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Lin C, Qin H, Liao Y, Chen J, Gao B. Chemical Synthesis and Insecticidal Activity Research Based on α-Conotoxins. Molecules 2024; 29:2846. [PMID: 38930912 PMCID: PMC11206848 DOI: 10.3390/molecules29122846] [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: 05/28/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The escalating resistance of agricultural pests to chemical insecticides necessitates the development of novel, efficient, and safe biological insecticides. Conus quercinus, a vermivorous cone snail, yields a crude venom rich in peptides for marine worm predation. This study screened six α-conotoxins with insecticidal potential from a previously constructed transcriptome database of C. quercinus, characterized by two disulfide bonds. These conotoxins were derived via solid-phase peptide synthesis (SPPS) and folded using two-step iodine oxidation for further insecticidal activity validation, such as CCK-8 assay and insect bioassay. The final results confirmed the insecticidal activities of the six α-conotoxins, with Qc1.15 and Qc1.18 exhibiting high insecticidal activity. In addition, structural analysis via homology modeling and functional insights from molecular docking offer a preliminary look into their potential insecticidal mechanisms. In summary, this study provides essential references and foundations for developing novel insecticides.
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Affiliation(s)
| | | | | | - Jiao Chen
- Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, International Joint Research Center of Human-Machine Intelligent Collaborative for Tumor Precision Diagnosis and Treatment of Hainan Province, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (C.L.); (H.Q.); (Y.L.)
| | - Bingmiao Gao
- Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, International Joint Research Center of Human-Machine Intelligent Collaborative for Tumor Precision Diagnosis and Treatment of Hainan Province, Hainan Key Laboratory for Research and Development of Tropical Herbs, School of Pharmacy, Hainan Medical University, Haikou 571199, China; (C.L.); (H.Q.); (Y.L.)
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2
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Timofeeva AM, Sedykh SE, Litvinova EA, Dolgushin SA, Matveev AL, Tikunova NV, Nevinsky GA. Binding of Natural Antibodies Generated after COVID-19 and Vaccination with Individual Peptides Corresponding to the SARS-CoV-2 S-Protein. Vaccines (Basel) 2024; 12:426. [PMID: 38675808 PMCID: PMC11053827 DOI: 10.3390/vaccines12040426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The rapid development of vaccines is a crucial objective in modern biotechnology and molecular pharmacology. In this context, conducting research to expedite the selection of a potent immunogen is imperative. The candidate vaccine should induce the production of antibodies that can recognize the immunogenic epitopes of the target protein, resembling the ones found in recovered patients. One major challenge in vaccine development is the absence of straightforward and reliable techniques to determine the extent to which the spectrum of antibodies produced after vaccination corresponds to antibodies found after recovery. This paper describes a newly developed method to detect antibodies specific to immunogenic epitopes of the target protein in blood plasma and to compare them with antibody spectra generated post vaccination. Comparing the antibody pool generated in the human body after recovering from an infectious disease with the pool formed through vaccination can become a universal method for screening candidate vaccines. This method will enable the identification of candidate vaccines that can induce the production of antibodies similar to those generated in response to a natural infection. Implementing this approach will facilitate the rapid development of new vaccines, even when faced with a pandemic.
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Affiliation(s)
- Anna M. Timofeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina A. Litvinova
- Physical Engineering Faculty, Novosibirsk State Technical University, Novosibirsk 630073, Russia
| | | | - Andrey L. Matveev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
| | - Nina V. Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
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3
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Schüttel M, Will E, Sangouard G, Zarda A, Habeshian S, Nielsen AL, Heinis C. Solid-phase peptide synthesis in 384-well plates. J Pept Sci 2024; 30:e3555. [PMID: 38220145 DOI: 10.1002/psc.3555] [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: 07/06/2023] [Revised: 08/31/2023] [Accepted: 11/03/2023] [Indexed: 01/16/2024]
Abstract
Newer solid-phase peptide synthesis and release strategies enable the production of short peptides with high purity, allowing direct screening for desired bioactivity without prior chromatographic purification. However, the maximum number of peptides that can currently be synthesized per microplate reactor is 96, allowing the parallel synthesis of 384 peptides in modern devices that have space for 4 microplate reactors. To synthesize larger numbers of peptides, we modified a commercially available peptide synthesizer to enable the production of peptides in 384-well plates, which allows the synthesis of 1,536 peptides in one run (4 × 384 peptides). We report new hardware components and customized software that allowed for the synthesis of 1,536 short peptides in good quantity (average > 0.5 μmol), at high concentration (average > 10 mM), and decent purity without purification (average > 80%). The high-throughput peptide synthesis, which we developed with peptide drug development in mind, may be widely used for peptide library synthesis and screening, antibody epitope scanning, epitope mimetic development, or protease/kinase substrate screening.
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Affiliation(s)
- Mischa Schüttel
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Edward Will
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gontran Sangouard
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anne Zarda
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sevan Habeshian
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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4
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Hananya N, Koren S, Muir TW. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet 2024; 25:255-271. [PMID: 37985791 PMCID: PMC11176933 DOI: 10.1038/s41576-023-00664-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2023] [Indexed: 11/22/2023]
Abstract
Genetic and genomic techniques have proven incredibly powerful for identifying and studying molecular players implicated in the epigenetic regulation of DNA-templated processes such as transcription. However, achieving a mechanistic understanding of how these molecules interact with chromatin to elicit a functional output is non-trivial, owing to the tremendous complexity of the biochemical networks involved. Advances in protein engineering have enabled the reconstitution of 'designer' chromatin containing customized post-translational modification patterns, which, when used in conjunction with sophisticated biochemical and biophysical methods, allow many mechanistic questions to be addressed. In this Review, we discuss how such tools complement established 'omics' techniques to answer fundamental questions on chromatin regulation, focusing on chromatin mark establishment and protein-chromatin interactions.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Shany Koren
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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5
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Jian M, Sun X, Zhang H, Li X, Li S, Wang Z. Development of a peptide microarray-based metal-enhanced fluorescence assay for ultrasensitive detection of multiple matrix metalloproteinase activities by using a gold nanorod-polymer substrate. Biosens Bioelectron 2024; 246:115871. [PMID: 38035516 DOI: 10.1016/j.bios.2023.115871] [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: 08/25/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
Matrix metalloproteinases (MMPs) are attractive biomarkers for cancer diagnosis and treatment, while it is still a challenge to precise analysis of MMP activities owing to their very low abundance in the biological samples, especially at the early stages of tumors. Herein, a peptide microarray-based metal-enhanced fluorescence assay (PMMEFA) is proposed to simultaneously detect MMP-1, -2, -3, -7, -9, and -13 activities. The assay involves immobilization of Förster resonance energy transfer dye pair decorated peptides (FRET-peptides) on a poly(glycidyl methacrylate-co-2-hydroxyethyl methacrylate) coated gold nanorod modified glass slide (GNR@P(GMA-HEMA)). To fabricate the GNR@P(GMA-HEMA) slide, GNRs are self-assembled onto an aminated glass slide, and a polymer brush (P(GMA-HEMA)) is grown through a surface-initiated atom transfer radical polymerization reaction (SI-ATRP). Upon the addition of MMPs, the FRET pairs are broken due to the specific cleavage of FRET-peptides by enzymes, resulting in the recovery of fluorescence signals and further enhancement by the MEF of GNRs. The fluorescence recovery degree provides a direct indicator for MMP activity. The PMMEFA exhibits excellent sensitivity, which enables to detect MMP-1, -2, -3, -7, -9, and -13 activities, with low limits of detection (LODs) of 1.7 fg mL-1, 0.3 fg mL-1, 2.0 fg mL-1, 1.8 fg mL-1, 2.2 fg mL-1 and 14.0 fg mL-1, respectively. To substantiate the practicability of PMMEFA, MMP activities were measured in a range of matrices, encompassing cell culture medium, serum, and tumor tissue homogenate, and MMP activities can be detected only in 0.15 μL serum and 0.025 mg tumor tissue.
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Affiliation(s)
- Minghong Jian
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China
| | - Xudong Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, PR China
| | - Hua Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China
| | - Xiaotong Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, PR China
| | - Shasha Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, PR China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, PR China; National Analytical Research Center of Electrochemistry and Spectroscopy, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China.
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6
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Terada Y, Akimoto M, Sakoda H, Yamamoto S, Kubota M, Motoyama T, Imanaka Y, Nakano S, Ito S, Kato S, Ito K. Comprehensive Epitope Analysis of Monoclonal Antibodies Binding to Hen Egg Ovalbumin Using a Peptide Array. Foods 2024; 13:407. [PMID: 38338542 PMCID: PMC10855139 DOI: 10.3390/foods13030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/06/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Food allergies are a significant health issue worldwide. In many countries, labeling of primary allergens in food products has been made mandatory to ensure consumer safety. In food manufacturing settings, the lateral flow immunoassay (LFI)-based on antigen-antibody reactions-is a rapid and accurate method for allergen testing and is widely used. Peptide arrays are tools that enable the synthesis of peptides of any sequence on a substrate and high-throughput analysis of their interactions with chemicals. This study aimed to investigate a new application of peptide arrays in the field of food technology, particularly in the development of antibodies for food allergen testing. First, monoclonal antibodies against hen egg ovalbumin, a major food allergen, were produced. Then, using a peptide array, the epitope and specificity of the antibodies were comprehensively and precisely analyzed. Finally, an LFI kit incorporating the antibodies demonstrated both high specificity and detection sensitivity for food allergen testing. These findings indicate that peptide arrays are valuable tools in the development of antibodies for food allergen testing, ensuring reliability and accuracy at the molecular level.
