that ligands also have been found to display promiscuity. Promiscuous behavior of proteins offers both challenges and opportunities to the drug discovery programs such as drug repurposing. Pathogens when exposed to antibiotics exploit protein promiscuity in several ways to develop resistance to the drug. There is increasing evidence now to support that the disorder in proteins is a major tool used by pathogens for virulence and evade drug action by exploiting protein promiscuity. This review provides a holistic view of this multi-faceted phenomenon called protein promiscuity.
Collapse
Affiliation(s)
- Munishwar N Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Anwar Alam
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Seyed E Hasnain
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Professor CR Rao Road, Hyderabad, 500046, India.
| |
Collapse
|
16
|
Atkins WM. Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters. FEBS J 2020; 287:1306-1322. [PMID: 31663687 PMCID: PMC7138722 DOI: 10.1111/febs.15116] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/04/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Detoxication, or 'drug-metabolizing', enzymes and drug transporters exhibit remarkable substrate promiscuity and catalytic promiscuity. In contrast to substrate-specific enzymes that participate in defined metabolic pathways, individual detoxication enzymes must cope with substrates of vast structural diversity, including previously unencountered environmental toxins. Presumably, evolution selects for a balance of 'adequate' kcat /KM values for a wide range of substrates, rather than optimizing kcat /KM for any individual substrate. However, the structural, energetic, and metabolic properties that achieve this balance, and hence optimize detoxication, are not well understood. Two features of detoxication enzymes that are frequently cited as contributions to promiscuity include the exploitation of highly reactive versatile cofactors, or cosubstrates, and a high degree of flexibility within the protein structure. This review examines these intuitive mechanisms in detail and clarifies the contributions of the classic ligand binding models 'induced fit' (IF) and 'conformational selection' (CS) to substrate promiscuity. The available literature data for drug metabolizing enzymes and transporters suggest that IF is exploited by these promiscuous detoxication enzymes, as it is with substrate-specific enzymes, but the detoxication enzymes uniquely exploit 'IFs' to retain a wide range of substrates at their active sites. In contrast, whereas CS provides no catalytic advantage to substrate-specific enzymes, promiscuous enzymes may uniquely exploit it to recruit a wide range of substrates. The combination of CS and IF, for recruitment and retention of substrates, can potentially optimize the promiscuity of drug metabolizing enzymes and drug transporters.
Collapse
Affiliation(s)
- William M. Atkins
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWAUSA
| |
Collapse
|
17
|
Velez Rueda AJ, Palopoli N, Zacarías M, Sommese LM, Parisi G. ProtMiscuity: a database of promiscuous proteins. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5606773. [PMID: 31650170 PMCID: PMC6813136 DOI: 10.1093/database/baz103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/02/2019] [Accepted: 08/01/2019] [Indexed: 11/30/2022]
Abstract
Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure–function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing catalytic promiscuity. ProtMiscuity contains information about canonical and promiscuous activities comprising 88 different reactions in 57 proteins from 40 different organisms. It can be searched or browsed by protein names, organisms and descriptions of canonical and promiscuous reactions. Entries provide information on reaction substrates, products and kinetic parameters, mapping of active sites to sequence and structure and links to external resources with biological and functional annotations. ProtMiscuity could assist in studying the underlying mechanisms of promiscuous reactions by offering a unique and curated collection of experimentally derived data that is otherwise hard to find, retrieve and validate from literature.
Collapse
Affiliation(s)
- Ana Julia Velez Rueda
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD Buenos Aires, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD Buenos Aires, Argentina
| | - Matías Zacarías
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD Buenos Aires, Argentina
| | - Leandro Matías Sommese
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD Buenos Aires, Argentina
| |
Collapse
|
18
|
González-Cuesta M, Goyard D, Nanba E, Higaki K, García Fernández JM, Renaudet O, Ortiz Mellet C. Multivalent glycoligands with lectin/enzyme dual specificity: self-deliverable glycosidase regulators. Chem Commun (Camb) 2019; 55:12845-12848. [PMID: 31596280 DOI: 10.1039/c9cc06376e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multivalent mannosides with inherent macrophage recognition abilities, built on β-cyclodextrin, RAFT cyclopeptide or peptide dendrimer cores, trigger selective inhibition of lysosomal β-glucocerebrosidase or α-mannosidase depending on valency and topology, offering new opportunities in multitargeted drug design.
