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Rhein S, Costalunga R, Inderhees J, Gürtzgen T, Faupel TC, Shaheryar Z, Arrulo Pereira A, Othman A, Begemann K, Binder S, Stölting I, Dorta V, Nawroth PP, Fleming T, Oexle K, Prevot V, Nogueiras R, Meyhöfer S, Meyhöfer SM, Schwaninger M. The reactive pyruvate metabolite dimethylglyoxal mediates neurological consequences of diabetes. Nat Commun 2024; 15:5745. [PMID: 38987239 PMCID: PMC11237006 DOI: 10.1038/s41467-024-50089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
Complications of diabetes are often attributed to glucose and reactive dicarbonyl metabolites derived from glycolysis or gluconeogenesis, such as methylglyoxal. However, in the CNS, neurons and endothelial cells use lactate as energy source in addition to glucose, which does not lead to the formation of methylglyoxal and has previously been considered a safer route of energy consumption than glycolysis. Nevertheless, neurons and endothelial cells are hotspots for the cellular pathology underlying neurological complications in diabetes, suggesting a cause that is distinct from other diabetes complications and independent of methylglyoxal. Here, we show that in clinical and experimental diabetes plasma concentrations of dimethylglyoxal are increased. In a mouse model of diabetes, ilvb acetolactate-synthase-like (ILVBL, HACL2) is the enzyme involved in formation of increased amounts of dimethylglyoxal from lactate-derived pyruvate. Dimethylglyoxal reacts with lysine residues, forms Nε-3-hydroxy-2-butanonelysine (HBL) as an adduct, induces oxidative stress more strongly than other dicarbonyls, causes blood-brain barrier disruption, and can mimic mild cognitive impairment in experimental diabetes. These data suggest dimethylglyoxal formation as a pathway leading to neurological complications in diabetes that is distinct from other complications. Importantly, dimethylglyoxal formation can be reduced using genetic, pharmacological and dietary interventions, offering new strategies for preventing CNS dysfunction in diabetes.
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Affiliation(s)
- Sina Rhein
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Riccardo Costalunga
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
- Bioanalytic Core Facility, Center for Brain Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Julica Inderhees
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany
- Bioanalytic Core Facility, Center for Brain Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Tammo Gürtzgen
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Teresa Christina Faupel
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Zaib Shaheryar
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Adriana Arrulo Pereira
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Alaa Othman
- Bioanalytic Core Facility, Center for Brain Behavior and Metabolism, University of Lübeck, Lübeck, Germany
- Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland
| | - Kimberly Begemann
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Sonja Binder
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Ines Stölting
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Valentina Dorta
- Department of Physiology, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de, Compostela, Spain
| | - Peter P Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Fleming
- Department of Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
| | - Konrad Oexle
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz, Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Vincent Prevot
- Univ. Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S 1172, DISTALZ, EGID, Lille, France
| | - Ruben Nogueiras
- Department of Physiology, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de, Compostela, Spain
| | - Svenja Meyhöfer
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
- Institute for Endocrinology and Diabetes, University of Lübeck, Lübeck, Germany
- Department of Medicine I, University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Sebastian M Meyhöfer
- German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
- Institute for Endocrinology and Diabetes, University of Lübeck, Lübeck, Germany
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany.
- German Research Centre for Cardiovascular Research (DZHK), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany.
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2
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Chatterjee A, Goswami S, Kumar R, Laha J, Das D. Emergence of a short peptide based reductase via activation of the model hydride rich cofactor. Nat Commun 2024; 15:4515. [PMID: 38802430 PMCID: PMC11130128 DOI: 10.1038/s41467-024-48930-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
In extant biology, large and complex enzymes employ low molecular weight cofactors such as dihydronicotinamides as efficient hydride transfer agents and electron carriers for the regulation of critical metabolic processes. In absence of complex contemporary enzymes, these molecular cofactors are generally inefficient to facilitate any reactions on their own. Herein, we report short peptide-based amyloid nanotubes featuring exposed arrays of cationic and hydrophobic residues that can bind small molecular weak hydride transfer agents (NaBH4) to facilitate efficient reduction of ester substrates in water. In addition, the paracrystalline amyloid phases loaded with borohydrides demonstrate recyclability, substrate selectivity and controlled reduction and surpass the capabilities of standard reducing agent such as LiAlH4. The amyloid microphases and their collaboration with small molecular cofactors foreshadow the important roles that short peptide-based assemblies might have played in the emergence of protometabolism and biopolymer evolution in prebiotic earth.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Surashree Goswami
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Raushan Kumar
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Janmejay Laha
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India.
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3
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Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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4
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Kim J, Kim EJ, Ko HJ, Lee YH, Hong SK, Shin M, Lee JH, Kwak W. Construction of Streptomyces coelicolor A3(2) mutants that exclusively produce NA4/NA6 intermediates of agarose metabolism through mutation induction. Sci Rep 2023; 13:18968. [PMID: 37923760 PMCID: PMC10624881 DOI: 10.1038/s41598-023-46410-7] [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: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023] Open
Abstract
NA4/NA6, an intermediate degradation product of β-agarase, is a high value-added product with anticancer, anti-obesity, and anti-diabetic effects. Therefore, a method that enables the efficient production of NA4/NA6 would be useful from economic and medical perspectives. In this study, we aimed to generate a Streptomyces coelicolor A3(2) mutant M22-2C43 that produces NA4/NA6 as a final product; this method serves as a more efficient alternative to the enzymatic conversion of β-agarase for the generation of these products. The M22-2C43 strain was generated through two rounds of mutagenesis and screening for increased β-agarase activity and effective production of NA4/NA6. We assembled the complete genomes of two mutants, M22 and M22-2C43, which were identified following a two-round screening. Large and small genetic changes were found in these two mutants, including the loss of two plasmids present in wild-type S. coelicolor A3(2) and chromosome circularization of mutant M22-2C43. These findings suggest that mutant M22-2C43 can produce NA4/NA6 as a degradation product due to functional inactivation of the dagB gene through a point mutation (G474A), ultimately preventing further degradation of NA4/NA6 to NA2. To our knowledge, this is the first report of a microbial strain that can effectively produce NA4/NA6 as the main degradation product of β-agarase, opening the door for the use of this species for the large-scale production of this valuable product.
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Affiliation(s)
- Jina Kim
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Eun Joo Kim
- Dyne Bio Inc., Seongnam-si, Gyeonggido, 13209, Republic of Korea
| | - Hye-Jeong Ko
- Dyne Bio Inc., Seongnam-si, Gyeonggido, 13209, Republic of Korea
| | - Yeon-Hee Lee
- Dyne Bio Inc., Seongnam-si, Gyeonggido, 13209, Republic of Korea
| | - Soon-Kwang Hong
- Department of Biological Science and Bioinformatics, Myongji University, 116 Myongji-Ro, Cheoin-gu, Yongin, 17058, Gyeonggido, Korea
| | - Miyoung Shin
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Je Hyeon Lee
- Dyne Bio Inc., Seongnam-si, Gyeonggido, 13209, Republic of Korea.