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Affiliation(s)
- Yuko Terada
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi 422-8526, Shizuoka, Japan; (Y.T.); (M.K.); (T.M.); (Y.I.); (S.N.); (S.I.)
| | - Masanobu Akimoto
- Research and Development Department, Prima Meat Packers, Ltd., 635 Nakamukaihara, Tsuchiura-shi 300-0841, Ibaraki, Japan; (M.A.); (H.S.); (S.Y.); (S.K.)
| | - Hirofumi Sakoda
- Research and Development Department, Prima Meat Packers, Ltd., 635 Nakamukaihara, Tsuchiura-shi 300-0841, Ibaraki, Japan; (M.A.); (H.S.); (S.Y.); (S.K.)
| | - Shunsuke Yamamoto
- Research and Development Department, Prima Meat Packers, Ltd., 635 Nakamukaihara, Tsuchiura-shi 300-0841, Ibaraki, Japan; (M.A.); (H.S.); (S.Y.); (S.K.)
| | - Mayuka Kubota
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi 422-8526, Shizuoka, Japan; (Y.T.); (M.K.); (T.M.); (Y.I.); (S.N.); (S.I.)
| | - Tomoharu Motoyama
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi 422-8526, Shizuoka, Japan; (Y.T.); (M.K.); (T.M.); (Y.I.); (S.N.); (S.I.)
| | - Yo Imanaka
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi 422-8526, Shizuoka, Japan; (Y.T.); (M.K.); (T.M.); (Y.I.); (S.N.); (S.I.)
| | - Shogo Nakano
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi 422-8526, Shizuoka, Japan; (Y.T.); (M.K.); (T.M.); (Y.I.); (S.N.); (S.I.)
| | - Sohei Ito
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi 422-8526, Shizuoka, Japan; (Y.T.); (M.K.); (T.M.); (Y.I.); (S.N.); (S.I.)
| | - Shigeki Kato
- Research and Development Department, Prima Meat Packers, Ltd., 635 Nakamukaihara, Tsuchiura-shi 300-0841, Ibaraki, Japan; (M.A.); (H.S.); (S.Y.); (S.K.)
| | - Keisuke Ito
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi 422-8526, Shizuoka, Japan; (Y.T.); (M.K.); (T.M.); (Y.I.); (S.N.); (S.I.)
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7
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Kelbauskas L, Legutki JB, Woodbury NW. Highly heterogenous humoral immune response in Lyme disease patients revealed by broad machine learning-assisted antibody binding profiling with random peptide arrays. Front Immunol 2024; 15:1335446. [PMID: 38318184 PMCID: PMC10838964 DOI: 10.3389/fimmu.2024.1335446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Lyme disease (LD), a rapidly growing public health problem in the US, represents a formidable challenge due to the lack of detailed understanding about how the human immune system responds to its pathogen, the Borrelia burgdorferi bacterium. Despite significant advances in gaining deeper insight into mechanisms the pathogen uses to evade immune response, substantial gaps remain. As a result, molecular tools for the disease diagnosis are lacking with the currently available tests showing poor performance. High interpersonal variability in immune response combined with the ability of the pathogen to use a number of immune evasive tactics have been implicated as underlying factors for the limited test performance. Methods This study was designed to perform a broad profiling of the entire repertoire of circulating antibodies in human sera at the single-individual level using planar arrays of short linear peptides with random sequences. The peptides sample sparsely, but uniformly the entire combinatorial sequence space of the same length peptides for profiling the humoral immune response to a B.burg. infection and compare them with other diseases with etiology similar to LD and healthy controls. Results The study revealed substantial variability in antibody binding profiles between individual LD patients even to the same antigen (VlsE protein) and strong similarity between individuals diagnosed with Lyme disease and healthy controls from the areas endemic to LD suggesting a high prevalence of seropositivity in endemic healthy control. Discussion This work demonstrates the utility of the approach as a valuable analytical tool for agnostic profiling of humoral immune response to a pathogen.
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Affiliation(s)
- L Kelbauskas
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
- Biomorph Technologies, Chandler, AZ, United States
| | - J B Legutki
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
- Biomorph Technologies, Chandler, AZ, United States
| | - N W Woodbury
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
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8
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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9
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Gurung V, Biswas S, Biswas I. Diverse nature of ClpX degradation motifs in Streptococcus mutans. Microbiol Spectr 2024; 12:e0345723. [PMID: 38051052 PMCID: PMC10782952 DOI: 10.1128/spectrum.03457-23] [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: 09/22/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Cytoplasmic Clp-related proteases play a major role in maintaining cellular proteome in bacteria. ClpX/P is one such proteolytic complex that is important for conserving protein homeostasis. In this study, we investigated the role of ClpX/P in Streptococcus mutans, an important oral pathogen. We identified several putative substrates whose cellular levels are regulated by ClpX/P in S. mutans and subsequently discovered several recognition motifs that are critical for degradation. Our study is the first comprehensive analysis of determining ClpX/P motifs in streptococci. We believe that identifying the substrates that are regulated by ClpX/P will enhance our understanding about virulence regulation in this important group of pathogens.
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Affiliation(s)
- Vivek Gurung
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Saswati Biswas
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
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10
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Lim C, Lee S, Shin Y, Cho S, Park C, Shin Y, Song EC, Kim WK, Ham C, Kim SB, Kwon YS, Oh KT. Development and application of novel peptide-formulated nanoparticles for treatment of atopic dermatitis. J Mater Chem B 2023; 11:10131-10146. [PMID: 37830254 DOI: 10.1039/d3tb01202f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Atopic dermatitis is a chronic inflammatory skin condition that is characterized by skin inflammation, itching, and redness. Although various treatments can alleviate symptoms, they often come with side effects, highlighting the need for new treatments. Here, we discovered a new peptide-based therapy using the intra-dermal delivery technology (IDDT) platform developed by Remedi Co., Ltd (REMEDI). The platform screens and identifies peptides derived from proteins in the human body that possess cell-penetrating peptide (CPP) properties. We screened over 1000-peptides and identified several derived from the Speckled protein (SP) family that have excellent CPP properties and have anti-inflammatory effects. We assessed these peptides for their potential as a treatment for atopic dermatitis. Among them, the RMSP1 peptide showed the most potent anti-inflammatory effects by inhibiting the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and signal transducer and activator of transcription 3 (STAT3) signaling pathways while possessing CPP properties. To further improve efficacy and stability, we developed a palmitoylated version called Pal-RMSP1. Formulation studies using liposomes (Pal-RMSP1 LP) and micelles (Pal-RMSP1 DP) demonstrated improved anti-inflammatory effects in vitro and enhanced therapeutic effects in vivo. Our study indicates that nano-formulated Pal-RMSP1 could have the potential to become a new treatment option for atopic dermatitis.
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Affiliation(s)
- Chaemin Lim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- College of Pharmacy, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, 13488 Gyeonggi-do, Republic of Korea
| | - Subin Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- Department of Global Innovative Drugs, The Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yuseon Shin
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- Department of Global Innovative Drugs, The Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seongmin Cho
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Chanho Park
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Yungyeong Shin
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Ee Chan Song
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Wan Ki Kim
- Remedi Co., Ltd. Research Center, Songdo 21990, Republic of Korea
| | - Cheolmin Ham
- Rare Isotope Science Project, Institute for Basic Science, Daejeon 34000, Republic of Korea
| | - Sang Bum Kim
- College of Pharmacy, Sahmyook University, Seoul 01795, Republic of Korea
| | - Yong-Su Kwon
- Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyung Taek Oh
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
- Department of Global Innovative Drugs, The Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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11
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Palma M. Epitopes and Mimotopes Identification Using Phage Display for Vaccine Development against Infectious Pathogens. Vaccines (Basel) 2023; 11:1176. [PMID: 37514992 PMCID: PMC10384025 DOI: 10.3390/vaccines11071176] [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: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Traditional vaccines use inactivated or weakened forms of pathogens which could have side effects and inadequate immune responses. To overcome these challenges, phage display has emerged as a valuable tool for identifying specific epitopes that could be used in vaccines. This review emphasizes the direct connection between epitope identification and vaccine development, filling a crucial gap in the field. This technique allows vaccines to be engineered to effectively stimulate the immune system by presenting carefully selected epitopes. Phage display involves screening libraries of random peptides or gene/genome fragments using serum samples from infected, convalescent, or vaccinated individuals. This method has been used to identify epitopes from various pathogens including SARS-CoV-2, Mycobacterium tuberculosis, hepatitis viruses, H5N1, HIV-1, Human T-lymphotropic virus 1, Plasmodium falciparum, Trypanosoma cruzi, and Dirofilaria repens. Bacteriophages offer advantages such as being immunogenic carriers, low production costs, and customization options, making them a promising alternative to traditional vaccines. The purpose of this study has been to highlight an approach that encompasses the entire process from epitope identification to vaccine production using a single technique, without requiring additional manipulation. Unlike conventional methods, phage display demonstrates exceptional efficiency and speed, which could provide significant advantages in critical scenarios such as pandemics.
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Affiliation(s)
- Marco Palma
- Institute for Globally Distributed Open Research and Education (IGDORE), 03181 Torrevieja, Spain
- Protheragen Inc., Ronkonkoma, NY 11779, USA
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12
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Chowdhury R, Taguchi AT, Kelbauskas L, Stafford P, Diehnelt C, Zhao ZG, Williamson PC, Green V, Woodbury NW. Modeling the sequence dependence of differential antibody binding in the immune response to infectious disease. PLoS Comput Biol 2023; 19:e1010773. [PMID: 37339137 DOI: 10.1371/journal.pcbi.1010773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/15/2023] [Indexed: 06/22/2023] Open
Abstract
Past studies have shown that incubation of human serum samples on high density peptide arrays followed by measurement of total antibody bound to each peptide sequence allows detection and discrimination of humoral immune responses to a variety of infectious diseases. This is true even though these arrays consist of peptides with near-random amino acid sequences that were not designed to mimic biological antigens. This "immunosignature" approach, is based on a statistical evaluation of the binding pattern for each sample but it ignores the information contained in the amino acid sequences that the antibodies are binding to. Here, similar array-based antibody profiles are instead used to train a neural network to model the sequence dependence of molecular recognition involved in the immune response of each sample. The binding profiles used resulted from incubating serum from 5 infectious disease cohorts (Hepatitis B and C, Dengue Fever, West Nile Virus and Chagas disease) and an uninfected cohort with 122,926 peptide sequences on an array. These sequences were selected quasi-randomly to represent an even but sparse sample of the entire possible combinatorial sequence space (~1012). This very sparse sampling of combinatorial sequence space was sufficient to capture a statistically accurate representation of the humoral immune response across the entire space. Processing array data using the neural network not only captures the disease-specific sequence-binding information but aggregates binding information with respect to sequence, removing sequence-independent noise and improving the accuracy of array-based classification of disease compared with the raw binding data. Because the neural network model is trained on all samples simultaneously, a highly condensed representation of the differential information between samples resides in the output layer of the model, and the column vectors from this layer can be used to represent each sample for classification or unsupervised clustering applications.
