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Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [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: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
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Park Y, Jin S, Noda I, Jung YM. Continuing progress in the field of two-dimensional correlation spectroscopy (2D-COS): Part III. Versatile applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 284:121636. [PMID: 36229084 DOI: 10.1016/j.saa.2022.121636] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 06/16/2023]
Abstract
In this review, the comprehensive summary of two-dimensional correlation spectroscopy (2D-COS) for the last two years is covered. The remarkable applications of 2D-COS in diverse fields using many types of probes and perturbations for the last two years are highlighted. IR spectroscopy is still the most popular probe in 2D-COS during the last two years. Applications in fluorescence and Raman spectroscopy are also very popularly used. In the external perturbations applied in 2D-COS, variations in concentration, pH, and relative compositions are dramatically increased during the last two years. Temperature is still the most used effect, but it is slightly decreased compared to two years ago. 2D-COS has been applied to diverse systems, such as environments, natural products, polymers, food, proteins and peptides, solutions, mixtures, nano materials, pharmaceuticals, and others. Especially, biological and environmental applications have significantly emerged. This survey review paper shows that 2D-COS is an actively evolving and expanding field.
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Affiliation(s)
- Yeonju Park
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sila Jin
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Isao Noda
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Young Mee Jung
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Republic of Korea; Department of Chemistry, and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea.
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Lin X, Shuang E, Chen X. Metal-organic framework/3,3',5,5'-tetramethylbenzidine based multidimensional spectral array platform for sensitive discrimination of protein phosphorylation. J Colloid Interface Sci 2021; 602:513-519. [PMID: 34144305 DOI: 10.1016/j.jcis.2021.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/21/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
A multifunctional metal-organic framework (MOF) hybrid Zr-FeTCPP-MOF is fabricated with 2-aminoterephthalic acid (NH2-BDC) and Fe (III) meso-Tetra (4-carboxyphenyl) porphine chloride (FeTCPPCl) participating in the coordination to Zr6 clusters via one-pot hydrothermal method. The adsorption of phosphoproteins on the surface of Zr-FeTCPP-MOF hybrid cause the chances on the absorbance (Abs), fluorescence (FL) and resonance light scattering (RLS) signals of Zr-FeTCPP-MOF/3,3',5,5'-Tetramethylbenzidine (TMB) system, and an array sensing platform is successfully built for sensitive identification of protein phosphorylation based on the three-dimensional spectral changes of MOF/TMB sensing system induced by the variations on the structure, size, and phosphorylation site of phosphoproteins. This array sensing system is robust in recognizing different phosphoprotein species, and shows high sensitivity in discriminating similar phosphoproteins of different phosphorylation distribution, i.e., caseins (α-, β- and κ-cas). The detection limit of this array sensing platform to individual phosphoprotein is low down to 5 nM. The practical application of this MOF/TMB-base sensing system is substantially demonstrated by identifying tau peptides with different phosphorylation distribution, and distinguishing cancer cells of abnormal phosphorylations from normal cells. This work proves the reliability, sensitivity, and practicality of the MOF/TMB-base sensing system platform for the diagnosis of phosphorylation-related diseases in clinical trials.
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Affiliation(s)
- Xin Lin
- College of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning, China; Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box332, Shenyang 110819, Liaoning, China
| | - E Shuang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box332, Shenyang 110819, Liaoning, China
| | - Xuwei Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box332, Shenyang 110819, Liaoning, China.
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Li Vigni M, Durante C, Michelini S, Nocetti M, Cocchi M. Preliminary Assessment of Parmigiano Reggiano Authenticity by Handheld Raman Spectroscopy. Foods 2020; 9:foods9111563. [PMID: 33126689 PMCID: PMC7692761 DOI: 10.3390/foods9111563] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 11/16/2022] Open
Abstract
Raman spectroscopy, and handheld spectrometers in particular, are gaining increasing attention in food quality control as a fast, portable, non-destructive technique. Furthermore, this technology also allows for measuring the intact sample through the packaging and, with respect to near infrared spectroscopy, it is not affected by the water content of the samples. In this work, we evaluate the potential of the methodology to model, by multivariate data analysis, the authenticity of Parmigiano Reggiano cheese, which is one of the most well-known and appreciated hard cheeses worldwide, with protected denomination of origin (PDO). On the other hand, it is also highly subject to counterfeiting. In particular, it is critical to assess the authenticity of grated cheese, to which, under strictly specified conditions, the PDO is extended. To this aim, it would be highly valuable to develop an authenticity model based on a fast, non-destructive technique. In this work, we present preliminary results obtained by a handheld Raman spectrometer and class-modeling (Soft Independent Modeling of Class Analogy, SIMCA), which are extremely promising, showing sensitivity and specificity of 100% for the test set. Moreover, another salient issue, namely the percentage of rind in grated cheese, was addressed by developing a multivariate calibration model based on Raman spectra. It was possible to obtain a prediction error around 5%, with 18% being the maximum content allowed by the production protocol.
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Affiliation(s)
- Mario Li Vigni
- Dipartimento Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (M.L.V.); (C.D.)
| | - Caterina Durante
- Dipartimento Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (M.L.V.); (C.D.)
| | - Sara Michelini
- Consorzio Parmigiano Reggiano, Via Kennedy 18, 42124 Reggio Emilia, Italy; (S.M.); (M.N.)
| | - Marco Nocetti
- Consorzio Parmigiano Reggiano, Via Kennedy 18, 42124 Reggio Emilia, Italy; (S.M.); (M.N.)
| | - Marina Cocchi
- Dipartimento Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (M.L.V.); (C.D.)
- Correspondence: ; Tel.: +39-0592058554
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Bao Y, Li Y, Ling L, Xiang X, Han X, Zhao B, Guo X. Label-Free and Highly Sensitive Detection of Native Proteins by Ag IANPs via Surface-Enhanced Raman Spectroscopy. Anal Chem 2020; 92:14325-14329. [DOI: 10.1021/acs.analchem.0c03165] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ying Bao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yang Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ling Ling
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xiaoxia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, P. R. China
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Townsend DJ, Middleton DA, Ashton L. Raman Spectroscopy with 2D Perturbation Correlation Moving Windows for the Characterization of Heparin-Amyloid Interactions. Anal Chem 2020; 92:13822-13828. [PMID: 32935978 DOI: 10.1021/acs.analchem.0c02390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It has been shown extensively that glycosaminoglycan (GAG)-protein interactions can induce, accelerate, and impede the clearance of amyloid fibrils associated with systemic and localized amyloidosis. Obtaining molecular details of these interactions is fundamental to our understanding of amyloid disease. Consequently, there is a need for analytical approaches that can identify protein conformational transitions and simultaneously characterize heparin interactions. By combining Raman spectroscopy with two-dimensional (2D) perturbation correlation moving window (2DPCMW) analysis, we have successfully identified changes in protein secondary structure during pH- and heparin-induced fibril formation of apolipoprotein A-I (apoA-I) associated with atherosclerosis. Furthermore, from the 2DPCMW, we have identified peak shifts and intensity variations in Raman peaks arising from different heparan sulfate moieties, indicating that protein-heparin interactions vary at different heparin concentrations. Raman spectroscopy thus reveals new mechanistic insights into the role of GAGs during amyloid fibril formation.
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Affiliation(s)
- David J Townsend
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - David A Middleton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Lorna Ashton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
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Ma H, Han XX, Zhao B. Enhanced Raman spectroscopic analysis of protein post-translational modifications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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