1
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Lan T, Dong Y, Jiang L, Zhang Y, Sui X. Analytical approaches for assessing protein structure in protein-rich food: A comprehensive review. Food Chem X 2024; 22:101365. [PMID: 38623506 PMCID: PMC11016869 DOI: 10.1016/j.fochx.2024.101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
This review focuses on changes in nutrition and functional properties of protein-rich foods, primarily attributed to alterations in protein structures. We provide a comprehensive overview and comparison of commonly used laboratory methods for protein structure identification, aiming to offer readers a convenient understanding of these techniques. The review covers a range of detection technologies employed in food protein analysis and conducts an extensive comparison to identify the most suitable method for various proteins. While these techniques offer distinct advantages for protein structure determination, the inherent complexity of food matrices presents ongoing challenges. Further research is necessary to develop and enhance more robust detection methods to improve accuracy in protein conformation and structure analysis.
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Affiliation(s)
- Tian Lan
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yabo Dong
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lianzhou Jiang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaonan Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
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2
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Osman R, Bossu M, Dauvillée D, Spriet C, Liu C, Zeeman SC, D'Hulst C, Bompard C. LIKE EARLY STARVATION 1 interacts with amylopectin during starch biosynthesis. PLANT PHYSIOLOGY 2024; 195:1851-1865. [PMID: 38573555 DOI: 10.1093/plphys/kiae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Starch is the major energy storage compound in plants. Both transient starch and long-lasting storage starch accumulate in the form of insoluble, partly crystalline granules. The structure of these granules is related to the structure of the branched polymer amylopectin: linear chains of glucose units organized in double helices that align to form semicrystalline lamellae, with branching points located in amorphous regions between them. EARLY STARVATION 1 (ESV1) and LIKE EARLY STARVATION 1 (LESV) proteins are involved in the maintenance of starch granule structure and in the phase transition of amylopectin, respectively, in Arabidopsis (Arabidopsis thaliana). These proteins contain a conserved tryptophan-rich C-terminal domain folded into an antiparallel β-sheet, likely responsible for binding of the proteins to starch, and different N-terminal domains whose structure and function are unknown. In this work, we combined biochemical and biophysical approaches to analyze the structures of LESV and ESV1 and their interactions with the different starch polyglucans. We determined that both proteins interact with amylopectin but not with amylose and that only LESV is capable of interacting with amylopectin during starch biosynthesis. While the C-terminal domain interacts with amylopectin in its semicrystalline form, the N-terminal domain of LESV undergoes induced conformational changes that are probably involved in its specific function of mediating glucan phase transition. These results clarify the specific mechanism of action of these 2 proteins in the biosynthesis of starch granules.
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Affiliation(s)
- Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mélanie Bossu
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - David Dauvillée
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Lille F-59000, France
| | - Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Christophe D'Hulst
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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3
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Longo E, Siligardi G, Hussain R. Interaction of Blenoxane and Congeners Bleomycins A2 and B2 with Human Plasma Proteins Using Circular Dichroism Spectroscopy. Int J Mol Sci 2023; 24:13598. [PMID: 37686404 PMCID: PMC10488149 DOI: 10.3390/ijms241713598] [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: 08/11/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Bleomycin is a glycopeptide congeners' family of antitumor antibiotics employed for the treatment of several types of tumors such as squamous cell carcinomas and malignant lymphomas. The general chemical structure is constituted by three main portions: (i) a metal binding domain that is recognized to be responsible for the DNA cleavage activity; (ii) a DNA binding domain via the 1-4' bithiazole moiety; and (iii) a carbohydrate domain thought to be responsible for the accumulation of bleomycin in some cancer cells. To date, a limited number of protein interactions with bleomycin have been studied, but the plasma binding has not yet been determined. Here, we explore this aspect of the protein binding capacity of bleomycin to the two most abundant plasma proteins, human serum albumin (HSA) and α1-acid glycoprotein (AGP), which are known to bind and to be carriers of many drug molecules using spectroscopic techniques, such as circular dichroism, UV-vis absorbance, and fluorescence. The results showed that bleomycin binds to plasma proteins with an order-of-magnitude higher affinity for AGP than HSA. This is particularly important as AGP is an acute phase protein and is overexpressed in cancer patients. This should be taken into consideration as it could affect the therapeutic effect of the bleomycin dosage.