| | - Woori Kwak
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
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5
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Leone D, Pohl R, Hubálek M, Kadeřábková M, Krömer M, Sýkorová V, Hocek M. Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins. Chemistry 2022; 28:e202104208. [DOI: 10.1002/chem.202104208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Marta Kadeřábková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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6
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Yi Z, Junwen L, Sijin W, Haiming C. Ion-imprinted guanidine-functionalized zeolite molecular sieves enhance the adsorption selectivity and antibacterial properties for uranium extraction. RSC Adv 2022; 12:15470-15478. [PMID: 35693237 PMCID: PMC9121788 DOI: 10.1039/d2ra01651f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/14/2022] [Indexed: 11/26/2022] Open
Abstract
The important properties in the development of adsorbents for uranium extraction from seawater include specific selectivity to uranium ions and anti-biofouling ability in the ocean environment. In this paper, we report a novel strategy for efficient selective extraction of uranium from aqueous solutions and good anti-bacterial properties by surface ion-imprinted zeolite molecular sieves. Guanidine-modified zeolite molecular sieves 13X (ZMS-G) were synthesized and used as the support for the preparation of uranium(vi) ion-imprinted adsorbents (IIZMS-G) by ligands with phosphonic groups. The prepared IIZMS-G adsorbent was characterized via Fourier transform infrared spectroscopy (FT-IR), scanning electronic microscopy (SEM), X-ray diffraction (XRD), and energy dispersive spectroscopy (EDS). The results showed that guanidine groups have been successfully introduced onto the support while its morphology structure was maintained. The adsorption performance and selectivity to U(vi) ions, antibacterial property, and reusability of IIZMS-G were evaluated. The results showed that the maximum adsorption capacity reached 141.09 mg g−1 when the initial concentration of metal ions was 50 mg L−1 at pH 6 and 20 °C. The adsorption process followed the pseudo-second-order kinetic model and Langmuir adsorption isotherm model. The IIZMS-G exhibits an efficient selective adsorption of U(vi) ions from aqueous solutions with competing ions. In addition, the IIZMS-G exhibited excellent inhibitory effects on Escherichia coli and Staphylococcus aureus, and the inhibitory rate was 99.99% and 98.96% respectively. These results suggest that the prepared IIZMS-G adsorbent may promote the development strategy of novel high selectivity and antifouling adsorbents for uranium recovery from seawater. The important properties in the development of adsorbents for uranium extraction from seawater include specific selectivity to uranium ions and anti-biofouling ability in the ocean environment.![]()
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Affiliation(s)
- Zhao Yi
- The Key Laboratory of Leather Chemistry and Engineering of Ministry of Education, Sichuan University, Chengdu 610065, China
- National Engineering Laboratory for Clean Technology of Leather Manufacture, Sichuan University, Chengdu 610065, Sichuan, China
| | - Li Junwen
- The Key Laboratory of Leather Chemistry and Engineering of Ministry of Education, Sichuan University, Chengdu 610065, China
| | - Wu Sijin
- The Key Laboratory of Leather Chemistry and Engineering of Ministry of Education, Sichuan University, Chengdu 610065, China
| | - Cheng Haiming
- The Key Laboratory of Leather Chemistry and Engineering of Ministry of Education, Sichuan University, Chengdu 610065, China
- National Engineering Laboratory for Clean Technology of Leather Manufacture, Sichuan University, Chengdu 610065, Sichuan, China
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7
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Pharmacokinetics of Azalomycin F, a Natural Macrolide Produced by Streptomycete Strains, in Rats. Molecules 2021; 26:molecules26216464. [PMID: 34770873 PMCID: PMC8588360 DOI: 10.3390/molecules26216464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 12/05/2022] Open
Abstract
As antimicrobial resistance has been increasing, new antimicrobial agents are desperately needed. Azalomycin F, a natural polyhydroxy macrolide, presents remarkable antimicrobial activities. To investigate its pharmacokinetic characteristics in rats, the concentrations of azalomycin F contained in biological samples, in vitro, were determined using a validated high-performance liquid chromatography–ultraviolet (HPLC-UV) method, and, in vivo, samples were assayed by an ultra-high performance liquid chromatography–tandem mass spectrometric (UPLC–MS/MS) method. Based on these methods, the pharmacokinetics of azalomycin F were first investigated. Its plasma concentration-time courses and pharmacokinetic parameters in rats were obtained by a non-compartment model for oral (26.4 mg/kg) and intravenous (2.2 mg/kg) administrations. The results indicate that the oral absolute bioavailability of azalomycin F is very low (2.39 ± 1.28%). From combinational analyses of these pharmacokinetic parameters, and of the results of the in-vitro absorption and metabolism experiments, we conclude that azalomycin F is absorbed relatively slowly and with difficulty by the intestinal tract, and subsequently can be rapidly distributed into the tissues and/or intracellular f of rats. Azalomycin F is stable in plasma, whole blood, and the liver, and presents plasma protein binding ratios of more than 90%. Moreover, one of the major elimination routes of azalomycin F is its excretion through bile and feces. Together, the above indicate that azalomycin F is suitable for administration by intravenous injection when used for systemic diseases, while, by oral administration, it can be used in the treatment of diseases of the gastrointestinal tract.
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Nubi T, Adewole TS, Agunbiade TO, Osukoya OA, Kuku A. Purification and erythrocyte-membrane perturbing activity of a ketose-specific lectin from Moringa oleifera seeds. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 31:e00650. [PMID: 34258240 PMCID: PMC8253949 DOI: 10.1016/j.btre.2021.e00650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 05/26/2021] [Accepted: 06/16/2021] [Indexed: 12/17/2022]
Abstract
This study purified a hemagglutinating protein (MoL) from Moringa oleifera seed, and investigated its hemolytic activity. Molecular weight and stability of MoL were also determined. Modification of some amino acid residues was carried out and the effect on MoL hemagglutinating activity determined. Other investigated parameters are the effects of temperature, concentration, incubation period, pH, and sugars on the protein's hemagglutinating and hemolytic activities. The native and subunit molecular weights were estimated as 30 and 27.5 kDa respectively. Hemagglutinating activity of MoL was slightly inhibited by fructose and sucrose, stable at temperature up to 90°C and within pH range of 2-4. Modification of tryptophan and arginine residues resulted in partial loss of hemagglutinating activity. The hemolytic activity of MoL was concentration, temperature, pH, and time-dependent. The study concluded that MoL showed hemolytic (membrane-perturbing) activity in moderate acidic conditions. This suggests its potential exploitation in improved intracellular delivery of bioactive compounds.
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Affiliation(s)
- Tolulope Nubi
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University Ile-Ife, PMB 13, Nigeria
| | | | | | | | - Adenike Kuku
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University Ile-Ife, PMB 13, Nigeria
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9
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Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021; 60:17383-17387. [PMID: 34107150 PMCID: PMC8362068 DOI: 10.1002/anie.202105126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Indexed: 12/28/2022]
Abstract
Linear or branched 1,3-diketone-linked thymidine 5'-O-mono- and triphosphate were synthesized through CuAAC click reaction of diketone-alkynes with 5-azidomethyl-dUMP or -dUTP. The triphosphates were good substrates for KOD XL DNA polymerase in primer extension synthesis of modified DNA. The nucleotide bearing linear 3,5-dioxohexyl group (HDO) efficiently reacted with arginine-containing peptides to form stable pyrimidine-linked conjugates, whereas the branched 2-acetyl-3-oxo-butyl (PDO) group was not reactive. Reaction with Lys or a terminal amino group formed enamine adducts that were prone to hydrolysis. This reactive HDO modification in DNA was used for bioconjugations and cross-linking with Arg-containing peptides or proteins (e.g. histones).