Collapse
Affiliation(s)
- Manuel González-Cuesta
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/Profesor García González 1, 41012 Seville, Spain.
| | - David Goyard
- Université Grenoble Alpes, CNRS, DCM UMR 5250, 3800 Grenoble, France.
| | - Eiji Nanba
- Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
| | - Katsumi Higaki
- Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
| | - José M García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Avda. Américo Vespucio 49, Isla de la Cartuja, 41092 Sevilla, Spain.
| | - Olivier Renaudet
- Université Grenoble Alpes, CNRS, DCM UMR 5250, 3800 Grenoble, France. and Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Carmen Ortiz Mellet
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/Profesor García González 1, 41012 Seville, Spain.
| |
Collapse
|
19
|
Lee LYH, Loscalzo J. Network Medicine in Pathobiology. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1311-1326. [PMID: 31014954 DOI: 10.1016/j.ajpath.2019.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022]
Abstract
The past decade has witnessed exponential growth in the generation of high-throughput human data across almost all known dimensions of biological systems. The discipline of network medicine has rapidly evolved in parallel, providing an unbiased, comprehensive biological framework through which to interrogate and integrate systematically these large-scale, multi-omic data to enhance our understanding of disease mechanisms and to design drugs that reflect a deep knowledge of molecular pathobiology. In this review, we discuss the key principles of network medicine and the human disease network and explore the latest applications of network medicine in this multi-omic era. We also highlight the current conceptual and technological challenges, which serve as exciting opportunities by which to improve and expand the network-based applications beyond the artificial boundaries of the current state of human pathobiology.
Collapse
Affiliation(s)
| | - Joseph Loscalzo
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| |
Collapse
|
20
|
Kreis W, Munkert J. Exploiting enzyme promiscuity to shape plant specialized metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1435-1445. [PMID: 30715457 DOI: 10.1093/jxb/erz025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/11/2018] [Accepted: 01/11/2019] [Indexed: 05/23/2023]
Abstract
The amazing variability of plant metabolism and its rapid divergence during evolution pose fundamental questions as to the driving forces, mechanisms, and players in metabolic differentiation. This review examines concepts that help us understand adaptive pathway evolution, with a particular emphasis on plant specialized metabolism, previously often termed secondary metabolism. Following a general introduction to pathway and metabolite evolution, the focus is directed to enzyme promiscuity and its classification. Promiscuous enzymes (or substrates), 'silent' elements of the metabolome, and the 'underground metabolism' may be used and combined to evolve 'new' metabolic pathways. It appears that new pathways rarely appear from scratch, but instead emerge from 'floppy' enzymes and elements of a 'messy' metabolism, and in this way a range of metabolites is generated, some of which may provide benefits to the plant.
Collapse
Affiliation(s)
| | - Jennifer Munkert
- Friedrich-Alexander University Erlangen-Nürnberg, Department of Biology, Division of Pharmaceutical Biology, Erlangen, Germany
| |
Collapse
|
21
|
Wang D, Weng J, Wang W. An unconventional ligand‐binding mechanism of substrate‐binding proteins: MD simulation and Markov state model analysis of BtuF. J Comput Chem 2019; 40:1440-1448. [DOI: 10.1002/jcc.25798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/22/2018] [Accepted: 01/28/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Dongdong Wang
- Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex System Fudan University Shanghai 200438 People's Republic of China
| | - Jingwei Weng
- Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex System Fudan University Shanghai 200438 People's Republic of China
| | - Wenning Wang
- Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex System Fudan University Shanghai 200438 People's Republic of China
| |
Collapse
|
22
|
Grünwald B, Schoeps B, Krüger A. Recognizing the Molecular Multifunctionality and Interactome of TIMP-1. Trends Cell Biol 2019; 29:6-19. [DOI: 10.1016/j.tcb.2018.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 01/31/2023]
|
23
|
Aissa R, Guezane-Lakoud S, Kolodziej E, Toffano M, Aribi-Zouioueche L. Diastereoselective synthesis of bis(α-aminophosphonates) by lipase catalytic promiscuity. NEW J CHEM 2019. [DOI: 10.1039/c8nj06235h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
New bis(α-aminophosphonates) were directly prepared with high diastereoselectivity by lipase catalytic promiscuity in the presence of immobilized Candida antarctica lipase.
