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Estiri H, Bhattacharya S, Buitrago JAR, Castagna R, Legzdiņa L, Casucci G, Ricci A, Parisini E, Gautieri A. Tailoring FPOX enzymes for enhanced stability and expanded substrate recognition. Sci Rep 2023; 13:18610. [PMID: 37903872 PMCID: PMC10616090 DOI: 10.1038/s41598-023-45428-1] [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: 07/13/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Fructosyl peptide oxidases (FPOX) are deglycating enzymes that find application as key enzymatic components in diabetes monitoring devices. Indeed, their use with blood samples can provide a measurement of the concentration of glycated hemoglobin and glycated albumin, two well-known diabetes markers. However, the FPOX currently employed in enzymatic assays cannot directly detect whole glycated proteins, making it necessary to perform a preliminary proteolytic treatment of the target protein to generate small glycated peptides that can act as viable substrates for the enzyme. This is a costly and time consuming step. In this work, we used an in silico protein engineering approach to enhance the overall thermal stability of the enzyme and to improve its catalytic activity toward large substrates. The final design shows a marked improvement in thermal stability relative to the wild type enzyme, a distinct widening of its access tunnel and significant enzymatic activity towards a range of glycated substrates.
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Affiliation(s)
- Hajar Estiri
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Shapla Bhattacharya
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
- Faculty of Materials Science and Applied Chemistry, Riga Technical University, Paula Valdena 3, Riga, 1048, Latvia
| | | | - Rossella Castagna
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Piazza L. da Vinci 32, 20133, Milano, Italy
| | - Linda Legzdiņa
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Giorgia Casucci
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia
| | - Andrea Ricci
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Emilio Parisini
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, 1006, Latvia.
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.
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2
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Song H, Ma H, Shi J, Liu Y, Kan C, Hou N, Han J, Sun X, Qiu H. Optimizing glycation control in diabetes: An integrated approach for inhibiting nonenzymatic glycation reactions of biological macromolecules. Int J Biol Macromol 2023:125148. [PMID: 37268079 DOI: 10.1016/j.ijbiomac.2023.125148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/16/2023] [Accepted: 05/27/2023] [Indexed: 06/04/2023]
Abstract
Diabetes is a multifactorial disorder that increases mortality and disability due to its complications. A key driver of these complications is nonenzymatic glycation, which generates advanced glycation end-products (AGEs) that impair tissue function. Therefore, effective nonenzymatic glycation prevention and control strategies are urgently needed. This review comprehensively describes the molecular mechanisms and pathological consequences of nonenzymatic glycation in diabetes and outlines various anti-glycation strategies, such as lowering plasma glucose, interfering with the glycation reaction, and degrading early and late glycation products. Diet, exercise, and hypoglycemic medications can reduce the onset of high glucose at the source. Glucose or amino acid analogs such as flavonoids, lysine and aminoguanidine competitively bind to proteins or glucose to block the initial nonenzymatic glycation reaction. In addition, deglycation enzymes such as amadoriase, fructosamine-3-kinase, parkinson's disease protein, glutamine amidotransferase-like class 1 domain-containing 3A and terminal FraB deglycase can eliminate existing nonenzymatic glycation products. These strategies involve nutritional, pharmacological, and enzymatic interventions that target different stages of nonenzymatic glycation. This review also emphasizes the therapeutic potential of anti-glycation drugs for preventing and treating diabetes complications.
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Affiliation(s)
- Hongwei Song
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Hongyan Ma
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Junfeng Shi
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yongping Liu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Chengxia Kan
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Ningning Hou
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jing Han
- College of Traditional Chinese Medicine, Weifang Medical University, Weifang 261053, Shandong, China
| | - Xiaodong Sun
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China.
| | - Hongyan Qiu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China.