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Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
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10
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Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3‐Diketone‐Modified Nucleotides and DNA for Cross‐Linking with Arginine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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11
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Patra P, Banerjee R, Chakrabarti J. Control of solvent exposure of cationic polypeptides in anionic environment. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Zhang GQ, Li YS, Zhao Y, Luo YX, Gao XF. A rapid and automated flow injection spectrophotometric determination method for pioglitazone/metformin hydrochloride in pharmaceutical preparation and to confirmation of its reaction principle using PCX column. Microchem J 2020. [DOI: 10.1016/j.microc.2020.104698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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14
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Zhang H, Zhang L, Han X, Kuang L, Hua D. Guanidine and Amidoxime Cofunctionalized Polypropylene Nonwoven Fabric for Potential Uranium Seawater Extraction with Antifouling Property. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.7b04687] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Huijun Zhang
- State
Key Laboratory of Radiation Medicine and Protection, School for Radiological
and Interdisciplinary Sciences (RAD−X), Soochow University, Suzhou 215123, China
| | - Lixia Zhang
- State
Key Laboratory of Radiation Medicine and Protection, School for Radiological
and Interdisciplinary Sciences (RAD−X), Soochow University, Suzhou 215123, China
| | - Xiaoli Han
- State
Key Laboratory of Radiation Medicine and Protection, School for Radiological
and Interdisciplinary Sciences (RAD−X), Soochow University, Suzhou 215123, China
| | - Liangju Kuang
- Department
of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Daoben Hua
- State
Key Laboratory of Radiation Medicine and Protection, School for Radiological
and Interdisciplinary Sciences (RAD−X), Soochow University, Suzhou 215123, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
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15
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Zong L, Tan CH. Phase-Transfer and Ion-Pairing Catalysis of Pentanidiums and Bisguanidiniums. Acc Chem Res 2017; 50:842-856. [PMID: 28379012 DOI: 10.1021/acs.accounts.6b00604] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Catalysts accelerate biological processes and organic reactions in a controlled and selective fashion. There are continuing efforts in asymmetric catalysis to develop efficient catalysts with broad reaction scope and industrial practicability. Among the various modes of asymmetric catalysis, phase-transfer catalysis has attracted intense interest due to its facile scale up and low catalyst loading. Chiral quaternary ammonium and phosphonium salts are well-studied classes of chiral phase-transfer catalysts, and they are typically composed of sp3-hybridized quaternary onium salts. In this Account, we describe our recent attempts to develop N-sp2-hybridized guanidinium-type salts as efficient phase-transfer catalysts as well as ion-pair catalysis based on N-sp2 hybridized bisguanidinium-type salts. The sp2-quaternized ammonium salts, pentanidiums, which contain five nitrogen atoms in conjugation, displayed remarkable phase-transfer catalytic efficiency. We have shown that pentanidium can catalyze Michael additions of tert-butyl glycinate-benzophenone Schiff bases with various α,β-unsaturated acceptors, such as vinyl ketones, acrylates, and chalcones, in high enantioselectivities. The structurally amendable pentanidium phase-transfer catalysts supply diverse reactivity and selectivity to various other organic transformations, such as α-hydroxylation of 3-substituted-2-oxindoles, Michael addition of 3-alkyloxindoles with vinyl sulfone, and alkylation reactions of sulfenate anions and dihydrocoumarins. Pentanidium salts are applicable to enantioselective transformations on a preparative scale at low catalyst loading, allowing for the synthesis of a broad range of enantiopure compounds. From computational and experimental results, we also proposed that the halogenated pentanidium catalysts participated in halogen bonding and that this contributed to the excellent stereocontrol in alkylation reactions. Subsequently, we determined that chiral cations can direct functional anions besides basic anions in traditional Brønsted basic phase-transfer reactions, including metal-centered anions. We identified dicationic bisguanidinium as an excellent ion-pairing catalyst, first demonstrating that bisguanidinium formed an ion pair with permanganate and directed the anion in enantioselective dihydroxylation and oxohydroxylation of a,β-unsaturated esters. This initial success led us to explore chiral cationic ion-pairing catalysis as a general mode of catalysis. This mode of catalysis is at the interphase between organocatalysis, phase-transfer catalysis and organometallic catalysis. We then identified bisguanidinium diphosphatobisperoxotungstate and bisguanidinium dinuclear oxodiperoxomolybdosulfate ion pairs as the active catalysts in enantioselective sulfoxidations using aqueous H2O2 as the oxidant. The structure of the bisguanidinium dinuclear oxodiperoxomolybdosulfate ion pair was elucidated using single-crystal X-ray analysis. Bisguanidinium-catalyzed sulfoxidations emerged as a practical methodology for the synthesis of enantioenriched sulfoxides including armodafinil and lansoprazole, which are commercial drugs. Finally, we are also able to show that pentanidium and bisguanidinium hypervalent silicates are intermediates in enantioselective alkylations using silylamide as a Brønsted probase.
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Affiliation(s)
- Lili Zong
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Choon-Hong Tan
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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16
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Wang A, Zhou R, Zhou L, Sun K, Zhou J, Wei S, Jiang J. Arginine-Substituted Phthalocyanine with Concentration-Driven Self-Disaggregation Performance: Synthesis, Properties and Mechanistic Study. Chem Asian J 2016; 11:3008-3013. [DOI: 10.1002/asia.201601133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Ao Wang
- Institute of Chemical Industry of Forest Products, CAF; Key Lab of Biomass Energy and Material, Jiangsu Province; National Engineering Lab. For Biomass Chemical Utilization; Key and Open Lab. Of Forest Chemical Engineering, SFA; Institute of Chemical Industry of Forest Products, CAF; No. 16, Suojin 5th Village Nanjing 210042 China
- School of Chemistry and Materials Science; Jiangsu Key Laboratory of Biofunctional Materials; Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials; Key Laboratory of Applied Photochemistry; Nanjing Normal University; Wenyuan Road No.1 Nanjing 210023 China
| | - Rongrong Zhou
- School of Chemistry and Materials Science; Jiangsu Key Laboratory of Biofunctional Materials; Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials; Key Laboratory of Applied Photochemistry; Nanjing Normal University; Wenyuan Road No.1 Nanjing 210023 China
| | - Lin Zhou
- School of Chemistry and Materials Science; Jiangsu Key Laboratory of Biofunctional Materials; Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials; Key Laboratory of Applied Photochemistry; Nanjing Normal University; Wenyuan Road No.1 Nanjing 210023 China
| | - Kang Sun
- Institute of Chemical Industry of Forest Products, CAF; Key Lab of Biomass Energy and Material, Jiangsu Province; National Engineering Lab. For Biomass Chemical Utilization; Key and Open Lab. Of Forest Chemical Engineering, SFA; Institute of Chemical Industry of Forest Products, CAF; No. 16, Suojin 5th Village Nanjing 210042 China
| | - Jiahong Zhou
- School of Chemistry and Materials Science; Jiangsu Key Laboratory of Biofunctional Materials; Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials; Key Laboratory of Applied Photochemistry; Nanjing Normal University; Wenyuan Road No.1 Nanjing 210023 China
| | - Shaohua Wei
- School of Chemistry and Materials Science; Jiangsu Key Laboratory of Biofunctional Materials; Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials; Key Laboratory of Applied Photochemistry; Nanjing Normal University; Wenyuan Road No.1 Nanjing 210023 China
| | - Jianchun Jiang
- Institute of Chemical Industry of Forest Products, CAF; Key Lab of Biomass Energy and Material, Jiangsu Province; National Engineering Lab. For Biomass Chemical Utilization; Key and Open Lab. Of Forest Chemical Engineering, SFA; Institute of Chemical Industry of Forest Products, CAF; No. 16, Suojin 5th Village Nanjing 210042 China
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17
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Delineation of the structural and functional role of Arg111 in GSTU4-4 from Glycine max by chemical modification and site-directed mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1315-21. [PMID: 27375050 DOI: 10.1016/j.bbapap.2016.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/20/2016] [Accepted: 06/29/2016] [Indexed: 12/16/2022]
Abstract
The structural and functional role of Arg111 in GSTU4-4 from Glycine max (GmGSTU4-4) was studied by chemical modification followed by site-directed mutagenesis. The arginine-specific reagent 2,3-butanedione (BTD) inactivates the enzyme in borate buffer at pH8.0, with pseudo-first-order saturation kinetics. The rate of inactivation exhibited a non-linear dependence on the concentration of BTD which can be described by reversible binding of reagent to the enzyme (KD 81.2±9.2mM) prior to the irreversible reaction, with maximum rate constants of 0.18±0.01min(-1). Protection from inactivation was afforded by substrate analogues demonstrating the specificity of the reaction. Structural analysis suggested that the modified residue is Arg111, which was confirmed by protein chemistry experiments. Site-directed mutagenesis was used in dissecting the role of Arg111 in substrate binding, specificity and catalytic mechanism. The mutant Arg111Ala enzyme exhibited unchanged Km value for GSH but showed reduced affinity for the xenobiotic substrates, higher kcat and specific activities towards aromatic substrates and lower specific activities towards aliphatic substrates. The biological significance of the specific modification of Arg111 by dicarbonyl compounds and the role of Arg111 as a target for engineering xenobiotic substrate specificity were discussed.
