1
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Guo Z, Chiesa G, Yin J, Sanford A, Meier S, Khalil AS, Cheng JX. Structural Mapping of Protein Aggregates in Live Cells Modeling Huntington's Disease. Angew Chem Int Ed Engl 2024:e202408163. [PMID: 38880765 DOI: 10.1002/anie.202408163] [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: 04/29/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
While protein aggregation is a hallmark of many neurodegenerative diseases, acquiring structural information on protein aggregates inside live cells remains challenging. Traditional microscopy does not provide structural information on protein systems. Routinely used fluorescent protein tags, such as Green Fluorescent Protein (GFP), might perturb native structures. Here, we report a counter-propagating mid-infrared photothermal imaging approach enabling mapping of secondary structure of protein aggregates in live cells modeling Huntington's disease. By comparing mid-infrared photothermal spectra of label-free and GFP-tagged huntingtin inclusions, we demonstrate that GFP fusions indeed perturb the secondary structure of aggregates. By implementing spectra with small spatial step for dissecting spectral features within sub-micrometer distances, we reveal that huntingtin inclusions partition into a β-sheet-rich core and a ɑ-helix-rich shell. We further demonstrate that this structural partition exists only in cells with the [RNQ+] prion state, while [rnq-] cells only carry smaller β-rich non-toxic aggregates. Collectively, our methodology has the potential to unveil detailed structural information on protein assemblies in live cells, enabling high-throughput structural screenings of macromolecular assemblies.
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Affiliation(s)
- Zhongyue Guo
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Giulio Chiesa
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Jiaze Yin
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Adam Sanford
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Stefan Meier
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
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2
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Herrera MG, Amundarain MJ, Dörfler PW, Dodero VI. The Celiac-Disease Superantigen Oligomerizes and Increases Permeability in an Enterocyte Cell Model. Angew Chem Int Ed Engl 2024; 63:e202317552. [PMID: 38497459 DOI: 10.1002/anie.202317552] [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: 11/17/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/19/2024]
Abstract
Celiac disease (CeD) is an autoimmune disorder triggered by gluten proteins, affecting approximately 1 % of the global population. The 33-mer deamidated gliadin peptide (DGP) is a metabolically modified wheat-gluten superantigen for CeD. Here, we demonstrate that the 33-mer DGP spontaneously assembles into oligomers with a diameter of approximately 24 nm. The 33-mer DGP oligomers present two main secondary structural motifs-a major polyproline II helix and a minor β-sheet structure. Importantly, in the presence of 33-mer DGP oligomers, there is a statistically significant increase in the permeability in the gut epithelial cell model Caco-2, accompanied by the redistribution of zonula occludens-1, a master tight junction protein. These findings provide novel molecular and supramolecular insights into the impact of 33-mer DGP in CeD and highlight the relevance of gliadin peptide oligomerization.
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Affiliation(s)
- Maria G Herrera
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, C1428EG, Argentina
| | - Maria J Amundarain
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Philipp W Dörfler
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Veronica I Dodero
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
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3
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Nascimento ALA, Guimarães AS, Rocha TDS, Goulart MOF, Xavier JDA, Santos JCC. Structural changes in hemoglobin and glycation. VITAMINS AND HORMONES 2024; 125:183-229. [PMID: 38997164 DOI: 10.1016/bs.vh.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Hemoglobin (Hb) is a hemeprotein found inside erythrocytes and is crucial in transporting oxygen and carbon dioxide in our bodies. In erythrocytes (Ery), the main energy source is glucose metabolized through glycolysis. However, a fraction of Hb can undergo glycation, in which a free amine group from the protein spontaneously binds to the carbonyl of glucose in the bloodstream, resulting in the formation of glycated hemoglobin (HbA1c), widely used as a marker for diabetes. Glycation leads to structural and conformational changes, compromising the function of proteins, and is intensified in the event of hyperglycemia. The main changes in Hb include structural alterations to the heme group, compromising its main function (oxygen transport). In addition, amyloid aggregates can form, which are strongly related to diabetic complications and neurodegenerative diseases. Therefore, this chapter discusses in vitro protocols for producing glycated Hb, as well as the main techniques and biophysical assays used to assess changes in the protein's structure before and after the glycation process. This more complete understanding of the effects of glycation on Hb is fundamental for understanding the complications associated with hyperglycemia and for developing more effective prevention and treatment strategies.
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Affiliation(s)
- Amanda Luise Alves Nascimento
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil
| | - Ari Souza Guimarães
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil
| | - Tauane Dos Santos Rocha
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil
| | | | - Jadriane de Almeida Xavier
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil.