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Affiliation(s)
| | | | - Rohanah Hussain
- B23 SRCD Beamline, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; (E.L.); (G.S.)
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4
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Kuwana R, Yamazawa R, Asada R, Ito K, Furuta M, Takamatsu H. Excessive ultraviolet C irradiation causes spore protein denaturation and prohibits the initiation of spore germination in Bacillus subtilis. JOURNAL OF MICROORGANISM CONTROL 2023; 28:15-25. [PMID: 37277954 DOI: 10.4265/jmc.28.1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultraviolet (UV) -C is widely used to kill bacteria as it damages chromosomal DNA. We analyzed the denaturation of the protein function of Bacillus subtilis spores after UV-C irradiation. Almost all of the B. subtilis spores germinated in Luria-Bertani (LB) liquid medium, but the colony-forming unit (CFU) of the spores on LB agar plates decreased to approximately 1/103 by 100 mJ/cm2 of UV-C irradiation. Some of the spores germinated in LB liquid medium under phase-contrast microscopy, but almost no colonies formed on the LB agar plates after 1 J/cm2 of UV-C irradiation. The fluorescence of the green fluorescent protein (GFP) -fused spore proteins, YeeK-GFP, YeeK is a coat protein, decreased following UV-C irradiation of over 1 J/cm2, while that of SspA-GFP, SspA is a core protein, decreased following UV-C irradiation of over 2 J/ cm2, respectively. These results revealed that UV-C affected on coat proteins more than core proteins. We conclude that 25 to 100 mJ/cm2 of UV-C irradiation can cause DNA damage, and more than 1 J/cm2 of UV-C irradiation can cause the denaturation of spore proteins involved in germination. Our study would contribute to improve the technology to detect the bacterial spores, especially after UV sterilization.
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Affiliation(s)
| | | | - Ryoko Asada
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Metropolitan University
| | - Kiyoshi Ito
- Faculty of Pharmaceutical Sciences, Setsunan University
| | - Masakazu Furuta
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Metropolitan University
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5
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Sharma A, Khamar D, Cullen S, Hayden A, Hughes H. Innovative Drying Technologies for Biopharmaceuticals. Int J Pharm 2021; 609:121115. [PMID: 34547393 DOI: 10.1016/j.ijpharm.2021.121115] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 01/30/2023]
Abstract
In the past two decades, biopharmaceuticals have been a breakthrough in improving the quality of lives of patients with various cancers, autoimmune, genetic disorders etc. With the growing demand of biopharmaceuticals, the need for reducing manufacturing costs is essential without compromising on the safety, quality, and efficacy of products. Batch Freeze-drying is the primary commercial means of manufacturing solid biopharmaceuticals. However, Freeze-drying is an economically unfriendly means of production with long production cycles, high energy consumption and heavy capital investment, resulting in high overall costs. This review compiles some potential, innovative drying technologies that have not gained popularity for manufacturing parenteral biopharmaceuticals. Some of these technologies such as Spin-freeze-drying, Spray-drying, Lynfinity® Technology etc. offer a paradigm shift towards continuous manufacturing, whereas PRINT® Technology and MicroglassificationTM allow controlled dry particle characteristics. Also, some of these drying technologies can be easily scaled-up with reduced requirement for different validation processes. The inclusion of Process Analytical Technology (PAT) and offline characterization techniques in tandem can provide additional information on the Critical Process Parameters (CPPs) and Critical Quality Attributes (CQAs) during biopharmaceutical processing. These processing technologies can be envisaged to increase the manufacturing capacity for biopharmaceutical products at reduced costs.