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18
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Hess AE, Beer PD. Chelated charge assisted halogen bonding enhanced halide recognition by a pyridinium-iodotriazolium axle containing [2]rotaxane. Org Biomol Chem 2016; 14:10193-10200. [DOI: 10.1039/c6ob01851c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A dicationic halogen bonding rotaxane displays enhanced binding and selectivity for bromide over other halides and nitrate and dihydrogen phosphate oxoanions in contrast to an all hydrogen bonding counterpart which is attributed to chelated charge assisted halogen bonding interactions.
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Affiliation(s)
- Alexander E. Hess
- Chemistry Research Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
| | - Paul D. Beer
- Chemistry Research Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
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19
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Abstract
Cyclic peptides provide excellent scaffolds for anion recognition and improved binding affinity and selectivity has been achieved through peptide backbone rigidification and the introduction of side chains bearing anion recognition groups.
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20
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A study on the nature of interactions of mixed-mode ligands HEA and PPA HyperCel using phenylglyoxal modified lysozyme. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 960:209-13. [DOI: 10.1016/j.jchromb.2014.04.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/23/2014] [Indexed: 11/20/2022]
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21
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Gupta P, Jairajpuri MA, Durani S. Redox specificity of 2-hydroxyacid-coupled NAD(+)/NADH dehydrogenases: a study exploiting "reactive" arginine as a reporter of protein electrostatics. PLoS One 2013; 8:e83505. [PMID: 24391777 PMCID: PMC3877072 DOI: 10.1371/journal.pone.0083505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/03/2013] [Indexed: 11/19/2022] Open
Abstract
With "reactive" arginine as a kinetic reporter, 2-hydroxyacid dehydrogenases are assessed in basis of their specialization as NAD(+)-reducing or NADH-oxidizing enzymes. Specifically, M4 and H4 lactate dehydrogenases (LDHs) and cytoplasmic and mitochondrial malate dehydrogenases (MDHs) are compared to assess if their coenzyme specificity may involve electrostatics of cationic or neutral nicotinamide structure as the basis. The enzymes from diverse eukaryote and prokaryote sources thus are assessed in "reactivity" of functionally-critical arginine as a function of salt concentration and pH. Electrostatic calculations were performed on "reactive" arginines and found good correspondence with experiment. The reductive and oxidative LDHs and MDHs are assessed in their count over ionizable residues and in placement details of the residues in their structures as proteins. The variants found to be high or low in ΔpKa of "reactive" arginine are found to be also strong or weak cations that preferentially oxidize NADH (neutral nicotinamide structure) or reduce NAD(+) (cationic nicotinamide structure). The ionized groups of protein structure may thus be important to redox specificity of the enzyme on basis of electrostatic preference for the oxidized (cationic nicotinamide) or reduced (neutral nicotinamide) coenzyme. Detailed comparisons of isozymes establish that the residues contributing in their redox specificity are scrambled in structure of the reductive enzyme.
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Affiliation(s)
- Pooja Gupta
- Department of Chemistry, Indian Institute of Biotechnology Bombay, Mumbai, India
| | - Mohamad Aman Jairajpuri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Biotechnology Bombay, Mumbai, India
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22
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Francis BR. Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J Mol Evol 2013; 77:134-58. [PMID: 23743924 DOI: 10.1007/s00239-013-9567-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/25/2013] [Indexed: 12/31/2022]
Abstract
Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids-valine, alanine, aspartic acid, and glycine-were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.
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Affiliation(s)
- Brian R Francis
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071-3944, USA,
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23
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Mendoza VL, Barón-Rodríguez MA, Blanco C, Vachet RW. Structural insights into the pre-amyloid tetramer of β-2-microglobulin from covalent labeling and mass spectrometry. Biochemistry 2011; 50:6711-22. [PMID: 21718071 DOI: 10.1021/bi2004894] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The main pathogenic process underlying dialysis-related amyloidosis is the accumulation of β-2-microglobulin (β2m) as amyloid fibrils in the musculoskeletal system, and some evidence suggests that Cu(II) may play a role in β2m amyloid formation. Cu(II)-induced β2m fibril formation is preceded by the formation of discrete, oligomeric intermediates, including dimers, tetramers, and hexamers. In this work, we use selective covalent labeling reactions combined with mass spectrometry to investigate the amino acids responsible for mediating tetramer formation in wild-type β2m. By comparing the labeling patterns of the monomer, dimer, and tetramer, we find evidence that the tetramer interface is formed by the interaction of D strands from one dimer unit and G strands from another dimer unit. These covalent labeling data along with molecular dynamics calculations allow the construction of a tetramer model that indicates how the protein might proceed to form even higher-order oligomers.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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24
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Potapovich MV, Eremin AN, Rubinov DB, Metelitza DI. Effect of herbicide tralkoxydim and 2-acylcyclohexane-1,3-diones on peroxidase activity. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683808010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Nygren P, Lundqvist M, Liedberg B, Jonsson BH, Ederth T. Secondary structure in de novo designed peptides induced by electrostatic interaction with a lipid bilayer membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:6437-6448. [PMID: 20349970 DOI: 10.1021/la100027n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We show that it is possible to induce a defined secondary structure in de novo designed peptides upon electrostatic attachment to negatively charged lipid bilayer vesicles without partitioning of the peptides into the membrane, and that the secondary structure can be varied via small changes in the primary amino acid sequence of the peptides. The peptides have a random-coil conformation in solution, and results from far-UV circular dichroism spectroscopy demonstrate that the structure induced by the interaction with silica nanoparticles is solely alpha-helical and also strongly pH-dependent. The present study shows that negatively charged vesicles, to which the peptides are electrostatically adsorbed via cationic amino acid residues, induce either alpha-helices or beta-sheets and that the conformation is dependent on both lipid composition and variations in peptide primary structure. The pH-dependence of the vesicle-induced peptide secondary structure is weak, which correlates well with small differences in the vesicles' electrophoretic mobility, and thus the surface charge, as the pH is varied.