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Affiliation(s)
- Robayet Chowdhury
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Laimonas Kelbauskas
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | - Phillip Stafford
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | - Chris Diehnelt
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | - Zhan-Gong Zhao
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | | | - Valerie Green
- Creative Testing Solutions, Tempe, Arizona, United States of America
| | - Neal W Woodbury
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
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13
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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14
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Hsueh HT, Chou RT, Rai U, Liyanage W, Kim YC, Appell MB, Pejavar J, Leo KT, Davison C, Kolodziejski P, Mozzer A, Kwon H, Sista M, Anders NM, Hemingway A, Rompicharla SVK, Edwards M, Pitha I, Hanes J, Cummings MP, Ensign LM. Machine learning-driven multifunctional peptide engineering for sustained ocular drug delivery. Nat Commun 2023; 14:2509. [PMID: 37130851 PMCID: PMC10154330 DOI: 10.1038/s41467-023-38056-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/12/2023] [Indexed: 05/04/2023] Open
Abstract
Sustained drug delivery strategies have many potential benefits for treating a range of diseases, particularly chronic diseases that require treatment for years. For many chronic ocular diseases, patient adherence to eye drop dosing regimens and the need for frequent intraocular injections are significant barriers to effective disease management. Here, we utilize peptide engineering to impart melanin binding properties to peptide-drug conjugates to act as a sustained-release depot in the eye. We develop a super learning-based methodology to engineer multifunctional peptides that efficiently enter cells, bind to melanin, and have low cytotoxicity. When the lead multifunctional peptide (HR97) is conjugated to brimonidine, an intraocular pressure lowering drug that is prescribed for three times per day topical dosing, intraocular pressure reduction is observed for up to 18 days after a single intracameral injection in rabbits. Further, the cumulative intraocular pressure lowering effect increases ~17-fold compared to free brimonidine injection. Engineered multifunctional peptide-drug conjugates are a promising approach for providing sustained therapeutic delivery in the eye and beyond.
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Affiliation(s)
- Henry T Hsueh
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Renee Ti Chou
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Usha Rai
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wathsala Liyanage
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yoo Chun Kim
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew B Appell
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Jahnavi Pejavar
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kirby T Leo
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Charlotte Davison
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Patricia Kolodziejski
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Ann Mozzer
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - HyeYoung Kwon
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Maanasa Sista
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Nicole M Anders
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA
| | - Avelina Hemingway
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA
| | - Sri Vishnu Kiran Rompicharla
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Malia Edwards
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ian Pitha
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Justin Hanes
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA
| | - Michael P Cummings
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
| | - Laura M Ensign
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA.
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15
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DeMarco AG, Hall MC. Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates. Molecules 2023; 28:3675. [PMID: 37175085 PMCID: PMC10180314 DOI: 10.3390/molecules28093675] [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: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.
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Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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16
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Aparna GM, Tetala KKR. Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays. Biomolecules 2023; 13:biom13040602. [PMID: 37189350 DOI: 10.3390/biom13040602] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018–2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.
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17
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Kamran DES, Hussain M, Mirza T. Investigating In Situ Expression of c-MYC and Candidate Ubiquitin-Specific Proteases in DLBCL and Assessment for Peptidyl Disruptor Molecule against c-MYC-USP37 Complex. Molecules 2023; 28:molecules28062441. [PMID: 36985413 PMCID: PMC10058055 DOI: 10.3390/molecules28062441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/30/2023] Open
Abstract
Diffuse Large B-Cell Lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma (NHL). Elevated expression of c-MYC in DLBCL is associated with poor prognosis of the disease. In different cancers, c-MYC has been found regulated by different ubiquitin-specific proteases (USPs), but to date, the role of USPs in c-MYC regulation has not been investigated in DLBCL. In this study, in situ co expression of c-MYC and three candidates USPs, USP28, USP36 and USP37, have been investigated in both the ABC and GCB subtypes of DLBCL. This shows that USP37 expression is positively correlated with the c-MYC expression in the ABC subtype of DLBCL. Structurally, both c-MYC and USP37 has shown large proportion of intrinsically disordered regions, minimizing their chances for full structure crystallization. Peptide array and docking simulations has shown that N-terminal region of c-MYC interacts directly with residues within and in proximity of catalytically active C19 domain of the USP37. Given the structural properties of the interaction sites in the c-MYC-USP37 complex, a peptidyl inhibitor has been designed. Molecular docking has shown that the peptide fits well in the targeted site of c-MYC, masking most of its residues involved in the binding with USP37. The findings could further be exploited to develop therapeutic interventions against the ABC subtype of DLBCL.
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Affiliation(s)
- Durr E Sameen Kamran
- Department of Pathology, Dow Ishrat-ul-Ebad Khan Institute of Oral Health Sciences, Dow University of Health Sciences, Karachi 75330, Pakistan
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi 75330, Pakistan
| | - Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi 75330, Pakistan
| | - Talat Mirza
- Department of Research, Ziauddin University, Karachi 75000, Pakistan
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18
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Holt BA, Lim HS, Sivakumar A, Phuengkham H, Su M, Tuttle M, Xu Y, Liakakos H, Qiu P, Kwong GA. Embracing enzyme promiscuity with activity-based compressed biosensing. CELL REPORTS METHODS 2023; 3:100372. [PMID: 36814844 PMCID: PMC9939361 DOI: 10.1016/j.crmeth.2022.100372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 10/11/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022]
Abstract
The development of protease-activatable drugs and diagnostics requires identifying substrates specific to individual proteases. However, this process becomes increasingly difficult as the number of target proteases increases because most substrates are promiscuously cleaved by multiple proteases. We introduce a method-substrate libraries for compressed sensing of enzymes (SLICE)-for selecting libraries of promiscuous substrates that classify protease mixtures (1) without deconvolution of compressed signals and (2) without highly specific substrates. SLICE ranks substrate libraries using a compression score (C), which quantifies substrate orthogonality and protease coverage. This metric is predictive of classification accuracy across 140 in silico (Pearson r = 0.71) and 55 in vitro libraries (r = 0.55). Using SLICE, we select a two-substrate library to classify 28 samples containing 11 enzymes in plasma (area under the receiver operating characteristic curve [AUROC] = 0.93). We envision that SLICE will enable the selection of libraries that capture information from hundreds of enzymes using fewer substrates for applications like activity-based sensors for imaging and diagnostics.
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Affiliation(s)
- Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hong Seo Lim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Anirudh Sivakumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hathaichanok Phuengkham
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Melanie Su
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - McKenzie Tuttle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Yilin Xu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Haley Liakakos
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Gabriel A. Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
- Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA 30332, USA
- Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA 30332, USA
- Integrated Cancer Research Center, Georgia Tech, Atlanta, GA 30332, USA
- Georgia ImmunoEngineering Consortium, Georgia Tech and Emory University, Atlanta, GA 30332, USA
- Emory School of Medicine, Atlanta, GA 30332, USA
- Emory Winship Cancer Institute, Atlanta, GA 30322, USA
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19
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Wang Z, Jian M, Li X. Profiling of Multiple Matrix Metalloproteinases Activities in the Progression of Osteosarcoma by Peptide Microarray-Based Fluorescence Assay on Polymer Brush-Coated Zinc Oxide Nanorod Substrate. Methods Mol Biol 2023; 2578:161-175. [PMID: 36152286 DOI: 10.1007/978-1-0716-2732-7_11] [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] [Indexed: 06/16/2023]
Abstract
Peptide microarray provides the ability to miniaturize, parallelize, and automate high-throughput screening substrate specificities of enzymes, profiling of multiple enzyme activities, discovery of disease biomarkers, and development of drugs. Matrix metalloproteinases (MMPs) are demonstrated as important biomarkers of tumor invasion and metastasis. Herein, a peptide microarray-based fluorescence assay is proposed to profile multiple MMPs (MMP-1, MMP-2, MMP-3, MMP-7, MMP-9, and MMP-13) activities in the culture medium of four human osteosarcoma (OS) cells and in the progression of OS by using the mouse-bearing xenograft OSs including U-2OS and Saos-2 human. This method has excellent selectivity and sensitivity, which enables to detect the activities of cellular secreted MMP-1, MMP-2, MMP-3, MMP-7, MMP-9, and MMP-13 with limit of detection downs to 10 pM, 30 pM, 113 pM, 13 pM, 93 pM, and 12 pM, respectively. Furthermore, it is demonstrated that the activity pattern of MMPs is serum closely relevant to the disease progression and type of tumor.