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Affiliation(s)
- Ashutosh Sharma
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland.
| | - Dikshitkumar Khamar
- Sanofi, Manufacturing Science, Analytics and Technology (MSAT), IDA Industrial Park, Waterford X91TP27, Ireland
| | - Sean Cullen
- Gilead Sciences, Commercial Manufacturing, IDA Business & Technology Park, Carrigtwohill, Co. Cork T45DP77, Ireland
| | - Ambrose Hayden
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
| | - Helen Hughes
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
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6
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Ruzza P, Honisch C, Hussain R, Siligardi G. Free Radical Generation in Far-UV Synchrotron Radiation Circular Dichroism Assays-Protein and Buffer Composition Contribution. Int J Mol Sci 2021; 22:11325. [PMID: 34768758 PMCID: PMC8583428 DOI: 10.3390/ijms222111325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022] Open
Abstract
A useful tool to analyze the ligands and/or environmental contribution to protein stability is represented by the Synchrotron Radiation Circular Dichroism UV-denaturation assay that consists in the acquisition of several consecutive repeated far-UV SRCD spectra. Recently we demonstrated that the prevailing mechanism of this denaturation involves the generation of free radicals and reactive oxygen species (ROS). In this work, we analyzed the effect of buffering agents commonly used in spectroscopic measurements, including MOPS (3-(N-morpholino) propanesulfonic acid), HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), TRIS-HCl (tris-hydroxymethil aminomethane hydrochloride), and phosphate, on the efficiency of protein denaturation caused by exposure to UV radiation. Fluorescence experiments confirmed the presence of ROS and were used to determine the rate of ROS generation. Our results indicate that the efficiency of the denaturation process is strongly influenced by the buffer composition with MOPS and HEPES acting also as scavengers and that the presence of proteins itself influenced the ROS formation rate.
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Affiliation(s)
- Paolo Ruzza
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo, 1, 35131 Padova, Italy;
| | - Claudia Honisch
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo, 1, 35131 Padova, Italy;
- Department of Chemical Sciences, University of Padua, via Marzolo, 1, 35131 Padova, Italy
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK;
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK;
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7
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Honisch C, Ragazzi E, Hussain R, Brazier J, Siligardi G, Ruzza P. Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study. Pharmaceutics 2021; 13:1104. [PMID: 34452065 PMCID: PMC8401852 DOI: 10.3390/pharmaceutics13081104] [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: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
G-quadruplex (G4) forming DNA sequences were recently found to play a crucial role in the regulation of genomic processes such as replication, transcription and translation, also related to serious diseases. Therefore, systems capable of controlling DNA and RNA G-quadruplex structures would be useful for the modulation of various cellular events. In particular, peptides represent good candidates for targeting G-quadruplex structures, since they are easily tailored to enhance their functionality. In this work, we analyzed, by circular dichroism and synchrotron radiation circular dichroism spectroscopies, the interaction of a 25-residue peptide deriving from RHAU helicases (Rhau25) with three G-quadruplex-forming oligonucleotide sequences, in both sodium- and potassium-containing buffers, the most relevant monovalent cations in physiological conditions. The peptide displayed greater affinity for the G4 sequences adopting a parallel structure. However, it showed the ability to also interact with antiparallel or hybrid G-quadruplex structures, inducing a conformation conversion to the parallel structure. The stability of the oligonucleotide structure alone or in presence of the Rhau25 peptide was studied by temperature melting and UV denaturation experiments, and the data showed that the interaction with the peptide stabilized the conformation of oligonucleotide sequences when subjected to stress conditions.
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Affiliation(s)
- Claudia Honisch
- Institute of Biomolecular Chemistry of CNR, Via F. Marzolo, 1, 35131 Padova, Italy;
- Department of Chemical Sciences, University of Padua, Via F. Marzolo, 1, 35131 Padova, Italy
| | - Eugenio Ragazzi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, 2, 35131 Padova, Italy;
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (R.H.); (G.S.)
| | - John Brazier
- School of Pharmacy, University of Reading, Reading RG6 6DX, UK;
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (R.H.); (G.S.)