Collapse
Affiliation(s)
- Rim Aissa
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE)
- Badji Mokhtar Annaba-University
- 23000 Annaba
- Algeria
| | - Samia Guezane-Lakoud
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE)
- Badji Mokhtar Annaba-University
- 23000 Annaba
- Algeria
| | - Emilie Kolodziej
- Equipe de Catalyse Moléculaire
- ICMMO
- UMR CNRS
- Bât 420
- Université Paris-Sud
| | - Martial Toffano
- Equipe de Catalyse Moléculaire
- ICMMO
- UMR CNRS
- Bât 420
- Université Paris-Sud
| | - Louisa Aribi-Zouioueche
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE)
- Badji Mokhtar Annaba-University
- 23000 Annaba
- Algeria
| |
Collapse
|
24
|
Macias-Contreras M, He H, Zhu L. Beyond O6-Benzylguanine: O6-(5-Pyridylmethyl)guanine as a Substrate for the Self-Labeling Enzyme SNAP-Tag. Bioconjug Chem 2018; 29:4104-4109. [DOI: 10.1021/acs.bioconjchem.8b00703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Miguel Macias-Contreras
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Huan He
- College of Medicine, Florida State University, Tallahassee, Florida 32306-4300, United States
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| |
Collapse
|
25
|
Reciprocal Perspective for Improved Protein-Protein Interaction Prediction. Sci Rep 2018; 8:11694. [PMID: 30076341 PMCID: PMC6076239 DOI: 10.1038/s41598-018-30044-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/20/2018] [Indexed: 02/06/2023] Open
Abstract
All protein-protein interaction (PPI) predictors require the determination of an operational decision threshold when differentiating positive PPIs from negatives. Historically, a single global threshold, typically optimized via cross-validation testing, is applied to all protein pairs. However, we here use data visualization techniques to show that no single decision threshold is suitable for all protein pairs, given the inherent diversity of protein interaction profiles. The recent development of high throughput PPI predictors has enabled the comprehensive scoring of all possible protein-protein pairs. This, in turn, has given rise to context, enabling us now to evaluate a PPI within the context of all possible predictions. Leveraging this context, we introduce a novel modeling framework called Reciprocal Perspective (RP), which estimates a localized threshold on a per-protein basis using several rank order metrics. By considering a putative PPI from the perspective of each of the proteins within the pair, RP rescores the predicted PPI and applies a cascaded Random Forest classifier leading to improvements in recall and precision. We here validate RP using two state-of-the-art PPI predictors, the Protein-protein Interaction Prediction Engine and the Scoring PRotein INTeractions methods, over five organisms: Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, and Mus musculus. Results demonstrate the application of a post hoc RP rescoring layer significantly improves classification (p < 0.001) in all cases over all organisms and this new rescoring approach can apply to any PPI prediction method.