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Affiliation(s)
- Patrik Nygren
- Division of Molecular Physics, IFM, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
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26
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27
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Mendoza VL, Antwi K, Barón-Rodríguez MA, Blanco C, Vachet RW. Structure of the preamyloid dimer of beta-2-microglobulin from covalent labeling and mass spectrometry. Biochemistry 2010; 49:1522-32. [PMID: 20088607 PMCID: PMC2848472 DOI: 10.1021/bi901748h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Beta-2-microglobulin (beta2m) self-associates into fibrillar amyloid deposits in the musculoskeletal system of patients undergoing hemodialysis treatment. Previous studies have shown that stoichiometric amounts of Cu(II) at near physiological conditions can cause beta2m to organize into native-like dimers prior to forming amyloid fibrils. Here, we report the results from selective covalent labeling reactions combined with mass spectrometry that provide insight into the amino acid residues that mediate dimer formation in the wild-type protein. Using three complementary covalent labeling reagents, we find that the dimer interface is formed by the antiparallel stacking of ABED beta-sheets from two beta2m monomers. In addition, our data clearly indicate that a dimer interface involving the interactions of D-D strands from separate protein units as seen in the recent crystal structures of two mutant beta2m oligomers is unlikely.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kwasi Antwi
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | | | | | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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28
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Mendoza VL, Vachet RW. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. MASS SPECTROMETRY REVIEWS 2009; 28:785-815. [PMID: 19016300 PMCID: PMC2768138 DOI: 10.1002/mas.20203] [Citation(s) in RCA: 270] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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29
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Lin TC, Lai CC, Chiu SH. A Guanidinium Ion-Based Anion- and Solvent Polarity-Controllable Molecular Switch. Org Lett 2008; 11:613-6. [DOI: 10.1021/ol802638k] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tzu-Chiun Lin
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan, 10617, R.O.C., and Institute of Molecular Biology, National Chung Hsing University and Department of Medical Genetics, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Chien-Chen Lai
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan, 10617, R.O.C., and Institute of Molecular Biology, National Chung Hsing University and Department of Medical Genetics, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Sheng-Hsien Chiu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan, 10617, R.O.C., and Institute of Molecular Biology, National Chung Hsing University and Department of Medical Genetics, China Medical University Hospital, Taichung, Taiwan, R.O.C
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30
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31
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Leach FR. A View on the Active Site of Firefly Luciferase. Nat Prod Commun 2008. [DOI: 10.1177/1934578x0800300908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The bioluminescent enzyme firefly luciferase has been the subject of detailed biochemical studies since the late 1940s. These studies have culminated in the cloning and sequence determination of some 161 different c-DNAs and/or genes for firefly luciferase and the determination of 6 crystallographic structures with and without reactants/products/analogs bound. This paper reviews these studies, searches for which amino acid residues are involved in the enzyme's action using chemical modification experiments, and analyzes the structure/function relationships of the various conserved amino acid residues. There are 71/550 amino acid residues conserved in the 161 different firefly luciferases. In my laboratory K-206, K-529, and R-437 were chemically modified; ATP inhibited these modifications suggesting that they are involved in the reaction. An integrated picture of the active site is postulated.
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Affiliation(s)
- Franklin R. Leach
- Department of Biochemistry and Molecular Biology, NRC246, Oklahoma State University, Stillwater, Oklahoma 74078—3035, USA
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32
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Zhang YM, Rock CO. Thematic review series: Glycerolipids. Acyltransferases in bacterial glycerophospholipid synthesis. J Lipid Res 2008; 49:1867-74. [PMID: 18369234 DOI: 10.1194/jlr.r800005-jlr200] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phospholipid biosynthesis is a vital facet of bacterial physiology that begins with the synthesis of the fatty acids by a soluble type II fatty acid synthase. The bacterial glycerol-phosphate acyltransferases utilize the completed fatty acid chains to form the first membrane phospholipid and thus play a critical role in the regulation of membrane biogenesis. The first bacterial acyltransferase described was PlsB, a glycerol-phosphate acyltransferase. PlsB is a key regulatory point that coordinates membrane phospholipid formation with cell growth and macromolecular synthesis. Phosphatidic acid is then produced by PlsC, a 1-acylglycerol-phosphate acyltransferase. These two acyltransferases use thioesters of either CoA or acyl carrier protein (ACP) as the acyl donors and have homologs that perform the same reactions in higher organisms. However, the most prevalent glycerol-phosphate acyltransferase in the bacterial world is PlsY, which uses a recently discovered acyl-phosphate fatty acid intermediate as an acyl donor. This unique activated fatty acid is formed from the acyl-ACP end products of the fatty acid biosynthetic pathway by PlsX, an acyl-ACP:phosphate transacylase.
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Affiliation(s)
- Yong-Mei Zhang
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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33
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Law CJ, Almqvist J, Bernstein A, Goetz RM, Huang Y, Soudant C, Laaksonen A, Hovmöller S, Wang DN. Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT. J Mol Biol 2008; 378:828-39. [PMID: 18395745 DOI: 10.1016/j.jmb.2008.03.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/05/2008] [Accepted: 03/13/2008] [Indexed: 10/22/2022]
Abstract
Active transport of substrates across cytoplasmic membranes is of great physiological, medical and pharmaceutical importance. The glycerol-3-phosphate (G3P) transporter (GlpT) of the E. coli inner membrane is a secondary active antiporter from the ubiquitous major facilitator superfamily that couples the import of G3P to the efflux of inorganic phosphate (P(i)) down its concentration gradient. Integrating information from a novel combination of structural, molecular dynamics simulations and biochemical studies, we identify the residues involved directly in binding of substrate to the inward-facing conformation of GlpT, thus defining the structural basis for the substrate-specificity of this transporter. The substrate binding mechanism involves protonation of a histidine residue at the binding site. Furthermore, our data suggest that the formation and breaking of inter- and intradomain salt bridges control the conformational change of the transporter that accompanies substrate translocation across the membrane. The mechanism we propose may be a paradigm for organophosphate:phosphate antiporters.
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Affiliation(s)
- Christopher J Law
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
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34
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Buche A, Picorel R. Spectral Changes Induced by Alkaline pH and Specific Chemical Modification of Amino Acid Residues in the Light-Harvesting II Antenna Complex from Ectothiorhodospira sp. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1999.tb03286.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Affiliation(s)
- Abigail G. Doyle
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Eric N. Jacobsen
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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36
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Leitner A, Lindner W. Functional probing of arginine residues in proteins using mass spectrometry and an arginine-specific covalent tagging concept. Anal Chem 2007; 77:4481-8. [PMID: 16013863 DOI: 10.1021/ac050217h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reactivity of arginine residues in model proteins (ubiquitin, cytochrome c, myoglobin, ribonuclease A, lysozyme) was examined using a selective tagging reaction in combination with on-line monitoring of the reaction progress by electrospray ionization mass spectrometry (ESI-MS). The kinetics of this reaction, based on the cyclization of the guanidine group of arginine with 2,3-butanedione and phenylboronic acid at pH 8-10, allow the grouping of arginines in "exposed" or "partially buried" residues, because they differ substantially in their reaction rate constants for the conversion of the guanidine groups. The method allows one to differentiate between different protein conformations as shown for myoglobin and its apo form and native and reduced ribonuclease A: Removal of the heme group in myoglobin resulted in an increased reactivity for the two partially buried arginines. For RNAse A, quantitative reduction of the disulfide bonds lead to the exposure of an additional arginine residue and two different conformations of the reduced protein were observed by ESI-MS that could be distinguished according to their charge-state distribution. Experimentally obtained accessibilities were compared with solvent-accessibility data calculated from 3D structures and substantial agreement between both techniques was observed.