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3
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Pizzi A, Sori L, Pigliacelli C, Gautieri A, Andolina C, Bergamaschi G, Gori A, Panine P, Grande AM, Linder MB, Baldelli Bombelli F, Soncini M, Metrangolo P. Emergence of Elastic Properties in a Minimalist Resilin-Derived Heptapeptide upon Bromination. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200807. [PMID: 35723172 DOI: 10.1002/smll.202200807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Bromination is herein exploited to promote the emergence of elastic behavior in a short peptide-SDSYGAP-derived from resilin, a rubber-like protein exerting its role in the jumping and flight systems of insects. Elastic and resilient hydrogels are obtained, which also show self-healing behavior, thanks to the promoted non-covalent interactions that limit deformations and contribute to the structural recovery of the peptide-based hydrogel. In particular, halogen bonds may stabilize the β-sheet organization working as non-covalent cross-links between nearby peptide strands. Importantly, the unmodified peptide (i.e., wild type) does not show such properties. Thus, SDSY(3,5-Br)GAP is a novel minimalist peptide elastomer.
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Affiliation(s)
- Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
| | - Lorenzo Sori
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
| | - Claudia Pigliacelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Puumiehenkuja2, Espoo, FI-00076, Finland
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, 20131, Italy
| | - Clara Andolina
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Puumiehenkuja2, Espoo, FI-00076, Finland
| | - Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche - National Research Council of Italy (SCITEC-CNR), Milan, 20131, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche - National Research Council of Italy (SCITEC-CNR), Milan, 20131, Italy
| | - Pierre Panine
- Xenocs SAS, 1-3 Allée du Nanomètre, Grenoble, 38000, France
| | - Antonio Mattia Grande
- Department of Aerospace Science and Technology, Politecnico di Milano, via La Masa 34, Milano, 20156, Italy
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
| | - Monica Soncini
- Biomolecular Engineering Lab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, 20131, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Puumiehenkuja2, Espoo, FI-00076, Finland
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4
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Gautieri A, Rigoldi F, Torretta A, Redaelli A, Parisini E. In Silico Engineering of Enzyme Access Tunnels. Methods Mol Biol 2022; 2397:203-225. [PMID: 34813066 DOI: 10.1007/978-1-0716-1826-4_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Enzyme engineering is a tailoring process that allows the modification of naturally occurring enzymes to provide them with improved catalytic efficiency, stability, or specificity. By introducing partial modifications to their sequence and to their structural features, enzyme engineering can transform natural enzymes into more efficient, specific and resistant biocatalysts and render them suitable for virtually countless industrial processes. Current enzyme engineering methods mostly target the active site of the enzyme, where the catalytic reaction takes place. Nonetheless, the tunnel that often connects the surface of an enzyme with its buried active site plays a key role in the activity of the enzyme as it acts as a gatekeeper and regulates the access of the substrate to the catalytic pocket. Hence, there is an increasing interest in targeting the sequence and the structure of substrate entrance tunnels in order to fine-tune enzymatic activity, regulate substrate specificity, or control reaction promiscuity.In this chapter, we describe the use of a rational in silico design and screening method to engineer the access tunnel of a fructosyl peptide oxidase with the aim to facilitate access to its catalytic site and to expand its substrate range. Our goal is to engineer this class of enzymes in order to utilize them for the direct detection of glycated proteins in diabetes monitoring devices. The design strategy involves remodeling of the backbone structure of the enzyme , a feature that is not possible with conventional enzyme engineering techniques such as single-point mutagenesis and that is highly unlikely to occur using a directed evolution approach.The proposed strategy, which results in a significant reduction in cost and time for the experimental production and characterization of candidate enzyme variants, represents a promising approach to the expedited identification of novel and improved enzymes. Rational enzyme design aims to provide in silico strategies for the fast, accurate, and inexpensive development of biocatalysts that can meet the needs of multiple industrial sectors, thus ultimately promoting the use of green chemistry and improving the efficiency of chemical processes.
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Affiliation(s)
- Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy.
| | - Federica Rigoldi
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Archimede Torretta
- Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Alberto Redaelli
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @Polimi, Istituto Italiano di Tecnologia, Milan, Italy.
- Latvian Institute of Organic Synthesis, Riga, Latvia.