Collapse
|
26
|
Chakraborty S. Inconclusive studies on possible CRISPR-Cas off-targets should moderate expectations about enzymes that have evolved to be non-specific. J Biosci 2018; 43:225-228. [PMID: 29872009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Sandeep Chakraborty
- R-44/1, Celia Engineers, T. T. C Industrial Area, Rabale, Navi Mumbai 400701, India,
| |
Collapse
|
27
|
Inconclusive studies on possible CRISPR-Cas off-targets should moderate expectations about enzymes that have evolved to be non-specific. J Biosci 2018. [DOI: 10.1007/s12038-018-9761-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
28
|
Bathellier C, Tcherkez G, Lorimer GH, Farquhar GD. Rubisco is not really so bad. PLANT, CELL & ENVIRONMENT 2018; 41:705-716. [PMID: 29359811 DOI: 10.1111/pce.13149] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the most widespread carboxylating enzyme in autotrophic organisms. Its kinetic and structural properties have been intensively studied for more than half a century. Yet important aspects of the catalytic mechanism remain poorly understood, especially the oxygenase reaction. Because of its relatively modest turnover rate (a few catalytic events per second) and the competitive inhibition by oxygen, Rubisco is often viewed as an inefficient catalyst for CO2 fixation. Considerable efforts have been devoted to improving its catalytic efficiency, so far without success. In this review, we re-examine Rubisco's catalytic performance by comparison with other chemically related enzymes. We find that Rubisco is not especially slow. Furthermore, considering both the nature and the complexity of the chemical reaction, its kinetic properties are unremarkable. Although not unique to Rubisco, oxygenation is not systematically observed in enolate and enamine forming enzymes and cannot be considered as an inevitable consequence of the mechanism. It is more likely the result of a compromise between chemical and metabolic imperatives. We argue that a better description of Rubisco mechanism is still required to better understand the link between CO2 and O2 reactivity and the rationale of Rubisco diversification and evolution.
Collapse
Affiliation(s)
- Camille Bathellier
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - Guillaume Tcherkez
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 27042, USA
| | - Graham D Farquhar
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| |
Collapse
|
29
|
Mortuza R, Aung HL, Taiaroa G, Opel-Reading HK, Kleffmann T, Cook GM, Krause KL. Overexpression of a newly identified d-amino acid transaminase inMycobacterium smegmatiscomplements glutamate racemase deletion. Mol Microbiol 2017; 107:198-213. [DOI: 10.1111/mmi.13877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Roman Mortuza
- Department of Biochemistry; University of Otago; Otago New Zealand
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - Htin Lin Aung
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - George Taiaroa
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | | | | | - Gregory M. Cook
- Department of Microbiology and Immunology; University of Otago; Otago New Zealand
| | - Kurt L. Krause
- Department of Biochemistry; University of Otago; Otago New Zealand
| |
Collapse
|
30
|
Guezane-Lakoud S, Toffano M, Aribi-Zouioueche L. Promiscuous lipase catalyzed a new P-C bond formation: Green and efficient protocol for one-pot synthesis of α-aminophosphonates. HETEROATOM CHEMISTRY 2017. [DOI: 10.1002/hc.21408] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Samia Guezane-Lakoud
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE); Badji Mokhtar Annaba-University; Annaba Algeria
| | - Martial Toffano
- Equipe de Catalyse Moléculaire-ICMMO- CNRS UMR8182 Bât 420; Université Paris-Sud; Orsay France
| | - Louisa Aribi-Zouioueche
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE); Badji Mokhtar Annaba-University; Annaba Algeria
| |
Collapse
|
31
|
Ryzhkova EP. Alternative enzymes as a special strategy for the adaptation of procaryotic organisms (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
32
|
Ortiz Mellet C, Nierengarten JF, García Fernández JM. Multivalency as an action principle in multimodal lectin recognition and glycosidase inhibition: a paradigm shift driven by carbon-based glyconanomaterials. J Mater Chem B 2017; 5:6428-6436. [PMID: 32264409 DOI: 10.1039/c7tb00860k] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The last decade has witnessed a series of discoveries that question the traditional paradigm of multivalency as a "safe" strategy to enhance the binding affinity of a lectin receptor to its cognate carbohydrate ligand. Upon following the initial reports on the supplementary effects operating in the presence of a third carbohydrate species (heteromultivalent effect), the observation of functional promiscuity of glyco(mimetic)ligands elicited by (hetero)multivalency, spreading from lectins to glycoprocessing enzymes (inhibitory multivalent effect), has raised concerns about the potential consequences of glyconanomaterials binding to non-cognate proteins and creating messiness or noise in the processes they participate in. Carbon-based glycomaterials, specifically glyconanodiamonds and glycofullerenes, have been instrumental in increasing our awareness of the frequency of these lectin-enzyme crosstalk behaviours elicited by multivalency, driving a reformulation of the rules and concepts in glycoscience towards a "generalized multivalency" scenario.