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry of CNR, Via F. Marzolo, 1, 35131 Padova, Italy;
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8
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Di Gaspero M, Ruzza P, Hussain R, Honisch C, Biondi B, Siligardi G, Marangon M, Curioni A, Vincenzi S. The Secondary Structure of a Major Wine Protein is Modified upon Interaction with Polyphenols. Molecules 2020; 25:E1646. [PMID: 32260104 PMCID: PMC7180857 DOI: 10.3390/molecules25071646] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 01/20/2023] Open
Abstract
Polyphenols are an important constituent of wines and they are largely studied due to their antioxidant properties and for their effects on wine quality and stability, which is also related to their capacity to bind to proteins. The effects of some selected polyphenols, including procyanidins B1 and B2, tannic acid, quercetin, and rutin, as well as those of a total white wine procyanidin extract on the conformational properties of the major wine protein VVTL1 (Vitis vinifera Thaumatin-Like-1) were investigated by Synchrotron Radiation Circular Dichroism (SRCD). Results showed that VVTL1 interacts with polyphenols as demonstrated by the changes in the secondary (far-UV) and tertiary (near-UV) structures, which were differently affected by different polyphenols. Additionally, polyphenols modified the two melting temperatures (TM) that were found for VVTL1 (32.2 °C and 53.9 °C for the protein alone). The circular dichroism (CD) spectra in the near-UV region revealed an involvement of the aromatic side-chains of the protein in the interaction with phenolics. The data demonstrate the existence of an interaction between polyphenols and VVTL1, which results in modification of its thermal and UV denaturation pattern. This information can be useful in understanding the behavior of wine proteins in presence of polyphenols, thus giving new insights on the phenomena that are involved in wine stability.
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Affiliation(s)
- Mattia Di Gaspero
- Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy;
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo 1, 35131 Padua, Italy; (P.R.); (C.H.); (B.B.)
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; (R.H.); (G.S.)
| | - Claudia Honisch
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo 1, 35131 Padua, Italy; (P.R.); (C.H.); (B.B.)
- Department of Chemical Sciences, University of Padua, Via Marzolo 1, 35131 Padua, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo 1, 35131 Padua, Italy; (P.R.); (C.H.); (B.B.)
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; (R.H.); (G.S.)
| | - Matteo Marangon
- Department of Agronomy, Food, Natural Resources Animals and Environment (DAFNAE), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy; (A.C.); (S.V.)
| | - Andrea Curioni
- Department of Agronomy, Food, Natural Resources Animals and Environment (DAFNAE), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy; (A.C.); (S.V.)
| | - Simone Vincenzi
- Department of Agronomy, Food, Natural Resources Animals and Environment (DAFNAE), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy; (A.C.); (S.V.)
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9
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Honisch C, Donadello V, Hussain R, Peterle D, De Filippis V, Arrigoni G, Gatto C, Giurgola L, Siligardi G, Ruzza P. Application of Circular Dichroism and Fluorescence Spectroscopies To Assess Photostability of Water-Soluble Porcine Lens Proteins. ACS OMEGA 2020; 5:4293-4301. [PMID: 32149259 PMCID: PMC7057709 DOI: 10.1021/acsomega.9b04234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
The eye lens is mainly composed of the highly ordered water-soluble (WS) proteins named crystallins. The aggregation and insolubilization of these proteins lead to progressive lens opacification until cataract onset. Although this is a well-known disease, the mechanism of eye lens protein aggregation is not well understood; however, one of the recognized causes of proteins modification is related to the exposure to UV light. For this reason, the spectroscopic properties of WS lens proteins and their stability to UV irradiation have been evaluated by different biophysical methods including synchrotron radiation circular dichroism, fluorescence, and circular dichroism spectroscopies. Moreover, dynamic light scattering, gel electrophoresis, transmission electron microscopy, and protein digestion followed by tandem LC-MS/MS analysis were used to study the morphological and structural changes in protein aggregates induced by exposure to UV light. Our results clearly indicated that the exposure to UV radiation modified the protein conformation, inducing a loss of ordered structure and aggregation. Furthermore, we confirmed that these changes were attributable to the generation of reactive oxygen species due to the irradiation of the protein sample. This approach, involving the photodenaturation of proteins, provides a benchmark in high-throughput screening of small molecules suitable to prevent protein denaturation and aggregation.