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5
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Bono N, Coloma Smith B, Moreschi F, Redaelli A, Gautieri A, Candiani G. In silico prediction of the in vitro behavior of polymeric gene delivery vectors. NANOSCALE 2021; 13:8333-8342. [PMID: 33900339 DOI: 10.1039/d0nr09052b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-viral gene delivery vectors have increasingly come under the spotlight, but their performaces are still far from being satisfactory. Therefore, there is an urgent need for forecasting tools and screening methods to enable the development of ever more effective transfectants. Here, coarse-grained (CG) models of gold standard transfectant poly(ethylene imine)s (PEIs) have been profitably used to investigate and highlight the effect of experimentally-relevant parameters, namely molecular weight (2 vs. 10 kDa) and topologies (linear vs. branched), protonation state, and ammine-to-phosphate ratios (N/Ps), on the complexation and the gene silencing efficiency of siRNA molecules. The results from the in vitro screening of cationic polymers and conditions were used to validate the in silico platform that we developed, such that the hits which came out of the CG models were of high practical relevance. We show that our in silico platform enables to foresee the most suitable conditions for the complexation of relevant siRNA-polycation assemblies, thereby providing a reliable predictive tool to test bench transfectants in silico, and foster the design and development of gene delivery vectors.
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Affiliation(s)
- Nina Bono
- GenT LΛB, Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131 Milan, Italy.
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6
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Lahham M, Jha S, Goj D, Macheroux P, Wallner S. The family of sarcosine oxidases: Same reaction, different products. Arch Biochem Biophys 2021; 704:108868. [PMID: 33812916 DOI: 10.1016/j.abb.2021.108868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
The subfamily of sarcosine oxidase is a set of enzymes within the larger family of amine oxidases. It is ubiquitously distributed among different kingdoms of life. The member enzymes catalyze the oxidization of an N-methyl amine bond of amino acids to yield unstable imine species that undergo subsequent spontaneous non-enzymatic reactions, forming an array of different products. These products range from demethylated simple species to complex alkaloids. The enzymes belonging to the sarcosine oxidase family, namely, monomeric and heterotetrameric sarcosine oxidase, l-pipecolate oxidase, N-methyltryptophan oxidase, NikD, l-proline dehydrogenase, FsqB, fructosamine oxidase and saccharopine oxidase have unique features differentiating them from other amine oxidases. This review highlights the key attributes of the sarcosine oxidase family enzymes, in terms of their substrate binding motif, type of oxidation reaction mediated and FAD regeneration, to define the boundaries of this group and demarcate these enzymes from other amine oxidase families.
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Affiliation(s)
- Majd Lahham
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria; Department of Biochemistry and Microbiology, Aljazeera Private University, Ghabagheb, Syria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Dominic Goj
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria.
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7
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Rigoldi F, Donini S, Torretta A, Carbone A, Redaelli A, Bandiera T, Parisini E, Gautieri A. Rational backbone redesign of a fructosyl peptide oxidase to widen its active site access tunnel. Biotechnol Bioeng 2020; 117:3688-3698. [PMID: 32797625 DOI: 10.1002/bit.27535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/27/2020] [Accepted: 08/09/2020] [Indexed: 12/31/2022]
Abstract
Fructosyl peptide oxidases (FPOXs) are enzymes currently used in enzymatic assays to measure the concentration of glycated hemoglobin and albumin in blood samples, which serve as biomarkers of diabetes. However, since FPOX are unable to work directly on glycated proteins, current enzymatic assays are based on a preliminary proteolytic digestion of the target proteins. Herein, to improve the speed and costs of the enzymatic assays for diabetes testing, we applied a rational design approach to engineer a novel enzyme with a wider access tunnel to the catalytic site, using a combination of Rosetta design and molecular dynamics simulations. Our final design, L3_35A, shows a significantly wider and shorter access tunnel, resulting from the deletion of five-amino acids lining the gate structures and from a total of 35 point mutations relative to the wild-type (WT) enzyme. Indeed, upon experimental testing, our engineered enzyme shows good structural stability and maintains significant activity relative to the WT.