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Affiliation(s)
- Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, China.
| | - Minghong Jian
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaotong Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, China
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20
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Hoekstra M, Ridgeway NH, Biggar KK. Characterization of KDM5 lysine demethylase family substrate preference and identification of novel substrates. J Biochem 2022; 173:31-42. [PMID: 36205465 DOI: 10.1093/jb/mvac081] [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: 06/17/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 12/29/2022] Open
Abstract
The KDM5/JARID1 sub-family are 2-oxoglutarate and Fe(II)-dependent lysine-specific histone demethylases that are characterized by their Jumonji catalytic domains. The KDM5 family is known to remove tri-/di-methyl modifications from lysine-4 of histone H3 (i.e. H3-K4me2/3), a mark associated with active gene expression. As a result, studies to date have revolved around the influence of KDM5 on disease through their ability to regulate H3-K4me2/3. Recent evidence demonstrates that KDM5 may influence disease beyond H3-K4 demethylation, making it critical to further investigate KDM5-mediated demethylation of non-histone proteins. To help identify potential non-histone substrates for the KDM5 family, we developed a library of 180 permutated peptide substrates, with sequences that are systematically altered from the wild-type H3-K4me3 substrate. From this library, we characterized recombinant KDM5A/B/C/D substrate preference and developed recognition motifs for each KDM5 demethylase. The recognition motifs developed were used to predict potential substrates for KDM5A/B/C/D and profiled to generate a list of high-ranking and medium/low-ranking substrates for further in vitro validation. Through this approach, we identified 66 high-ranking substrates in which KDM5 demethylases displayed significant in vitro activity towards.
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Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Nashira H Ridgeway
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
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21
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Hotop SK, Reimering S, Shekhar A, Asgari E, Beutling U, Dahlke C, Fathi A, Khan F, Lütgehetmann M, Ballmann R, Gerstner A, Tegge W, Cicin-Sain L, Bilitewski U, McHardy AC, Brönstrup M. Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2. Emerg Microbes Infect 2022; 11:1037-1048. [PMID: 35320064 PMCID: PMC9009950 DOI: 10.1080/22221751.2022.2057874] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The coronavirus SARS-CoV-2 is the causative agent for the disease COVID-19. To capture the IgA, IgG, and IgM antibody response of patients infected with SARS-CoV-2 at individual epitope resolution, we constructed planar microarrays of 648 overlapping peptides that cover the four major structural proteins S(pike), N(ucleocapsid), M(embrane), and E(nvelope). The arrays were incubated with sera of 67 SARS-CoV-2 positive and 22 negative control samples. Specific responses to SARS-CoV-2 were detectable, and nine peptides were associated with a more severe course of the disease. A random forest model disclosed that antibody binding to 21 peptides, mostly localized in the S protein, was associated with higher neutralization values in cellular anti-SARS-CoV-2 assays. For antibodies addressing the N-terminus of M, or peptides close to the fusion region of S, protective effects were proven by antibody depletion and neutralization assays. The study pinpoints unusual viral binding epitopes that might be suited as vaccine candidates.
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Affiliation(s)
| | - Susanne Reimering
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Aditya Shekhar
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ehsaneddin Asgari
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany
| | - Ulrike Beutling
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christine Dahlke
- University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research, Germany
| | - Anahita Fathi
- University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research, Germany
| | - Fawad Khan
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marc Lütgehetmann
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research, Germany.,Center for Diagnostics, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie du Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Andreas Gerstner
- Klinikum Braunschweig, Hals-, Nasen-, Ohrenklinik, Braunschweig, Germany
| | - Werner Tegge
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luka Cicin-Sain
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany
| | | | - Alice C McHardy
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,Partner Site Hannover-Braunschweig, German Centre for Infection Research (DZIF), Germany.,Biomolecular Drug Research Center (BMWZ), Hannover, Germany
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22
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Deo S, Turton KL, Kainth T, Kumar A, Wieden HJ. Strategies for improving antimicrobial peptide production. Biotechnol Adv 2022; 59:107968. [PMID: 35489657 DOI: 10.1016/j.biotechadv.2022.107968] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 01/10/2023]
Abstract
Antimicrobial peptides (AMPs) found in a wide range of animal, insect, and plant species are host defense peptides forming an integral part of their innate immunity. Although the exact mode of action of some AMPs is yet to be deciphered, many exhibit membrane lytic activity or interact with intracellular targets. The ever-growing threat of antibiotic resistance has brought attention to research on AMPs to enhance their clinical use as a therapeutic alternative. AMPs have several advantages over antibiotics such as broad range of antimicrobial activities including anti-fungal, anti-viral and anti-bacterial, and have not reported to contribute to resistance development. Despite the numerous studies to develop efficient production methods for AMPs, limitations including low yield, degradation, and loss of activity persists in many recombinant approaches. In this review, we outline available approaches for AMP production and various expression systems used to achieve higher yield and quality. In addition, recent advances in recombinant strategies, suitable fusion protein partners, and other molecular engineering strategies for improved AMP production are surveyed.
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Affiliation(s)
- Soumya Deo
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kristi L Turton
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W., Lethbridge, AB T1K 3M4, Canada
| | - Tajinder Kainth
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayush Kumar
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hans-Joachim Wieden
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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23
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Huang CF, Gottardi CJ, Mrksich M. Tyrosine phosphatase activity is restricted by basic charge substituting mutation of substrates. Sci Rep 2022; 12:15095. [PMID: 36064958 PMCID: PMC9445012 DOI: 10.1038/s41598-022-19133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Phosphorylation controls important cellular signals and its dysregulation leads to disease. While most phospho-regulation studies are focused on kinases, phosphatases are comparatively overlooked. Combining peptide arrays with SAMDI mass spectrometry, we show that tyrosine phosphatase activity is restricted by basic amino acids adjacent to phosphotyrosines. We validate this model using two β-catenin mutants associated with cancer (T653R/K) and a mouse model for intellectual disability (T653K). These mutants introduce a basic residue next to Y654, an established phosphorylation site where modification shifts β-catenin from cell-cell adhesions and towards its essential nuclear role as Wnt-signaling effector. We show that T653-basic mutant β-catenins are less efficiently dephosphorylated by phosphatases, leading to sustained Y654 phosphorylation and elevated Wnt signals, similar to those observed for Y654E phospho-mimic mutant mice. This model rationalizes how basic mutations proximal to phosphotyrosines can restrict counter-regulation by phosphatases, providing new mechanismistic and treatment insights for 6000+ potentially relevant cancer mutations.
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Affiliation(s)
- Che-Fan Huang
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Cara J Gottardi
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA.
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Department of Cell & Developmental Biology, Northwestern University, Chicago, IL, 60611, USA.
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24
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Radwan O, Brothers MC, Coyle V, Chapleau ME, Chapleau RR, Kim SS, Ruiz ON. Electrochemical biosensor for rapid detection of fungal contamination in fuel systems. Biosens Bioelectron 2022; 211:114374. [DOI: 10.1016/j.bios.2022.114374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
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25
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Planar Junctionless Field-Effect Transistor for Detecting Biomolecular Interactions. SENSORS 2022; 22:s22155783. [PMID: 35957340 PMCID: PMC9371156 DOI: 10.3390/s22155783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 02/01/2023]
Abstract
Label-free field-effect transistor-based immunosensors are promising candidates for proteomics and peptidomics-based diagnostics and therapeutics due to their high multiplexing capability, fast response time, and ability to increase the sensor sensitivity due to the short length of peptides. In this work, planar junctionless field-effect transistor sensors (FETs) were fabricated and characterized for pH sensing. The device with SiO2 gate oxide has shown voltage sensitivity of 41.8 ± 1.4, 39.9 ± 1.4, 39.0 ± 1.1, and 37.6 ± 1.0 mV/pH for constant drain currents of 5, 10, 20, and 50 nA, respectively, with a drain to source voltage of 0.05 V. The drift analysis shows a stability over time of −18 nA/h (pH 7.75), −3.5 nA/h (pH 6.84), −0.5 nA/h (pH 4.91), 0.5 nA/h (pH 3.43), corresponding to a pH drift of −0.45, −0.09, −0.01, and 0.01 per h. Theoretical modeling and simulation resulted in a mean value of the surface states of 3.8 × 1015/cm2 with a standard deviation of 3.6 × 1015/cm2. We have experimentally verified the number of surface sites due to APTES, peptide, and protein immobilization, which is in line with the theoretical calculations for FETs to be used for detecting peptide-protein interactions for future applications.
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26
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Xie T, Brady A, Velarde C, Vaccarello DN, Callahan NW, Marino JP, Orski SV. Selective C-Terminal Conjugation of Protease-Derived Native Peptides for Proteomic Measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9119-9128. [PMID: 35856835 DOI: 10.1021/acs.langmuir.2c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bottom-up proteomic experiments often require selective conjugation or labeling of the N- and/or C-termini of peptides resulting from proteolytic digestion. For example, techniques based on surface fluorescence imaging are emerging as a promising route to high-throughput protein sequencing but require the generation of peptide surface arrays immobilized through single C-terminal point attachment while leaving the N-terminus free. While several robust approaches are available for selective N-terminal conjugation, it has proven to be much more challenging to implement methods for selective labeling or conjugation of the C-termini that can discriminate between the C-terminal carboxyl group and other carboxyl groups on aspartate and glutamate residues. Further, many approaches based on conjugation through amide bond formation require protection of the N-terminus to avoid unwanted cross-linking reactions. To overcome these challenges, herein, we describe a new strategy for single-point selective immobilization of peptides generated by protease digestion via the C-terminus. The method involves immobilization of peptides via lysine amino acids which are found naturally at the C-terminal end of cleaved peptides from digestions of certain serine endoproteinases, like LysC. This lysine and the N-terminus, the sole two primary amines in the peptide fragments, are chemically reacted with a custom phenyl isothiocyanate (EPITC) that contains an alkyne handle. Subsequent exposure of the double-modified peptides to acid selectively cleaves the N-terminal amino acid, while the modified C-terminus lysine remains unchanged. The alkyne-modified peptides with free N-termini can then be immobilized on an azide surface through standard click chemistry. Using this general approach, surface functionalization is demonstrated using a combination of X-ray photoelectron spectroscopy (XPS), ellipsometry, and atomic force microscopy (AFM).