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Affiliation(s)
- Alexander Leitner
- Christian Doppler Laboratory for Molecular Recognition Materials, Institute of Analytical Chemistry and Food Chemistry, University of Vienna, 1090 Vienna, Austria.
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Abstract
Diacetyl is a diketone flavouring agent that is commonly employed for buttery taste as well as other purposes. Industrial exposure to flavouring agents, particularly diacetyl, has recently been associated with bronchiolitis obliterans, a severe respiratory illness producing fibrosis and obstruction of the small airways. This has been most commonly reported in the microwave popcorn production industry, but it has occurred elsewhere. In addition to bronchiolitis obliterans, spirometry abnormalities (fixed airflow obstruction) and respiratory symptoms have been associated with exposure. A direct effect on the respiratory epithelium with the disorganised fibrotic repair appears most likely as the underlying mechanism. Current data suggest that diacetyl is the agent responsible, although it is possible that diacetyl is simply a marker for another causative agent.
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Affiliation(s)
- Philip Harber
- Division of Occupational and Environmental Medicine, Department of Family Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California 90024, USA.
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Lu YJ, Zhang F, Grimes KD, Lee RE, Rock CO. Topology and active site of PlsY: the bacterial acylphosphate:glycerol-3-phosphate acyltransferase. J Biol Chem 2007; 282:11339-46. [PMID: 17308305 DOI: 10.1074/jbc.m700374200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The most widely distributed biosynthetic pathway to initiate phosphatidic acid formation in bacterial membrane phospholipid biosynthesis involves the conversion of acyl-acyl carrier protein to acylphosphate by PlsX and the transfer of the acyl group from acylphosphate to glycerol 3-phosphate by an integral membrane protein, PlsY. The membrane topology of Streptococcus pneumoniae PlsY was determined using the substituted cysteine accessibility method. PlsY has five membrane-spanning segments with the amino terminus and two short loops located on the external face of the membrane. Each of the three larger cytoplasmic domains contains a highly conserved sequence motif. Site-directed mutagenesis revealed that each conserved domain was critical for PlsY catalysis. Motif 1 had an essential serine and arginine residue. Motif 2 had the characteristics of a phosphate-binding loop. Mutations of the conserved glycines in motif 2 to alanines resulted in a Km defect for glycerol 3-phosphate binding leading to the conclusion that this motif corresponded to the glycerol 3-phosphate binding site. Motif 3 contained a conserved histidine and asparagine that were important for activity and a glutamate that was critical to the structural integrity of PlsY. PlsY was noncompetitively inhibited by palmitoyl-CoA. These data define the membrane architecture and the critical active site residues in the PlsY family of bacterial acyltransferases.
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Affiliation(s)
- Ying-Jie Lu
- Department of Infectious Diseases, St. Jude Children's Research Hospital, and Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38105-2794, USA
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39
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Ercan A, Park HI, Ming LJ. A "moonlighting" dizinc aminopeptidase from Streptomyces griseus: mechanisms for peptide hydrolysis and the 4 x 10(10)-fold acceleration of the alternative phosphodiester hydrolysis. Biochemistry 2007; 45:13779-93. [PMID: 17105197 DOI: 10.1021/bi061086x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A unique "enzyme catalytic promiscuity" has recently been observed, wherein a phosphodiester and a phosphonate ester are hydrolyzed by a dinuclear aminopeptidase and its metal derivatives from Streptomyces griseus (SgAP) [Park, H. I., Ming, L.-J. (1999) Angew. Chem., Int. Ed. Engl. 38, 2914-2916 and Ercan, A., Park, H. I., Ming, L.-J. (2000) Chem. Commun. 2501-2502]. Because tetrahedral phosphocenters often serve as transition-state inhibitors toward the hydrolysis of the peptide, phosphoester hydrolysis by peptidases is thus not expected to occur effectively and must take place through a unique mechanism. Owing to the very different structures and mechanistic requirements between phosphoesters and peptides during hydrolysis, the study of this effective phosphodiester hydrolysis by SgAP may provide further insight into the action of this enzyme that is otherwise not obtainable from regular peptide substrates. We present herein a detailed investigation of both peptide and phosphodiester hydrolyses catalyzed by SgAP. The latter exhibits a first-order rate enhancement of 4 x 10(10)-fold compared to the uncatalyzed reaction at pH 7.0 and 25 degrees C. The results suggest that peptide and phosphodiester hydrolyses by SgAP may share a common reaction mechanism to a certain extent. However, their differences in pH dependence, phosphate and fluoride inhibition patterns, and proton inventory reflect that they must follow different pathways. Mechanisms for the two hydrolyses are drawn on the basis of the results, which provide the foundation for further investigation of the catalytic promiscuity of this enzyme by means of physical and molecular biology methods. The catalytic versatility of SgAP suggests that this enzyme may serve as a unique "natural model system" for further investigation of dinuclear hydrolysis. A better understanding of enzyme catalytic promiscuity is also expected to shed light on the evolution and action of enzymes.
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Affiliation(s)
- Altan Ercan
- Department of Chemistry and Institute for Biomolecular Science, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250, USA
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40
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Leitner A, Amon S, Rizzi A, Lindner W. Use of the arginine-specific butanedione/phenylboronic acid tag for analysis of peptides and protein digests using matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:1321-30. [PMID: 17340573 DOI: 10.1002/rcm.2967] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We have applied an arginine-specific labeling technique to the study of peptides by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The reaction converts the guanidine group of the arginine side chain by reacting it with 2,3-butanedione and an arylboronic acid. Despite the general chemical lability of the tag under acidic conditions, it was possible to employ acidic matrices like alpha-cyano-4-hydroxycinnamic acid without adverse effects, using the thin-layer technique for preparation. After optimizing the method using arginine-containing model peptides--for which sensitivity down to the low fmol range was demonstrated--the procedure was applied to enzymatic digests of several model proteins in solution and to protein spots in gels obtained by two-dimensional electrophoretic separation of cell lysate samples. Information on the presence of arginine in peptides can be easily obtained from the mass spectra by the characteristic mass shift and the isotope pattern resulting from the incorporation of boron. This information might serve as a valuable additional search constraint for achieving a higher degree of confidence for protein identification by peptide mass fingerprinting.
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Affiliation(s)
- Alexander Leitner
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria.