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Affiliation(s)
- Federica Rigoldi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Biomolecular Engineering Lab, Politecnico di Milano, Milano, Italy
| | - Stefano Donini
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Milano, Italy
| | - Archimede Torretta
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Milano, Italy
| | - Anna Carbone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.,D3-PharmaChemistry, Istituto Italiano di Tecnologia, Genova, Italy
| | - Alberto Redaelli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Biomolecular Engineering Lab, Politecnico di Milano, Milano, Italy
| | - Tiziano Bandiera
- D3-PharmaChemistry, Istituto Italiano di Tecnologia, Genova, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Milano, Italy.,Biotechnology Group, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Alfonso Gautieri
- Dipartimento di Elettronica, Informazione e Bioingegneria, Biomolecular Engineering Lab, Politecnico di Milano, Milano, Italy
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The Anti-Amyloidogenic Action of Doxycycline: A Molecular Dynamics Study on the Interaction with Aβ42. Int J Mol Sci 2019; 20:ijms20184641. [PMID: 31546787 PMCID: PMC6769662 DOI: 10.3390/ijms20184641] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
The pathological aggregation of amyloidogenic proteins is a hallmark of many neurological diseases, including Alzheimer’s disease and prion diseases. We have shown both in vitro and in vivo that doxycycline can inhibit the aggregation of Aβ42 amyloid fibrils and disassemble mature amyloid fibrils. However, the molecular mechanisms of the drug’s anti-amyloidogenic property are not understood. In this study, a series of molecular dynamics simulations were performed to explain the molecular mechanism of the destabilization of Aβ42 fibrils by doxycycline and to compare the action of doxycycline with those of iododoxorubicin (a toxic structural homolog of tetracyclines), curcumin (known to have anti-amyloidogenic activity) and gentamicin (an antibiotic with no experimental evidence of anti-amyloidogenic properties). We found that doxycycline tightly binds the exposed hydrophobic amino acids of the Aβ42 amyloid fibrils, partly leading to destabilization of the fibrillar structure. Clarifying the molecular determinants of doxycycline binding to Aβ42 may help devise further strategies for structure-based drug design for Alzheimer’s disease.
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Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep 2019; 9:942. [PMID: 30700768 PMCID: PMC6353924 DOI: 10.1038/s41598-018-37806-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/11/2018] [Indexed: 11/30/2022] Open
Abstract
The currently available haemoglobin A1c (HbA1c) enzymatic assay consists of two specific steps: proteolysis of HbA1c and oxidation of the liberated fructosyl peptide by fructosyl peptide oxidase (FPOX). To develop a more convenient and high throughput assay, we devised novel protease-free assay system employing modified FPOX with HbA1c oxidation activity, namely HbA1c direct oxidase (HbA1cOX). AnFPOX-15, a modified FPOX from Aspergillus nidulans, was selected for conversion to HbA1cOX. As deduced from the crystal structure of AnFPOX-15, R61 was expected to obstruct the entrance of bulky substrates. An R61G mutant was thus constructed to open the gate at the active site. The prepared mutant exhibited significant reactivity for fructosyl hexapeptide (F-6P, N-terminal amino acids of HbA1c), and its crystal structure revealed a wider gate observed for AnFPOX-15. To improve the reactivity for F-6P, several mutagenesis approaches were performed. The ultimately generated AnFPOX-47 exhibited the highest F-6P reactivity and possessed HbA1c oxidation activity. HbA1c levels in blood samples as measured using the direct assay system using AnFPOX-47 were highly correlated with the levels measured using the conventional HPLC method. In this study, FPOX was successfully converted to HbA1cOX, which could represent a novel in vitro diagnostic modality for diabetes mellitus.