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Affiliation(s)
- Tian Xie
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
- Georgetown University, Washington, District of Columbia, 20057, United States
| | - Alexandria Brady
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - Cecilia Velarde
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - David N Vaccarello
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - Nicholas W Callahan
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - John P Marino
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - Sara V Orski
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
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27
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Gutman I, Gutman R, Sidney J, Chihab L, Mishto M, Liepe J, Chiem A, Greenbaum J, Yan Z, Sette A, Koşaloğlu-Yalçın Z, Peters B. Predicting the Success of Fmoc-Based Peptide Synthesis. ACS OMEGA 2022; 7:23771-23781. [PMID: 35847273 PMCID: PMC9280948 DOI: 10.1021/acsomega.2c02425] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Synthetic peptides are commonly used in biomedical science for many applications in basic and translational research. While peptide synthesis is generally easy and reliable, the chemical nature of some amino acids as well as the many steps and chemical compounds involved can render the synthesis of some peptide sequences difficult. Identification of these problematic sequences and mitigation of issues they may present can be important for the reliable use of peptide reagents in several contexts. Here, we assembled a large dataset of peptides that were synthesized using standard Fmoc chemistry and whose identity was validated using mass spectrometry. We analyzed the mass spectra to identify errors in peptide syntheses and sought to develop a computational tool to predict the likelihood that any given peptide sequence would be synthesized accurately. Our model, named Peptide Synthesis Score (PepSySco), is able to predict the likelihood that a peptide will be successfully synthesized based on its amino acid sequence.
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Affiliation(s)
- Ilanit Gutman
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Ron Gutman
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - John Sidney
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Leila Chihab
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Michele Mishto
- Centre
for Inflammation Biology and Cancer Immunology (CIBCI) & Peter
Gorer Department of Immunobiology, King’s
College London, London SE1 1UL, U.K.
- Francis
Crick Institute, London NW1 1AT, U.K.
| | - Juliane Liepe
- Max-Planck-Institute
for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Anthony Chiem
- TC
Peptide Lab, San Diego, California 92121-4708, United States
| | - Jason Greenbaum
- Bioinformatics
Core Facility, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Zhen Yan
- Bioinformatics
Core Facility, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Alessandro Sette
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
- Department
of Medicine, University of California San
Diego, La Jolla, California 92037-1387, United States
| | - Zeynep Koşaloğlu-Yalçın
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
| | - Bjoern Peters
- Center
for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California 92037-1387, United States
- Department
of Medicine, University of California San
Diego, La Jolla, California 92037-1387, United States
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28
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Gervais T, Temiz Y, Aubé L, Delamarche E. Large-Scale Dried Reagent Reconstitution and Diffusion Control Using Microfluidic Self-Coalescence Modules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105939. [PMID: 35307960 DOI: 10.1002/smll.202105939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/13/2022] [Indexed: 06/14/2023]
Abstract
The positioning and manipulation of large numbers of reagents in small aliquots are paramount to many fields in chemistry and the life sciences, such as combinatorial screening, enzyme activity assays, and point-of-care testing. Here, a capillary microfluidic architecture based on self-coalescence modules capable of storing thousands of dried reagent spots per square centimeter is reported, which can all be reconstituted independently without dispersion using a single pipetting step and ≤5 μL of a solution. A simple diffusion-based mathematical model is also provided to guide the spotting of reagents in this microfluidic architecture at the experimental design stage to enable either compartmentalization, mixing, or the generation of complex multi-reagent chemical patterns. Results demonstrate the formation of chemical patterns with high accuracy and versatility, and simple methods for integrating reagents and imaging the resulting chemical patterns.
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Affiliation(s)
- Thomas Gervais
- IBM Research Europe - Zurich, Rueschlikon, 8803, Switzerland
- Polytechnique Montréal, Montreal, H3C 3A7, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, H2X0A9, Canada
| | - Yuksel Temiz
- IBM Research Europe - Zurich, Rueschlikon, 8803, Switzerland
| | - Lucas Aubé
- Polytechnique Montréal, Montreal, H3C 3A7, Canada
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29
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Düzgüneş N, Fernandez-Fuentes N, Konopka K. Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design. Pathogens 2021; 10:1599. [PMID: 34959554 PMCID: PMC8709411 DOI: 10.3390/pathogens10121599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Fusion of lipid-enveloped viruses with the cellular plasma membrane or the endosome membrane is mediated by viral envelope proteins that undergo large conformational changes following binding to receptors. The HIV-1 fusion protein gp41 undergoes a transition into a "six-helix bundle" after binding of the surface protein gp120 to the CD4 receptor and a co-receptor. Synthetic peptides that mimic part of this structure interfere with the formation of the helix structure and inhibit membrane fusion. This approach also works with the S spike protein of SARS-CoV-2. Here we review the peptide inhibitors of membrane fusion involved in infection by influenza virus, HIV-1, MERS and SARS coronaviruses, hepatitis viruses, paramyxoviruses, flaviviruses, herpesviruses and filoviruses. We also describe recent computational methods used for the identification of peptide sequences that can interact strongly with protein interfaces, with special emphasis on SARS-CoV-2, using the PePI-Covid19 database.
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Affiliation(s)
- Nejat Düzgüneş
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, UK;
| | - Krystyna Konopka
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
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30
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Singh PP, Gupta V, Prakash B. Recent advancement in functional properties and toxicity assessment of plant-derived bioactive peptides using bioinformatic approaches. Crit Rev Food Sci Nutr 2021:1-19. [PMID: 34783283 DOI: 10.1080/10408398.2021.2002807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nowadays, biopeptides have gained considerable interest by the food industries, given their potent biological effect on health. BPs, when released from the sequence of their precursors by proteolytic enzymes, improved the various physiological functions of the body. Diabetic and hypertension are the two most common life-threatening diseases linked to dietary patterns. Angiotensin-converting enzyme (ACE) (hypertension-responsible glycoprotein) and dipeptidyl peptidase IV (DPP-IV) (proline-specific dimeric aminopeptidase) have been widely used as molecular target sites of action of bioactive compounds possessing antihypertensive and antidiabetic effects. Although, BPs possess considerable biological properties (antioxidant, antimicrobial, antiviral, immunomodulating, antiproliferative, antidiabetic, and antihypertensive effects), most of them possess inherent lacunae such as toxicity, allergenicity, bitterness, and lack of detailed mechanistic investigation, limiting their commercial application. The present review provides an overview on various sources of bioactive peptides, conventional and modern methods of extraction, and challenges that need to be addressed before its commercial application. In addition, bioinformatics' role in exploring the functional properties of biopeptides (ACE and DPP-IV inhibitory effects) toxicity, the target site of action with special reference to plant-based peptides, and recent burgeoning proficiencies in biopeptide research have been discussed.
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Affiliation(s)
- Prem Pratap Singh
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Vishal Gupta
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Bhanu Prakash
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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31
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Hoekstra M, Biggar KK. Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference. Anal Biochem 2021; 633:114429. [PMID: 34678252 DOI: 10.1016/j.ab.2021.114429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/30/2021] [Accepted: 10/17/2021] [Indexed: 01/25/2023]
Abstract
A major regulatory influence over gene expression is the dynamic post translational methylation of histone proteins, with major implications from both lysine methylation and demethylation. The KDM5/JARID1 sub-family of Fe(II)/2-oxoglutarate dependent lysine-specific demethylases is, in part, responsible for the removal of tri/dimethyl modifications from lysine 4 of histone H3 (i.e., H3K4me3/2), a mark associated with active gene expression. Although the relevance of KDM5 activity to disease progression has been primarily established through its ability to regulate gene expression via histone methylation, there is evidence that these enzymes may also target non-histone proteins. To aid in the identification of new non-histone substrates, we examined KDM5A in vitro activity towards a library of 180 permutated peptide substrates derived from the H3K4me3 sequence. From this data, a recognition motif was identified and used to predict candidate KDM5A substrates from the methyllysine proteome. High-ranking candidate substrates were then validated for in vitro KDM5A activity using representative trimethylated peptides. Our approach correctly identified activity towards 90% of high-ranked substrates. Here, we have demonstrated the usefulness of our method in identifying candidate substrates that is applicable to any Fe(II)- and 2-oxoglutarate dependent demethylase.
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Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
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32
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Hu J, Liu F, Chen Y, Shangguan G, Ju H. Mass Spectrometric Biosensing: A Powerful Approach for Multiplexed Analysis of Clinical Biomolecules. ACS Sens 2021; 6:3517-3535. [PMID: 34529414 DOI: 10.1021/acssensors.1c01394] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid and sensitive detection of clinical biomolecules in a multiplexed fashion is of great importance for accurate diagnosis of diseases. Mass spectrometric (MS) approaches are exceptionally suitable for clinical analysis due to its high throughput, high sensitivity, and reliable qualitative and quantitative capabilities. To break through the bottleneck of MS technique for detecting high-molecular-weight substances with low ionization efficiency, the concept of mass spectrometric biosensing has been put forward by adopting mass spectrometric chips to recognize the targets and mass spectrometry to detect the signals switched by the recognition. In this review, the principle of mass spectrometric sensing, the construction of different mass tags used for biosensing, and the typical combination mode of mass spectrometric imaging (MSI) technique are summarized. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to promote the advancements and practical applications of mass spectrometric biosensing.
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Affiliation(s)
- Junjie Hu
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Guoqiang Shangguan
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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33
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Parker Cates Z, Facciuolo A, Hogan D, Griebel PJ, Napper S, Kusalik AJ. EPIphany—A Platform for Analysis and Visualization of Peptide Immunoarray Data. FRONTIERS IN BIOINFORMATICS 2021; 1:694324. [PMID: 36303765 PMCID: PMC9581008 DOI: 10.3389/fbinf.2021.694324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies are critical effector molecules of the humoral immune system. Upon infection or vaccination, populations of antibodies are generated which bind to various regions of the invading pathogen or exogenous agent. Defining the reactivity and breadth of this antibody response provides an understanding of the antigenic determinants and enables the rational development and assessment of vaccine candidates. High-resolution analysis of these populations typically requires advanced techniques such as B cell receptor repertoire sequencing, mass spectrometry of isolated immunoglobulins, or phage display libraries that are dependent upon equipment and expertise which are prohibitive for many labs. High-density peptide microarrays representing diverse populations of putative linear epitopes (immunoarrays) are an effective alternative for high-throughput examination of antibody reactivity and diversity. While a promising technology, widespread adoption of immunoarrays has been limited by the need for, and relative absence of, user-friendly tools for consideration and visualization of the emerging data. To address this limitation, we developed EPIphany, a software platform with a simple web-based user interface, aimed at biological users, that provides access to important analysis parameters, data normalization options, and a variety of unique data visualization options. This platform provides researchers the greatest opportunity to extract biologically meaningful information from the immunoarray data, thereby facilitating the discovery and development of novel immuno-therapeutics.