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Affiliation(s)
- Claudia Honisch
- Institute
of Biomolecular Chemistry of CNR, Padua
Unit, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Viola Donadello
- Institute
of Biomolecular Chemistry of CNR, Padua
Unit, 35131 Padova, Italy
| | - Rohanah Hussain
- Diamond
Light Source Ltd., Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Daniele Peterle
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Vincenzo De Filippis
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Giorgio Arrigoni
- Department
of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Proteomics
Center, University of Padova and Azienda
Ospedaliera di Padova, 35129 Padova, Italy
| | - Claudio Gatto
- Alchilife
Srl, R&D, Viale Austria
14, 35020 Ponte
San Nicolò (PD), Italy
| | - Laura Giurgola
- Alchilife
Srl, R&D, Viale Austria
14, 35020 Ponte
San Nicolò (PD), Italy
| | - Giuliano Siligardi
- Diamond
Light Source Ltd., Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Paolo Ruzza
- Institute
of Biomolecular Chemistry of CNR, Padua
Unit, 35131 Padova, Italy
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10
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Honisch C, Hussain R, Siligardi G, Ruzza P. Influence of small molecules on the photo-stability of water soluble porcine lens proteins. Chirality 2020; 32:611-618. [PMID: 32114715 DOI: 10.1002/chir.23210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/07/2022]
Abstract
The eye lens is a biconvex structure composed of lens fibres, cells that lack of blood and nerve supply and of any organelle, allowing for a high concentration of water soluble proteins that determine the lens transparency and refractive index. The lens water soluble protein pool in mammals is composed of α-, β-, and γ-crystallins, the latter being involved in calcium homeostasis and having structural importance, the first playing a crucial role in preventing protein aggregation and the consequent lens obfuscation, which leads to the clinical outcome of cataract. Among different factors, oxidative stress, free radicals, and reactive oxygen species (ROSs) generated by the exposure to UV light are widely recognized to cause cataract formation. Taking advantage of synchrotron radiation circular dichroism, fluorescence, and circular dichroism spectroscopies, in the present study we investigate the influence of different small molecules with the potential to either quench ROS generation or to stabilize protein conformation. Therefore, ascorbic acid, an excellent antioxidant agent already present in the eye aqueous humour, has been tested along with ceftriaxone, mannitol and trehalose, which osmolyte activity was demonstrated interfering with model proteins misfolding. Our results showed that ascorbic acid strongly inhibits the ROS production without, however, preserving the native protein structure, whereas mannitol had no effect on the ROS production but retained better the secondary structure of WS proteins. Collectively, the use of a mixture of ascorbic acid and mannitol could be used to better protect eye lens proteins from ROS damage preventing the cataract onset.
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Affiliation(s)
- Claudia Honisch
- Institute of Biomolecular Chemistry, National Research Council (CNR), Padova, Italy.,Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Rohanah Hussain
- Soft Condensed Matter Village, Diamond Light Source Ltd, Didcot, UK
| | | | - Paolo Ruzza
- Institute of Biomolecular Chemistry, National Research Council (CNR), Padova, Italy
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11
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Enzyme-Ligand Interaction Monitored by Synchrotron Radiation Circular Dichroism. Methods Mol Biol 2019. [PMID: 31773649 DOI: 10.1007/978-1-0716-0163-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the global conformational changes, the secondary structure content, and protein folding and in the near-UV region the local tertiary structure changes probed by the local environment of the aromatic side chains, prosthetic groups (hemes, flavones, carotenoids), the dihedral angle of disulfide bonds, and the ligand chromophore moieties, the latter occurring as a result of protein-ligand binding interaction. Qualitative and quantitative investigations into ligand-binding interactions in both the far- and near-UV regions using CD spectroscopy provide unique and direct information whether induced conformational changes upon ligand binding occur and of what nature that are unattainable with other techniques such as fluorescence, ITC, SPR, and AUC.This chapter provides an overview of how to perform circular dichroism (CD) experiments, detailing methods, hints and tips for successful CD measurements. Descriptions of different experimental designs are discussed using CD to investigate ligand-binding interactions. This includes standard qualitative CD measurements conducted in both single-measurement mode and high-throughput 96-well plate mode, CD titrations, and UV protein denaturation assays with and without ligand.The highly collimated micro-beam available at B23 beamline for synchrotron radiation circular dichroism (SRCD) at Diamond Light Source (DLS) offers many advantages to benchtop instruments. The synchrotron light source is ten times brighter than a standard xenon arc light source of benchtop instruments. The small diameter of the synchrotron beam can be up to 160 times smaller than that of benchtop light beams; this has enabled the use of small aperture cuvette cells and flat capillary tubes reducing substantially the amount of volume sample to be investigated. Methods, hints and tips, and golden rules to measure good quality, artifact-free SRCD and CD data will be described in this chapter in particular for the study of protein-ligand interactions and protein photostability.