Collapse
Affiliation(s)
- Carmen Ortiz Mellet
- Department of Organic Chemistry, Faculty of Chemistry, University of Sevilla, c/ Profesor García González 1, 41011 Sevilla, Spain.
| | | | | |
Collapse
|
33
|
Adamski CJ, Palzkill T. BLIP-II Employs Differential Hotspot Residues To Bind Structurally Similar Staphylococcus aureus PBP2a and Class A β-Lactamases. Biochemistry 2017; 56:1075-1084. [PMID: 28182405 DOI: 10.1021/acs.biochem.6b00978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interaction of β-lactamase inhibitory protein II (BLIP-II) with β-lactamases serves as a model system to investigate the principles underlying protein-protein interactions. Previous studies have focused on identifying the determinants of binding affinity and specificity between BLIP-II and class A β-lactamases. However, interactions between BLIP-II and other bacterial proteins have yet to be explored. Here, we provide evidence that BLIP-II binds penicillin binding protein 2a (PBP2a) from methicillin-resistant Staphylococcus aureus (MRSA) with a KD in the low micromolar range. In comparison to the binding constants for the potent interaction between BLIP-II and TEM-1 β-lactamase (KD = 0.5 pM), the on-rate for BLIP-II binding PBP2a is 44 000 times slower and the off-rate is 170 times faster. Therefore, a slow association rate is a limiting factor for the potency of the interaction between BLIP-II and PBP2a. Results from alanine scanning mutagenesis of the predicted interface residues of BLIP-II indicate that charged residues on the periphery of the BLIP-II interface play a critical role for binding PBP2a, in contrast to previous findings that aromatic residues at the center of the BLIP-II interface are critical for the interaction with β-lactamases. Interestingly, many of the alanine mutants at the BLIP-II interface increase kon for binding PBP2a, consistent with the association rate being a limiting factor for affinity. In summary, the results of the study reveal that BLIP-II binds PBP2a, although weakly compared to binding of β-lactamases, and provides insights into the different binding strategies used for these targets.
Collapse
Affiliation(s)
- Carolyn J Adamski
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmacology, Baylor College of Medicine , Houston, Texas 77030, United States
| | - Timothy Palzkill
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmacology, Baylor College of Medicine , Houston, Texas 77030, United States
| |
Collapse
|
34
|
|
35
|
Musille PM, Kossmann BR, Kohn JA, Ivanov I, Ortlund EA. Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity. J Biol Chem 2015; 291:1411-26. [PMID: 26553876 DOI: 10.1074/jbc.m115.662874] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/06/2022] Open
Abstract
Phospholipids (PLs) are unusual signaling hormones sensed by the nuclear receptor liver receptor homolog-1 (LRH-1), which has evolved a novel allosteric pathway to support appropriate interaction with co-regulators depending on ligand status. LRH-1 plays an important role in controlling lipid and cholesterol homeostasis and is a potential target for the treatment of metabolic and neoplastic diseases. Although the prospect of modulating LRH-1 via small molecules is exciting, the molecular mechanism linking PL structure to transcriptional co-regulator preference is unknown. Previous studies showed that binding to an activating PL ligand, such as dilauroylphosphatidylcholine, favors LRH-1's interaction with transcriptional co-activators to up-regulate gene expression. Both crystallographic and solution-based structural studies showed that dilauroylphosphatidylcholine binding drives unanticipated structural fluctuations outside of the canonical activation surface in an alternate activation function (AF) region, encompassing the β-sheet-H6 region of the protein. However, the mechanism by which dynamics in the alternate AF influences co-regulator selectivity remains elusive. Here, we pair x-ray crystallography with molecular modeling to identify an unexpected allosteric network that traverses the protein ligand binding pocket and links these two elements to dictate selectivity. We show that communication between the alternate AF region and classical AF2 is correlated with the strength of the co-regulator interaction. This work offers the first glimpse into the conformational dynamics that drive this unusual PL-mediated nuclear hormone receptor activation.
Collapse
Affiliation(s)
- Paul M Musille
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | - Bradley R Kossmann
- the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302
| | - Jeffrey A Kohn
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | - Ivaylo Ivanov
- the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302
| | - Eric A Ortlund
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
| |
Collapse
|