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Affiliation(s)
- Zoe Parker Cates
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Philip J. Griebel
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Scott Napper,
| | - Anthony J. Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
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34
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Ryzhov IM, Tuzikov AB, Nizovtsev AV, Baidakova LK, Galanina OE, Shilova NV, Ziganshina MM, Dolgushina NV, Bayramova GR, Sukhikh GT, Williams EC, Nagappan R, Henry SM, Bovin NV. SARS-CoV-2 Peptide Bioconjugates Designed for Antibody Diagnostics. Bioconjug Chem 2021; 32:1606-1616. [PMID: 34181851 DOI: 10.1021/acs.bioconjchem.1c00186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the near future, the increase in the number of required tests for COVID-19 antibodies is expected to be many hundreds of millions. Obviously, this will be done using a variety of analytical methods and using different antigens, including peptides. In this work, we compare three method variations for detecting specific immunoglobulins directed against peptides of approximately 15-aa of the SARS-CoV-2 spike protein. These linear peptide epitopes were selected using antigenicity algorithms, and were synthesized with an additional terminal cysteine residue for their bioconjugation. In two of the methods, constructs were prepared where the peptide (F, function) is attached to a negatively charged hydrophilic spacer (S) linked to a dioleoylphosphatidyl ethanolamine residue (L, lipid) to create a function-spacer-lipid construct (FSL). These FSLs were easily and controllably incorporated into erythrocytes for serologic testing or in a lipid bilayer deposited on a polystyrene microplate for use in an enzyme immunoassays (EIA). The third method, also an EIA, used polyacrylamide conjugated peptides (peptide-PAA) prepared by controlled condensation of the cysteine residue of the peptide with the maleimide-derived PAA polymer which were immobilized on polystyrene microplates by physisorption of the polymer. In this work, we describe the synthesis of the PAA and FSL peptide bioconjugates, design of test systems, and comparison of the bioassays results, and discuss potential reasons for higher performance of the FSL conjugates, particularly in the erythrocyte-based serologic assay.
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Affiliation(s)
- Ivan M Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Alexander B Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Alexey V Nizovtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Ludmila K Baidakova
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
| | - Oxana E Galanina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Nadezhda V Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation.,National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Marina M Ziganshina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Nataliya V Dolgushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Guldana R Bayramova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Gennady T Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Eleanor C Williams
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
| | - Radhika Nagappan
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
| | - Stephen M Henry
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
| | - Nicolai V Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation.,Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
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35
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Pepscan Approach for the Identification of Protein-Protein Interfaces: Lessons from Experiment. Biomolecules 2021; 11:biom11060772. [PMID: 34063976 PMCID: PMC8224071 DOI: 10.3390/biom11060772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
PEPscan is an old approach that has recently gained renewed interest for the identification of interfering peptides (IPs), i.e., peptides able to interfere with protein-protein interactions (PPIs). Its principle is to slice a protein sequence as a series of short overlapping peptides that are synthesized on a peptide array and tested for their ability to bind a partner, with positive spots corresponding to candidate IPs. PEPscan has been applied with a rather large success in various contexts, but the structural determinants underlying this success remain obscure. Here, we analyze the results of 14 PEPscan experiments, and confront the in vitro results with the available structural information. PEPscan identifies candidate IPs in limited numbers that in all cases correspond to solvent-accessible regions of the structures, their location at the protein-protein interface remaining to be further demonstrated. A strong point of PEPscan seems to be its ability to identify specific IPs. IPs identified from the same protein differ depending on the target PPI, and correspond to patches not frequently involved in the interactions seen in the 3D structures available. Overall, PEPscan seems to provide a cheap and rapid manner to identify candidate IPs, that also comes with room for improvement.
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36
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Lukinović V, Biggar KK. Deconvoluting complex protein interaction networks through reductionist strategies in peptide biochemistry: Modern approaches and research questions. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110616. [PMID: 34000427 DOI: 10.1016/j.cbpb.2021.110616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
Following the decoding of the first human genome, researchers have vastly improved their understanding of cell biology and its regulation. As a result, it has become clear that it is not merely genetic information, but the aberrant changes in the functionality and connectivity of its encoded proteins that drive cell response to periods of stress and external cues. Therefore, proper utilization of refined methods that help to describe protein signalling or regulatory networks (i.e., functional connectivity), can help us understand how change in the signalling landscape effects the cell. However, given the vast complexity in 'how and when' proteins communicate or interact with each other, it is extremely difficult to define, characterize, and understand these interaction networks in a tangible manner. Herein lies the challenge of tackling the functional proteome; its regulation is encoded in multiple layers of interaction, chemical modification and cell compartmentalization. To address and refine simple research questions, modern reductionist strategies in protein biochemistry have successfully used peptide-based experiments; their summation helping to simplify the overall complexity of these protein interaction networks. In this way, peptides are powerful tools used in fundamental research that can be readily applied to comparative biochemical research. Understanding and defining how proteins interact is one of the key aspects towards understanding how the proteome functions. To date, reductionist peptide-based research has helped to address a wide range of proteome-related research questions, including the prediction of enzymes substrates, identification of posttranslational modifications, and the annotation of protein interaction partners. Peptide arrays have been used to identify the binding specificity of reader domains, which are able to recognise the posttranslational modifications; forming dynamic protein interactions that are dependent on modification state. Finally, representing one of the fastest growing classes of inhibitor molecules, peptides are now begin explored as "disruptors" of protein-protein interactions or enzyme activity. Collectively, this review will discuss the use of peptides, peptide arrays, peptide-oriented computational biochemistry as modern reductionist strategies in deconvoluting the functional proteome.
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Affiliation(s)
- Valentina Lukinović
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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37
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Li S, Song G, Bai Y, Song N, Zhao J, Liu J, Hu C. Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases. Front Immunol 2021; 12:645632. [PMID: 34012435 PMCID: PMC8126629 DOI: 10.3389/fimmu.2021.645632] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/13/2021] [Indexed: 01/18/2023] Open
Abstract
Dysregulated autoantibodies and cytokines were deemed to provide important cues for potential illnesses, such as various carcinomas and autoimmune diseases. Increasing biotechnological approaches have been applied to screen and identify the specific alterations of these biomolecules as distinctive biomarkers in diseases, especially autoimmune diseases. As a versatile and robust platform, protein microarray technology allows researchers to easily profile dysregulated autoantibodies and cytokines associated with autoimmune diseases using various biological specimens, mainly serum samples. Here, we summarize the applications of protein microarrays in biomarker discovery for autoimmune diseases. In addition, the key issues in the process of using this approach are presented for improving future studies.
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Affiliation(s)
- Siting Li
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yina Bai
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Ning Song
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jian Liu
- Department of Rheumatology, Aerospace Center Hospital, Aerospace, Clinical Medical College, Peking University, Beijing, China
| | - Chaojun Hu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
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38
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Heidepriem J, Dahlke C, Kobbe R, Santer R, Koch T, Fathi A, Seco BMS, Ly ML, Schmiedel S, Schwinge D, Serna S, Sellrie K, Reichardt NC, Seeberger PH, Addo MM, Loeffler FF. Longitudinal Development of Antibody Responses in COVID-19 Patients of Different Severity with ELISA, Peptide, and Glycan Arrays: An Immunological Case Series. Pathogens 2021; 10:438. [PMID: 33917609 PMCID: PMC8067489 DOI: 10.3390/pathogens10040438] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/08/2023] Open
Abstract
The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). A better understanding of its immunogenicity can be important for the development of improved diagnostics, therapeutics, and vaccines. Here, we report the longitudinal analysis of three COVID-19 patients with moderate (#1) and mild disease (#2 and #3). Antibody serum responses were analyzed using spike glycoprotein enzyme linked immunosorbent assay (ELISA), full-proteome peptide, and glycan microarrays. ELISA immunoglobulin A, G, and M (IgA, IgG, and IgM) signals increased over time for individuals #1 and #2, whereas #3 only showed no clear positive IgG and IgM result. In contrast, peptide microarrays showed increasing IgA/G signal intensity and epitope spread only in the moderate patient #1 over time, whereas early but transient IgA and stable IgG responses were observed in the two mild cases #2 and #3. Glycan arrays showed an interaction of antibodies to fragments of high-mannose and core N-glycans, present on the viral shield. In contrast to protein ELISA, microarrays allow for a deeper understanding of IgA, IgG, and IgM antibody responses to specific epitopes of the whole proteome and glycans of SARS-CoV-2 in parallel. In the future, this may help to better understand and to monitor vaccination programs and monoclonal antibodies as therapeutics.
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Affiliation(s)
- Jasmin Heidepriem
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany; (J.H.); (B.M.S.S.); (K.S.); (P.H.S.)
| | - Christine Dahlke
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (R.K.); (T.K.); (A.F.); (M.L.L.); (S.S.)
- Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, 20251 Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, 20251 Hamburg, Germany
| | - Robin Kobbe
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (R.K.); (T.K.); (A.F.); (M.L.L.); (S.S.)
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany;
| | - Till Koch
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (R.K.); (T.K.); (A.F.); (M.L.L.); (S.S.)
- Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, 20251 Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, 20251 Hamburg, Germany
| | - Anahita Fathi
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (R.K.); (T.K.); (A.F.); (M.L.L.); (S.S.)
- Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, 20251 Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, 20251 Hamburg, Germany
| | - Bruna M. S. Seco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany; (J.H.); (B.M.S.S.); (K.S.); (P.H.S.)
| | - My L. Ly
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (R.K.); (T.K.); (A.F.); (M.L.L.); (S.S.)
- Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, 20251 Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, 20251 Hamburg, Germany
| | - Stefan Schmiedel
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (R.K.); (T.K.); (A.F.); (M.L.L.); (S.S.)
| | - Dorothee Schwinge
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany;
| | - Sonia Serna
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain; (S.S.); (N.-C.R.)
| | - Katrin Sellrie
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany; (J.H.); (B.M.S.S.); (K.S.); (P.H.S.)
| | - Niels-Christian Reichardt
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain; (S.S.); (N.-C.R.)
- CIBER-BBN, Paseo Miramón 182, 20014 San Sebastián, Spain
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany; (J.H.); (B.M.S.S.); (K.S.); (P.H.S.)
| | - Marylyn M. Addo
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (R.K.); (T.K.); (A.F.); (M.L.L.); (S.S.)
- Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, 20251 Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, 20251 Hamburg, Germany
| | - Felix F. Loeffler
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany; (J.H.); (B.M.S.S.); (K.S.); (P.H.S.)
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39
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Chiodi E, Marn AM, Geib MT, Ünlü MS. The Role of Surface Chemistry in the Efficacy of Protein and DNA Microarrays for Label-Free Detection: An Overview. Polymers (Basel) 2021; 13:1026. [PMID: 33810267 PMCID: PMC8036480 DOI: 10.3390/polym13071026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The importance of microarrays in diagnostics and medicine has drastically increased in the last few years. Nevertheless, the efficiency of a microarray-based assay intrinsically depends on the density and functionality of the biorecognition elements immobilized onto each sensor spot. Recently, researchers have put effort into developing new functionalization strategies and technologies which provide efficient immobilization and stability of any sort of molecule. Here, we present an overview of the most widely used methods of surface functionalization of microarray substrates, as well as the most recent advances in the field, and compare their performance in terms of optimal immobilization of the bioreceptor molecules. We focus on label-free microarrays and, in particular, we aim to describe the impact of surface chemistry on two types of microarray-based sensors: microarrays for single particle imaging and for label-free measurements of binding kinetics. Both protein and DNA microarrays are taken into consideration, and the effect of different polymeric coatings on the molecules' functionalities is critically analyzed.
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Affiliation(s)
- Elisa Chiodi
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.T.G.); (M.S.Ü.)
| | - Allison M. Marn
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.T.G.); (M.S.Ü.)
| | - Matthew T. Geib
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.T.G.); (M.S.Ü.)
| | - M. Selim Ünlü
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (A.M.M.); (M.T.G.); (M.S.Ü.)
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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40
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Antonescu ON, Rasmussen A, Damm NAM, Heidemann DF, Popov R, Nesterov-Mueller A, Johansson KE, Winther JR. Substitutional landscape of a split fluorescent protein fragment using high-density peptide microarrays. PLoS One 2021; 16:e0241461. [PMID: 33534832 PMCID: PMC7857580 DOI: 10.1371/journal.pone.0241461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/21/2020] [Indexed: 11/23/2022] Open
Abstract
Split fluorescent proteins have wide applicability as biosensors for protein-protein interactions, genetically encoded tags for protein detection and localization, as well as fusion partners in super-resolution microscopy. We have here established and validated a novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) in high throughput and with rapid turnover. We have screened more than 12,000 variants of the beta-strand split fragment using high-density peptide microarrays for binding and functional complementation in Green Fluorescent Protein. We studied the effect of peptide length and the effect of different linkers to the solid support. We further mapped the effect of all possible amino acid substitutions on each position as well as in the context of some single and double amino acid substitutions. As all peptides were tested in 12 duplicates, the analysis rests on a firm statistical basis allowing for confirmation of the robustness and precision of the method. Based on experiments in solution, we conclude that under the given conditions, the signal intensity on the peptide microarray faithfully reflects the binding affinity between the split fragments. With this, we are able to identify a peptide with 9-fold higher affinity than the starting peptide.
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Affiliation(s)
- Oana N. Antonescu
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Andreas Rasmussen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Nicole A. M. Damm
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Ditte F. Heidemann
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Roman Popov
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Kristoffer E. Johansson
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
| | - Jakob R. Winther
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, University for Copenhagen, Copenhagen, Denmark
- * E-mail:
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41
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Nutrient transceptors physically interact with the yeast S6/protein kinase B homolog, Sch9, a TOR kinase target. Biochem J 2021; 478:357-375. [PMID: 33394033 PMCID: PMC7850899 DOI: 10.1042/bcj20200722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Multiple starvation-induced, high-affinity nutrient transporters in yeast function as receptors for activation of the protein kinase A (PKA) pathway upon re-addition of their substrate. We now show that these transceptors may play more extended roles in nutrient regulation. The Gap1 amino acid, Mep2 ammonium, Pho84 phosphate and Sul1 sulfate transceptors physically interact in vitro and in vivo with the PKA-related Sch9 protein kinase, the yeast homolog of mammalian S6 protein kinase and protein kinase B. Sch9 is a phosphorylation target of TOR and well known to affect nutrient-controlled cellular processes, such as growth rate. Mapping with peptide microarrays suggests specific interaction domains in Gap1 for Sch9 binding. Mutagenesis of the major domain affects the upstart of growth upon the addition of L-citrulline to nitrogen-starved cells to different extents but apparently does not affect in vitro binding. It also does not correlate with the drop in L-citrulline uptake capacity or transceptor activation of the PKA target trehalase by the Gap1 mutant forms. Our results reveal a nutrient transceptor-Sch9-TOR axis in which Sch9 accessibility for phosphorylation by TOR may be affected by nutrient transceptor-Sch9 interaction under conditions of nutrient starvation or other environmental challenges.
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42
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Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors. Int J Mol Sci 2021; 22:ijms22020812. [PMID: 33467468 PMCID: PMC7831021 DOI: 10.3390/ijms22020812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/17/2022] Open
Abstract
The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.
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43
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Anderson SE, Longbotham JE, O'Kane PT, Ugur FS, Fujimori DG, Mrksich M. Exploring the Ligand Preferences of the PHD1 Domain of Histone Demethylase KDM5A Reveals Tolerance for Modifications of the Q5 Residue of Histone 3. ACS Chem Biol 2021; 16:205-213. [PMID: 33314922 PMCID: PMC8168426 DOI: 10.1021/acschembio.0c00891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the ligand preferences of epigenetic reader domains enables identification of modification states of chromatin with which these domains associate and can yield insight into recruitment and catalysis of chromatin-acting complexes. However, thorough exploration of the ligand preferences of reader domains is hindered by the limitations of traditional protein-ligand binding assays. Here, we evaluate the binding preferences of the PHD1 domain of histone demethylase KDM5A using the protein interaction by SAMDI (PI-SAMDI) assay, which measures protein-ligand binding in a high-throughput and sensitive manner via binding-induced enhancement in the activity of a reporter enzyme, in combination with fluorescence polarization. The PI-SAMDI assay was validated by confirming its ability to accurately profile the relative binding affinity of a set of well-characterized histone 3 (H3) ligands of PHD1. The assay was then used to assess the affinity of PHD1 for 361 H3 mutant ligands, a select number of which were further characterized by fluorescence polarization. Together, these experiments revealed PHD1's tolerance for H3Q5 mutations, including an unexpected tolerance for aromatic residues in this position. Motivated by this finding, we further demonstrate a high-affinity interaction between PHD1 and recently identified Q5-serotonylated H3. This work yields interesting insights into permissible PHD1-H3 interactions and demonstrates the value of interfacing PI-SAMDI and fluorescence polarization in investigations of protein-ligand binding.
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Affiliation(s)
- Sarah E Anderson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Patrick T O'Kane
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Cell and Developmental Biology, Northwestern University, Evanston, Illinois 60208, United States
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44
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Moreno-Yruela C, Bæk M, Vrsanova AE, Schulte C, Maric HM, Olsen CA. Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases. Nat Commun 2021; 12:62. [PMID: 33397936 PMCID: PMC7782793 DOI: 10.1038/s41467-020-20250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone-reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Adela-Eugenie Vrsanova
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Institute of Applied Biosciences & Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Adenauerring 20a, D-76131, Karlsruhe, Germany.,Division of Proteomics of Stem Cells and Cancer, DKFZ German Cancer Research Center, Im Neuenhemier Feld 581, D-69120, Heidelberg, Germany
| | - Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany.
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.
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45
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Sugai H, Tomita S, Ishihara S, Yoshioka K, Kurita R. Microfluidic Sensing System with a Multichannel Surface Plasmon Resonance Chip: Damage-Free Characterization of Cells by Pattern Recognition. Anal Chem 2020; 92:14939-14946. [PMID: 33112611 DOI: 10.1021/acs.analchem.0c02220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of a versatile sensing strategy for the damage-free characterization of cultured cells is of great importance for both fundamental biological research and industrial applications. Here, we present a pattern-recognition-based cell-sensing approach using a multichannel surface plasmon resonance (SPR) chip. The chip, in which five cysteine derivatives with different structures are immobilized on Au films, is capable of generating five unique SPR sensorgrams for the cell-secreted molecules that are contained in cell culture media. An automatic statistical program was built to acquire kinetic parameters from the SPR sensorgrams and to select optimal parameters as "pattern information" for subsequent multivariate analysis. Our system rapidly (∼10 min) provides the complex information by merely depositing a small amount of cell culture media (∼25 μL) onto the chip, and the amount of information obtained is comparable to that furnished by a combination of conventional laborious biochemical assays. This noninvasive pattern-recognition-based cell-sensing approach could potentially be employed as a versatile tool for characterizing cells.