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12
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Lalande M, Schwob L, Vizcaino V, Chirot F, Dugourd P, Schlathölter T, Poully J. Direct Radiation Effects on the Structure and Stability of Collagen and Other Proteins. Chembiochem 2019; 20:2972-2980. [DOI: 10.1002/cbic.201900202] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/28/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Mathieu Lalande
- CIMAP LaboratoryUMR 6252CEA/CNRS/ENSICAEN/Université de Caen Normandie) Boulevard Becquerel 14070 Caen France
| | - Lucas Schwob
- Helmholtz AssociationDeutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 22607 Hamburg Germany
| | - Violaine Vizcaino
- CIMAP LaboratoryUMR 6252CEA/CNRS/ENSICAEN/Université de Caen Normandie) Boulevard Becquerel 14070 Caen France
| | - Fabien Chirot
- Université Claude Bernard Lyon 1ENS de LyonUMR 5280 Institut des Sciences Analytiques 5, rue de la Doua 69100 Villeurbanne France
| | - Philippe Dugourd
- Université Claude Bernard Lyon 1CNRSUMR 5306 Institut Lumière Matière 10 rue Ada Byron 69622 Villeurbanne Cedex France
| | - Thomas Schlathölter
- Zernike Institute for Advanced MaterialsUniversity of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Jean‐Christophe Poully
- CIMAP LaboratoryUMR 6252CEA/CNRS/ENSICAEN/Université de Caen Normandie) Boulevard Becquerel 14070 Caen France
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Siligardi G, Hughes CS, Hussain R. Characterisation of sensor kinase by CD spectroscopy: golden rules and tips. Biochem Soc Trans 2018; 46:1627-1642. [PMID: 30514767 PMCID: PMC6299240 DOI: 10.1042/bst20180222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 01/22/2023]
Abstract
This is a review that describes the golden rules and tips on how to characterise the molecular interactions of membrane sensor kinase proteins with ligands using mainly circular dichroism (CD) spectroscopy. CD spectroscopy is essential for this task as any conformational change observed in the far-UV (secondary structures (α-helix, β-strands, poly-proline of type II, β-turns, irregular and folding) and near-UV regions [local environment of the aromatic side-chains of amino acid residues (Phe, Tyr and Trp) and ligands (drugs) and prosthetic groups (porphyrins, cofactors and coenzymes (FMN, FAD, NAD))] upon ligand addition to the protein can be used to determine qualitatively and quantitatively ligand-binding interactions. Advantages of using CD versus other techniques will be discussed. The difference CD spectra of the protein-ligand mixtures calculated subtracting the spectra of the ligand at various molar ratios can be used to determine the type of conformational changes induced by the ligand in terms of the estimated content of the various elements of protein secondary structure. The highly collimated microbeam and high photon flux of Diamond Light Source B23 beamline for synchrotron radiation circular dichroism (SRCD) enable the use of minimal amount of membrane proteins (7.5 µg for a 0.5 mg/ml solution) for high-throughput screening. Several examples of CD titrations of membrane proteins with a variety of ligands are described herein including the protocol tips that would guide the choice of the appropriate parameters to conduct these titrations by CD/SRCD in the best possible way.
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Affiliation(s)
- Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, U.K
| | - Charlotte S Hughes
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, U.K
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, U.K.
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