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10
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Lahham M, Pavkov-Keller T, Fuchs M, Niederhauser J, Chalhoub G, Daniel B, Kroutil W, Gruber K, Macheroux P. Oxidative cyclization of N-methyl-dopa by a fungal flavoenzyme of the amine oxidase family. J Biol Chem 2018; 293:17021-17032. [PMID: 30194285 PMCID: PMC6222107 DOI: 10.1074/jbc.ra118.004227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/06/2018] [Indexed: 11/19/2022] Open
Abstract
Flavin-dependent enzymes catalyze many oxidations, including formation of ring structures in natural products. The gene cluster for biosynthesis of fumisoquins, secondary metabolites structurally related to isoquinolines, in the filamentous fungus Aspergillus fumigatus harbors a gene that encodes a flavoprotein of the amine oxidase family, termed fsqB (fumisoquin biosynthesis gene B). This enzyme catalyzes an oxidative ring closure reaction that leads to the formation of isoquinoline products. This reaction is reminiscent of the oxidative cyclization reported for berberine bridge enzyme and tetrahydrocannabinol synthase. Despite these similarities, amine oxidases and berberine bridge enzyme–like enzymes possess distinct structural properties, prompting us to investigate the structure–function relationships of FsqB. Here, we report the recombinant production and purification of FsqB, elucidation of its crystal structure, and kinetic analysis employing five putative substrates. The crystal structure at 2.6 Å resolution revealed that FsqB is a member of the amine oxidase family with a covalently bound FAD cofactor. N-methyl-dopa was the best substrate for FsqB and was completely converted to the cyclic isoquinoline product. The absence of the meta-hydroxyl group, as e.g. in l-N-methyl-tyrosine, resulted in a 25-fold lower rate of reduction and the formation of the demethylated product l-tyrosine, instead of a cyclic product. Surprisingly, FsqB did not accept the d-stereoisomer of N-methyltyrosine, in contrast to N-methyl-dopa, for which both stereoisomers were oxidized with similar rates. On the basis of the crystal structure and docking calculations, we postulate a substrate-dependent population of distinct binding modes that rationalizes stereospecific oxidation in the FsqB active site.
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Affiliation(s)
- Majd Lahham
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Tea Pavkov-Keller
- the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, and
| | - Michael Fuchs
- the Institute of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
| | - Johannes Niederhauser
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Gabriel Chalhoub
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Bastian Daniel
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Wolfgang Kroutil
- the Institute of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
| | - Karl Gruber
- the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, and
| | - Peter Macheroux
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz,
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11
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Thermal stabilization of the deglycating enzyme Amadoriase I by rational design. Sci Rep 2018; 8:3042. [PMID: 29445091 PMCID: PMC5813194 DOI: 10.1038/s41598-018-19991-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/03/2018] [Indexed: 11/16/2022] Open
Abstract
Amadoriases are a class of FAD-dependent enzymes that are found in fungi, yeast and bacteria and that are able to hydrolyze glycated amino acids, cleaving the sugar moiety from the amino acidic portion. So far, engineered Amadoriases have mostly found practical application in the measurement of the concentration of glycated albumin in blood samples. However, these engineered forms of Amadoriases show relatively low absolute activity and stability levels, which affect their conditions of use. Therefore, enzyme stabilization is desirable prior to function-altering molecular engineering. In this work, we describe a rational design strategy based on a computational screening method to evaluate a library of potentially stabilizing disulfide bonds. Our approach allowed the identification of two thermostable Amadoriase I mutants (SS03 and SS17) featuring a significantly higher T50 (55.3 °C and 60.6 °C, respectively) compared to the wild-type enzyme (52.4 °C). Moreover, SS17 shows clear hyperstabilization, with residual activity up to 95 °C, whereas the wild-type enzyme is fully inactive at 55 °C. Our computational screening method can therefore be considered as a promising approach to expedite the design of thermostable enzymes.