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Datta R, Das I, Sen B, Chakraborty A, Adak S, Mandal C, Datta A. Mutational analysis of the active-site residues crucial for catalytic activity of adenosine kinase from Leishmania donovani. Biochem J 2006; 387:591-600. [PMID: 15606359 PMCID: PMC1134988 DOI: 10.1042/bj20041733] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Leishmania donovani adenosine kinase (LdAdK) plays a pivotal role in scavenging of purines from the host. Exploiting interspecies homology and structural co-ordinates of the enzyme from other sources, we generated a model of LdAdK that led us to target several amino acid residues (namely Gly-62, Arg-69, Arg-131 and Asp-299). Replacement of Gly-62 with aspartate caused a drastic reduction in catalytic activity, with decreased affinity for either substrate. Asp-299 was found to be catalytically indispensable. Mutation of either Arg-131 or Arg-69 caused a significant reduction in kcat. R69A (Arg-69-->Ala) and R131A mutants exhibited unaltered K(m) for either substrate, whereas ATP K(m) for R69K increased 6-fold. Importance of both of the arginine residues was reaffirmed by the R69K/R131A double mutant, which exhibited approx. 0.5% residual activity with a large increase in ATP K(m). Phenylglyoxal, which inhibits the wild-type enzyme, also inactivated the arginine mutants to different extents. Adenosine protected both of the Arg-69 mutants, but not the R131A variant, from inactivation. Binding experiments revealed that the AMP-binding property of R69K or R69A and D299A mutants remained largely unaltered, but R131A and R69K/R131A mutants lost their AMP binding ability significantly. The G62D mutant did not bind AMP at all. Free energy calculations indicated that Arg-69 and Arg-131 are functionally independent. Thus, apart from the mandatory requirement of flexibility around the diglycyl (Gly-61-Gly-62) motif, our results identified Asp-299 and Arg-131 as key catalytic residues, with the former functioning as the proton abstractor from the 5'-OH of adenosine, while the latter acts as a bidentate electrophile to stabilize the negative charge on the leaving group during the phosphate transfer. Moreover, the positive charge distribution of Arg-69 probably helps in maintaining the flexibility of the alpha-3 helix needed for proper domain movement. These findings provide the first comprehensive biochemical evidence implicating the mechanistic roles of the functionally important residues of this chemotherapeutically exploitable enzyme.
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Affiliation(s)
- Rupak Datta
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Ishita Das
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Banibrata Sen
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Anutosh Chakraborty
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Subrata Adak
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Chhabinath Mandal
- †Division of Drug Design, Development and Molecular Modelling, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Alok K. Datta
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
- To whom correspondence should be addressed (email )
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Fackelmayer FO. Protein arginine methyltransferases: guardians of the Arg? Trends Biochem Sci 2005; 30:666-71. [PMID: 16257219 DOI: 10.1016/j.tibs.2005.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 09/21/2005] [Accepted: 10/10/2005] [Indexed: 12/01/2022]
Abstract
The recent discovery of enzymes that convert methylated arginine residues in proteins to citrulline has catapulted arginine methylation into the attention of cell-signaling researchers. Long considered a rather static post-translational modification of marginal interest, it seems that arginine methylation has now joined the group of signaling pathways that operate via pairs of antagonistic enzymes. However, many questions remain unanswered, especially concerning the removal mechanism and its implication for the physiological role of arginine methylation. I propose that, in addition to the broadly discussed function as regulator of protein activity, arginine methylation might serve a second purpose: protection of arginine residues against attack by endogenous reactive dicarbonyl agents, such as methylglyoxal, which are natural by-products of normal metabolic pathways. Inefficient detoxification of these highly cytotoxic compounds results in inactivation of proteins that is causally linked to diabetes, cancer, neurodegenerative diseases and pathophysiologies of aging. This new concept of 'arginine protection' might have far-reaching implications for the development of drugs that exploit a natural protection mechanism for medical purposes.
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Affiliation(s)
- Frank O Fackelmayer
- Department of Molecular Cell Biology, Heinrich-Pette-Institute, Martinistrasse 52, 20251 Hamburg, Germany.
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43
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Foettinger A, Leitner A, Lindner W. Solid-phase capture and release of arginine peptides by selective tagging and boronate affinity chromatography. J Chromatogr A 2005; 1079:187-96. [PMID: 16038304 DOI: 10.1016/j.chroma.2005.03.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A method for the selection of arginine-containing peptides from a mixture by a solid phase capture and release technique is presented. The method is based on the covalent modification of the guanidine group of arginine with 2,3-butanedione and phenylboronic acid under alkaline conditions. Using polymeric materials with immobilised phenylboronic acid the arginine-peptides can be captured on a solid support while arginine-free peptides are not covalently bound and can be washed away. Finally, the arginine-peptides can be cleaved again from the boronic acid beads due to the reversibility of the reaction. The recovered peptides are then analysed by liquid chromatography-tandem mass spectrometry. The method was optimised with model peptides with regard to the non-specific binding of arginine-free peptides and quantitative cleavage of the label after the selection step. Using an adequate protocol, the applicability towards more complex samples was successfully tested with a tryptic digest of a mixture of three standard proteins.
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Affiliation(s)
- A Foettinger
- Christian Doppler Laboratory for Molecular Recognition Materials, Institute of Analytical Chemistry, University of Vienna, Vienna, Austria
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44
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MÄKINEN KK, MÄKINEN PL, WILKES SH, BAYLISS ME, PRESCOTT JM. Chemical Modification of AeromonasAminopeptidase. ACTA ACUST UNITED AC 2005. [DOI: 10.1111/j.1432-1033.1982.tb06960.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Green ME. A possible role for phosphate in complexing the arginines of S4 in voltage gated channels. J Theor Biol 2004; 233:337-41. [PMID: 15652143 DOI: 10.1016/j.jtbi.2004.10.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 09/24/2004] [Accepted: 10/08/2004] [Indexed: 11/19/2022]
Abstract
Phosphate ions are known to complex guanidinium groups, which are the side chains of arginine. Voltage gated channels that allow passage of ions through cell membranes, producing, for example the nerve impulse, are in many cases composed of four domains, each with six transmembrane segments. The S4 transmembrane segments of these channels have arginines placed in such a way that they would be expected to complex phosphate. Known phosphate-arginine complexes are reasonably strong. Here, an ab initio calculation reinforces the expectation that a strong complex could form. As a consequence, if the S4 moved, it would carry either no charge, or at most half of what is expected from fully charged arginines. This suggests that it may be necessary to rethink voltage gating models in which the gating current is produced by physical motion of the S4 transmembrane segments.
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Affiliation(s)
- Michael E Green
- Department of Chemistry, City College of the City University of New York, New York, NY 10031, USA.
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46
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Abramson J, Kaback HR, Iwata S. Structural comparison of lactose permease and the glycerol-3-phosphate antiporter: members of the major facilitator superfamily. Curr Opin Struct Biol 2004; 14:413-9. [PMID: 15313234 DOI: 10.1016/j.sbi.2004.07.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Structural knowledge of the major facilitator superfamily has dramatically increased during the past year with the emergence of the structures of three members of this family of transporters. All three structures reveal 12 transmembrane helices forming two distinct domains, and could imply that members of this superfamily have preserved both secondary and tertiary structure elements during evolution.