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Affiliation(s)
- Hiroka Sugai
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Sayaka Ishihara
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kyoko Yoshioka
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Ryoji Kurita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-41, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.,Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
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46
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Heiss K, Heidepriem J, Fischer N, Weber LK, Dahlke C, Jaenisch T, Loeffler FF. Rapid Response to Pandemic Threats: Immunogenic Epitope Detection of Pandemic Pathogens for Diagnostics and Vaccine Development Using Peptide Microarrays. J Proteome Res 2020; 19:4339-4354. [PMID: 32892628 PMCID: PMC7640972 DOI: 10.1021/acs.jproteome.0c00484] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/18/2022]
Abstract
Emergence and re-emergence of pathogens bearing the risk of becoming a pandemic threat are on the rise. Increased travel and trade, growing population density, changes in urbanization, and climate have a critical impact on infectious disease spread. Currently, the world is confronted with the emergence of a novel coronavirus SARS-CoV-2, responsible for yet more than 800 000 deaths globally. Outbreaks caused by viruses, such as SARS-CoV-2, HIV, Ebola, influenza, and Zika, have increased over the past decade, underlining the need for a rapid development of diagnostics and vaccines. Hence, the rational identification of biomarkers for diagnostic measures on the one hand, and antigenic targets for vaccine development on the other, are of utmost importance. Peptide microarrays can display large numbers of putative target proteins translated into overlapping linear (and cyclic) peptides for a multiplexed, high-throughput antibody analysis. This enabled for example the identification of discriminant/diagnostic epitopes in Zika or influenza and mapping epitope evolution in natural infections versus vaccinations. In this review, we highlight synthesis platforms that facilitate fast and flexible generation of high-density peptide microarrays. We further outline the multifaceted applications of these peptide array platforms for the development of serological tests and vaccines to quickly encounter pandemic threats.
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Affiliation(s)
- Kirsten Heiss
- PEPperPRINT
GmbH, Rischerstrasse
12, 69123 Heidelberg, Germany
| | - Jasmin Heidepriem
- Max
Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Nico Fischer
- Section
Clinical Tropical Medicine, Department of Infectious Diseases, Heidelberg University Hospital, INF 324, 69120 Heidelberg, Germany
| | - Laura K. Weber
- PEPperPRINT
GmbH, Rischerstrasse
12, 69123 Heidelberg, Germany
- Institute
of Microstructure Technology, Karlsruhe
Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christine Dahlke
- Division
of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Department
of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German
Center for Infection Research, Partner Site
Hamburg-Lübeck-Borstel-Riems, 38124 Braunschweig, Germany
| | - Thomas Jaenisch
- Heidelberg
Institute of Global Health (HIGH), Heidelberg
University Hospital, Im Neuenheimer Feld 130, 69120 Heidelberg, Germany
- Center
for Global Health, Colorado School of Public Health, University of Colorado, Aurora, Colorado 80045, United States
- Department
of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, Colorado 80045, United States
| | - Felix F. Loeffler
- Max
Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Muehlenberg 1, 14476 Potsdam, Germany
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47
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Xie Z, Gan T, Fang L, Zhou X. Recent progress in creating complex and multiplexed surface-grafted macromolecular architectures. SOFT MATTER 2020; 16:8736-8759. [PMID: 32969442 DOI: 10.1039/d0sm01043j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Surface-grafted macromolecules, including polymers, DNA, peptides, etc., are versatile modifications to tailor the interfacial functions in a wide range of fields. In this review, we aim to provide an overview of the most recent progress in engineering surface-grafted chains for the creation of complex and multiplexed surface architectures over micro- to macro-scopic areas. A brief introduction to surface grafting is given first. Then the fabrication of complex surface architectures is summarized with a focus on controlled chain conformations, grafting densities and three-dimensional structures. Furthermore, recent advances are highlighted for the generation of multiplexed arrays with designed chemical composition in both horizontal and vertical dimensions. The applications of such complicated macromolecular architectures are then briefly discussed. Finally, some perspective outlooks for future studies and challenges are suggested. We hope that this review will be helpful to those just entering this field and those in the field requiring quick access to useful reference information about the progress in the properties, processing, performance, and applications of functional surface-grafted architectures.
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Affiliation(s)
- Zhuang Xie
- School of Materials Science and Engineering, and Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Sun Yat-sen University, Xingangxi Road No. 135, Guangzhou, Guangdong Province 510275, P. R. China.
| | - Tiansheng Gan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Shenzhen, Guangdong Province 518055, P. R. China.
| | - Lvye Fang
- School of Materials Science and Engineering, and Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Sun Yat-sen University, Xingangxi Road No. 135, Guangzhou, Guangdong Province 510275, P. R. China.
| | - Xuechang Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Shenzhen, Guangdong Province 518055, P. R. China.
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48
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Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, Nussenzweig MC, DeRisi JL, Wilson MR. ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens. CELL REPORTS MEDICINE 2020; 1:100123. [PMID: 32995758 PMCID: PMC7513813 DOI: 10.1016/j.xcrm.2020.100123] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/17/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
Comprehensive understanding of the serological response to SARS-CoV-2 infection is important for both pathophysiologic insight and diagnostic development. Here, we generate a pan-human coronavirus programmable phage display assay to perform proteome-wide profiling of coronavirus antigens enriched by 98 COVID-19 patient sera. Next, we use ReScan, a method to efficiently sequester phage expressing the most immunogenic peptides and print them onto paper-based microarrays using acoustic liquid handling, which isolates and identifies nine candidate antigens, eight of which are derived from the two proteins used for SARS-CoV-2 serologic assays: spike and nucleocapsid proteins. After deployment in a high-throughput assay amenable to clinical lab settings, these antigens show improved specificity over a whole protein panel. This proof-of-concept study demonstrates that ReScan will have broad applicability for other emerging infectious diseases or autoimmune diseases that lack a valid biomarker, enabling a seamless pipeline from antigen discovery to diagnostic using one recombinant protein source. ReScan is a whole proteome screen to isolate and identify serologic assay targets Antibodies to linear peptides in COVID-19 sera bind spike and nucleocapsid proteins Rapid workflow that seamlessly translates biomarkers into a functional diagnostic Multiplexing linear S and N SARS-CoV-2 peptides can increase diagnostic specificity
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Affiliation(s)
- Colin R Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jayant V Rajan
- Division of Experimental Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco, CA, USA
| | | | - Sabrina A Mann
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Rita P Loudermilk
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Gavin M Sowa
- University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Bonny D Alvarenga
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Philip J Norris
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Dianna Ng
- Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
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49
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Natural variants of α-gliadin peptides within wheat proteins with reduced toxicity in coeliac disease. Br J Nutr 2020; 123:1382-1389. [PMID: 32100654 DOI: 10.1017/s0007114520000768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The only generally accepted treatment of coeliac disease (CD) is a lifelong gluten-free diet. Wheat gluten proteins include gliadins, low and high molecular weight glutenins. However, we have found significant structural variations within these protein families among different cultivars. To determine which structural motifs might be less toxic than others, we assessed five variants of α-gliadin immunodominant CD-toxic peptides synthesised as 16mers in CD T cell stimulation assays with gluten-sensitive T cell lines generated from duodenal biopsies from CD-affected individuals. The peptides harboured the overlapping T cell epitopes DQ 2.5-glia-α-2 and naturally occurring variants that differed in certain amino acids (AA). The results revealed that introduction of two selected AA substitutions in α-gliadin peptides reduced immunogenicity. A peptide with three AA substitutions involving two glutamic acids (E) and one glutamine residue (G) revealed the peptide was negative in 5:5 samples. We used CD small-intestinal organ culture to assess CD toxicity that revealed two peptides with selected substitution of both glutamic acid (E) and proline (P) residues abrogated evidence of CD toxicity.
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50
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Heidepriem J, Krähling V, Dahlke C, Wolf T, Klein F, Addo MM, Becker S, Loeffler FF. Epitopes of Naturally Acquired and Vaccine-Induced Anti-Ebola Virus Glycoprotein Antibodies in Single Amino Acid Resolution. Biotechnol J 2020; 15:e2000069. [PMID: 32463974 DOI: 10.1002/biot.202000069] [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: 02/14/2020] [Revised: 04/29/2020] [Indexed: 12/26/2022]
Abstract
The Ebola virus (EBOV) can cause severe infections in humans, leading to a fatal outcome in a high percentage of cases. Neutralizing antibodies against the EBOV surface glycoprotein (GP) can prevent infections, demonstrating a straightforward way for an efficient vaccination strategy. Meanwhile, many different anti-EBOV antibodies have been identified, whereas the exact binding epitopes are often unknown. Here, the analysis of serum samples from an EBOV vaccine trial with the recombinant vesicular stomatitis virus-Zaire ebolavirus (rVSV-ZEBOV) and an Ebola virus disease survivor, using high-density peptide arrays, is presented. In this proof-of-principle study, distinct IgG and IgM antibodies binding to different epitopes of EBOV GP is detected: By mapping the whole GP as overlapping peptide fragments, new epitopes and confirmed epitopes from the literature are found. Furthermore, the highly selective binding epitope of a neutralizing monoclonal anti-EBOV GP antibody could be validated. This shows that peptide arrays can be a valuable tool to study the humoral immune response to vaccines in patients and to support Ebola vaccine development.
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Affiliation(s)
- Jasmin Heidepriem
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Potsdam, 14476, Germany
| | - Verena Krähling
- Institute of Virology, Faculty of Medicine, Philipps University Marburg, Marburg, 35043, Germany.,German Center for Infection Research, partner site Gießen-Marburg-Langen, Marburg, 35043, Germany
| | - Christine Dahlke
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany.,Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, 20359, Germany
| | - Timo Wolf
- Department of Medicine, Infectious Diseases Unit, Goethe University Hospital, Frankfurt, 60590, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, 50931, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine, Cologne, 50931, Germany.,German Center for Infection Research, partner site Bonn-Cologne, Cologne, 50931, Germany
| | - Marylyn M Addo
- Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany.,Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, 20359, Germany
| | - Stephan Becker
- Institute of Virology, Faculty of Medicine, Philipps University Marburg, Marburg, 35043, Germany.,German Center for Infection Research, partner site Gießen-Marburg-Langen, Marburg, 35043, Germany
| | - Felix F Loeffler
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Potsdam, 14476, Germany
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