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X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction. Sci Rep 2017; 7:2790. [PMID: 28584265 PMCID: PMC5459902 DOI: 10.1038/s41598-017-02657-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 04/18/2017] [Indexed: 01/07/2023] Open
Abstract
Current enzymatic systems for quantifying glycated hemoglobin are based on the FAD-containing enzyme fructosyl peptide oxidase (FPOX). FPOX has substrate specificity for fructosyl-α N-valyl-histidine derived from proteolytic digestion of the N-terminus of the HbA1c β-chain. This study reports the X-ray structures of the wild-type and Asn56Ala (N56A) mutant of Phaeosphaeria nodorum fructosyl peptide oxidase (PnFPOX) to elucidate the residues responsible for the oxidative half-reaction. N56A showed decreased oxidase activity compared to the wild -type, while its dye-mediated dehydrogenase activity was higher than that of wild type. In wild-type PnFPOX, Asn56 forms a hydrogen bond with Lys274, thereby preventing it from forming a salt bridge with Asp54. By contrast, Lys274 of PnFPOX N56A moves toward Asp54, and they approach each other to form a salt bridge at a distance of 2.92-3.35 Å. Site-directed mutagenesis studies and protein channel analysis suggest that Asp54 assists in accepting oxygen properly at the position of the bound water molecule in the main oxygen channel. These results reveal that Asn56 in PnFPOX is essential for maintaining an effective oxygen accession path, and support the role of Asp54 as a gate keeper that cooperates with Lys274 to enable oxygen to reach the active site properly.
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Abstract
Genomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being 'predicted', while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'HôpitalParis75013France
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Advanced glycation end-products: Mechanics of aged collagen from molecule to tissue. Matrix Biol 2016; 59:95-108. [PMID: 27616134 DOI: 10.1016/j.matbio.2016.09.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 01/03/2023]
Abstract
Concurrent with a progressive loss of regenerative capacity, connective tissue aging is characterized by a progressive accumulation of Advanced Glycation End-products (AGEs). Besides being part of the typical aging process, type II diabetics are particularly affected by AGE accumulation due to abnormally high levels of systemic glucose that increases the glycation rate of long-lived proteins such as collagen. Although AGEs are associated with a wide range of clinical disorders, the mechanisms by which AGEs contribute to connective tissue disease in aging and diabetes are still poorly understood. The present study harnesses advanced multiscale imaging techniques to characterize a widely employed in vitro model of ribose induced collagen aging and further benchmarks these data against experiments on native human tissues from donors of different age. These efforts yield unprecedented insight into the mechanical changes in collagen tissues across hierarchical scales from molecular, to fiber, to tissue-levels. We observed a linear increase in molecular spacing (from 1.45nm to 1.5nm) and a decrease in the D-period length (from 67.5nm to 67.1nm) in aged tissues, both using the ribose model of in vitro glycation and in native human probes. Multiscale mechanical analysis of in vitro glycated tendons strongly suggests that AGEs reduce tissue viscoelasticity by severely limiting fiber-fiber and fibril-fibril sliding. This study lays an important foundation for interpreting the functional and biological effects of AGEs in collagen connective tissues, by exploiting experimental models of AGEs crosslinking and benchmarking them for the first time against endogenous AGEs in native tissue.
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Rigoldi F, Spero L, Dalle Vedove A, Redaelli A, Parisini E, Gautieri A. Molecular dynamics simulations provide insights into the substrate specificity of FAOX family members. MOLECULAR BIOSYSTEMS 2016; 12:2622-33. [DOI: 10.1039/c6mb00405a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Enzymatic assays based on Fructosyl Amino Acid Oxidases (FAOX) represent a potential, rapid and economical strategy to measure glycated hemoglobin (HbA1c), which is in turn a reliable method to monitor the insurgence and the development of diabetes mellitus.
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Affiliation(s)
- Federica Rigoldi
- Dipartimento di Elettronica
- Informazione e Bioingegneria
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Ludovica Spero
- Dipartimento di Elettronica
- Informazione e Bioingegneria
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Andrea Dalle Vedove
- Center for Nano Science and Technology @Polimi
- Istituto Italiano di Tecnologia
- 20133 Milano
- Italy
- Dipartimento di Chimica
| | - Alberto Redaelli
- Dipartimento di Elettronica
- Informazione e Bioingegneria
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @Polimi
- Istituto Italiano di Tecnologia
- 20133 Milano
- Italy
| | - Alfonso Gautieri
- Dipartimento di Elettronica
- Informazione e Bioingegneria
- Politecnico di Milano
- 20133 Milano
- Italy
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