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Affiliation(s)
- Jeff Abramson
- Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK
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47
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Leitner A, Lindner W. Probing of arginine residues in peptides and proteins using selective tagging and electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:891-899. [PMID: 12938110 DOI: 10.1002/jms.477] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A general labelling method is presented which allows the determination of the number of guanidine groups (related to arginine and homoarginine in peptides and proteins) by means of mass spectrometry. It implies a guanidine-selective derivatization step with 2,3-butanedione and an arylboronic acid under aqueous, alkaline conditions (pH 8-10). The reaction mixture is then directly analysed by electrospray ionization mass spectrometry without further sample pretreatment. Other amino acids are not affected by this reaction although it is demonstrated that lysine side-chains may be unambiguously identified when they are converted to homoarginine prior to derivatization. Guanidine functionalities, as e.g. in the amino acid arginine, are easily identified by the characteristic mass shift between underivatized and derivatized analyte. The tagging procedure is straightforward and selective for guanidine groups. The influence of several experimental parameters, especially the pH of the solution and the choice of reagents, is examined and the method is applied to various arginine-containing peptides and to lysozyme as a representative protein. Possible applications of this technique and its limitations are discussed.
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Affiliation(s)
- Alexander Leitner
- Christian Doppler Laboratory for Molecular Recognition Materials, Institute of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
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48
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Gong X, Linsdell P. Molecular determinants and role of an anion binding site in the external mouth of the CFTR chloride channel pore. J Physiol 2003; 549:387-97. [PMID: 12679372 PMCID: PMC2342941 DOI: 10.1113/jphysiol.2002.038232] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chloride permeation through the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel is blocked by highly lyotropic permeant anions which bind tightly within the pore. Here we show that several different substitutions of a positively charged amino acid residue, arginine R334, in the putative outer mouth of the CFTR pore, greatly reduce the block caused by lyotropic Au(CN)2- ions applied to the intracellular side of the channel. Fixed positive charge at this site appears to play a role in Au(CN)2- binding, as judged by multiple substitutions of differently charged amino acid side chains and also by the pH dependence of block conferred by the R334H mutant. However, non-charge-dependent effects also appear to contribute to Au(CN)2- binding. Mutation of R334 also disrupts the apparent electrostatic interaction between intracellular Au(CN)2- ions and extracellular permeant anions, an interaction which normally acts to relieve channel block. All six mutations studied at R334 significantly weakened this interaction, suggesting that arginine possesses a unique ability to coordinate ion-ion interactions at this site in the pore. Our results suggest that lyotropic anions bind tightly to a site in the outer mouth of the CFTR pore that involves interaction with a fixed positive charge. Binding to this site is also involved in coordination of multiple permeant anions within the pore, suggesting that anion binding in the outer mouth of the pore is an important aspect in the normal anion permeation mechanism.
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Affiliation(s)
- Xiandi Gong
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
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49
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Schwöppe C, Winkler HH, Neuhaus HE. Connection of transport and sensing by UhpC, the sensor for external glucose-6-phosphate in Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1450-7. [PMID: 12654000 DOI: 10.1046/j.1432-1033.2003.03507.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
UhpC is a membrane-bound sensor protein in Escherichia coli required for recognizing external glucose-6-phosphate (Glc6P) and induction of the transport protein UhpT. Recently, it was shown that UhpC is also able to transport Glc6P. In this study we investigated whether these transport and sensing activities are obligatorily coupled in UhpC. We expressed a His-UhpC protein in a UhpC-deficient E. coli strain and verified that this construct does not alter the basic biochemical properties of the Glc6P sensor system. The effects of arginine replacements, mutations of the central loop, and introduction of a salt bridge in UhpC on transport and sensing were compared. The exchanges R46C, R266C and R149C moderately affected transport by UhpC but strongly decreased the sensing ability. This suggested that the affinity for Glc6P as a transported substrate is uncoupled in UhpC from its affinity for Glc6P as an inducer. Four of the 11 arginine mutants showed a constitutive phenotype but had near wild-type transport activity suggesting that Glc6P can be transported by a molecule locked in the inducing conformation. Introduction of an intrahelical salt bridge increased the transport activity of UhpC but abolished sensing. Three conserved residues from the central loop were mutated and although none of these showed transport, one exhibited increased affinity for sensing. Taken together, these data show that transport by UhpC is not required for sensing, that conserved arginine residues are important for sensing and not for transport, and that residues located in the central hydrophilic loop are critical for transport and for sensing.
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Affiliation(s)
- Christian Schwöppe
- Pflanzenphysiologie, Universität Kaiserslautern, Kaiserslautern, Germany
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50
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Konozy EHE, Bernardes ES, Rosa C, Faca V, Greene LJ, Ward RJ. Isolation, purification, and physicochemical characterization of a D-galactose-binding lectin from seeds of Erythrina speciosa. Arch Biochem Biophys 2003; 410:222-9. [PMID: 12573281 DOI: 10.1016/s0003-9861(02)00695-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A lectin was isolated from the saline extract of Erythrina speciosa seeds by affinity chromatography on lactose-Sepharose. The lectin content was about 265 mg/100g dry flour. E. speciosa seed lectin (EspecL) agglutinated all human RBC types, showing no human blood group specificity; however a slight preference toward the O blood group was evident. The lectin also agglutinated rabbit, sheep, and mouse blood cells and showed no effect on horse erythrocytes. Lactose was the most potent inhibitor of EspecL hemagglutinating activity (minimal inhibitory concentration (MIC)=0.25 mM) followed by N-acetyllactosamine, MIC=0.5mM, and then p-nitrophenyl alpha-galactopyranoside, MIC=2 mM. The lectin was a glycoprotein with a neutral carbohydrate content of 5.5% and had two pI values of 5.8 and 6.1 and E(1%)(1 cm) of 14.5. The native molecular mass of the lectin detected by hydrodynamic light scattering was 58 kDa and when examined by mass spectroscopy and SDS-PAGE it was found to be composed of two identical subunits of molecular mass of 27.6 kDa. The amino acid composition of the lectin revealed that it was rich in acidic and hydroxyl amino acids, contained a lesser amount of methionine, and totally lacked cysteine. The N-terminal of the lectin shared major similarities with other reported Erythrina lectins. The lectin was a metaloprotein that needed both Ca(2+) and Mn(2+) ions for its activity. Removal of these metals by EDTA rendered the lectin inactive whereas their addition restored the activity. EspecL was acidic pH sensitive and totally lost its activity when incubated with all pH values between pH 3 and pH 6. Above pH 6 and to pH 9.6 there was no effect on the lectin activity. At 65 degrees C for more than 90 min the lectin was fairly stable; however, when heated at 70 degrees C for 10 min it lost more than 80% of its original activity and was totally inactivated at 80 degrees C for less than 10 min. Fluorescence studies of EspecL indicated that tryptophan residues were present in a highly hydrophobic environment, and binding of lactose to EspecL neither quenched tryptophan fluorescence nor altered lambda(max) position. Treating purified EspecL with NBS an affinity-modifying reagent specific for tryptophan totally inactivated the lectin with total modification of three tryptophan residues. Of these residues only the third modified residue seemed to play a crucial role in the lectin activity. Addition of lactose to the assay medium did not provide protection against NBS modification which indicated that tryptophan might not be directly involved in the binding of haptenic sugar D-galactose. Modification of tyrosine with N-acetylimidazole led to a 50% drop in EspecL activity with concomitant acetylation of six tyrosine residues. The secondary structure of EspecL as studied by circular dichroism was found to be a typical beta-pleated-sheet structure which is comparable to the CD structure of Erythrina corallodendron lectin. Binding of lactose did not alter the EspecL secondary structure as revealed by CD examination.
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Affiliation(s)
- Emadeldin H E Konozy
- Departamento de Biologia e Celular e Molecular e Bioagentes Patognicos, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, CEP 14049-900, SP, Brazil.
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