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4
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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5
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Bashir S, Aiman A, Chaudhary AA, Khan N, Ahanger IA, Sami N, Almugri EA, Ali MA, Khan SUD, Shahid M, Basir SF, Hassan MI, Islam A. Probing protein aggregation through spectroscopic insights and multimodal approaches: A comprehensive review for counteracting neurodegenerative disorders. Heliyon 2024; 10:e27949. [PMID: 38689955 PMCID: PMC11059433 DOI: 10.1016/j.heliyon.2024.e27949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Aberrant accumulation of protein misfolding can cause aggregation and fibrillation and is one of the primary characteristic features of neurodegenerative diseases. Because they are disordered, misfolded, and aggregated proteins pose a significant setback in drug designing. The structural study of intermediate steps in these kinds of aggregated proteins will allow us to determine the conformational changes as well as the probable pathways encompassing various neurodegenerative disorders. The analysis of protein aggregates involved in neurodegenerative diseases relies on a diverse toolkit of biophysical techniques, encompassing both morphological and non-morphological methods. Additionally, Thioflavin T (ThT) assays and Circular Dichroism (CD) spectroscopy facilitate investigations into aggregation kinetics and secondary structure alterations. The collective application of these biophysical techniques empowers researchers to comprehensively unravel the intricate nature of protein aggregates associated with neurodegeneration. Furthermore, the topics covered in this review have summed up a handful of well-established techniques used for the structural analysis of protein aggregation. This multifaceted approach advances our fundamental understanding of the underlying mechanisms driving neurodegenerative diseases and informs potential therapeutic strategies.
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Affiliation(s)
- Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ayesha Aiman
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nashrah Khan
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Neha Sami
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Eman Abdullah Almugri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Mohamed A.M. Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic Universi-ty (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, AlKharj, 11942, Saudi Arabia
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
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6
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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7
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Miller A, Chia S, Klimont E, Knowles TPJ, Vendruscolo M, Ruggeri FS. Maturation-dependent changes in the size, structure and seeding capacity of Aβ42 amyloid fibrils. Commun Biol 2024; 7:153. [PMID: 38321144 PMCID: PMC10847148 DOI: 10.1038/s42003-024-05858-7] [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: 05/17/2023] [Accepted: 01/26/2024] [Indexed: 02/08/2024] Open
Abstract
Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile functional biomaterials. Thus, protein self-assembly has been widely studied to shed light on the properties of fibrils and their intermediates. A still open question in the field concerns the microscopic processes that underlie the long-time behaviour and properties of amyloid fibrillar assemblies. Here, we use atomic force microscopy with angstrom-sensitivity to observe that amyloid fibrils undergo a maturation process, associated with an increase in both fibril length and thickness, leading to a decrease of their density, and to a change in their cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein-based materials.
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Affiliation(s)
- Alyssa Miller
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sean Chia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ewa Klimont
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Francesco Simone Ruggeri
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen, 6703 WE, the Netherlands.
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen University, Stippeneng 4, Wageningen, 6703 WE, the Netherlands.
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8
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Hu J, Yu B, Yuan C, Tao H, Wu Z, Dong D, Lu Y, Zhang Z, Cao Y, Zhao H, Cheng Y, Cui B. Influence of heat treatment before and/or after high-pressure homogenization on the structure and emulsification properties of soybean protein isolate. Int J Biol Macromol 2023; 253:127411. [PMID: 37838131 DOI: 10.1016/j.ijbiomac.2023.127411] [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: 07/27/2023] [Revised: 09/17/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
This study investigates the effects of heat treatment before high-pressure homogenization (HHPH) and heat treatment after high-pressure homogenization (HPHH) at different pressures (20, 60, and 100 MPa) on the structural and emulsification properties of soy protein isolate (SPI). The results indicate that HHPH treatment increases the surface hydrophobicity (H0) of the SPI, reduces β-fold and irregular curls, leading to the formation of soluble aggregates, increased adsorbed protein content, and subsequent improvements in emulsification activity index (EAI) and emulsion stability index (ESI). In contrast, the HPHH treatment promoted the exchange of SH/SS bonds between protein molecules and facilitated the interaction of basic peptides and β-subunits, leading to larger particle sizes of the soluble aggregates compared to the HHPH-treated samples. However, excessive aggregation in HPHH-treated aggregates leads to decreased H0 and adsorbed protein content, and increased interfacial tension, negatively affecting the emulsification properties. Compared to the HPHH treatment, HHPH treatment at homogenization pressures of 20 to 100 MPa increases EAI and ESI by 5.81-29.6 % and 5.31-25.9 %, respectively. These findings provide a fundamental basis for soybean protein manufacturers to employ appropriate processing procedures aimed at improving emulsification properties.
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Affiliation(s)
- Jiyong Hu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Bin Yu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Chao Yuan
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Haiteng Tao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Zhengzong Wu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Die Dong
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Yanmin Lu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Zheng Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Yungang Cao
- School of Food Science and Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Haibo Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
| | - Yunhui Cheng
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, Hunan 410114, China.
| | - Bo Cui
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
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Freitas CDT, Souza DP, Grangeiro TB, Sousa JS, Lima IVM, Souza PFN, Lima CS, Gomes ADS, Monteiro-Moreira ACO, Aguiar TKB, Ramos MV. Proteomic analysis of Cryptostegia grandiflora latex, purification, characterization, and biological activity of two osmotin isoforms. Int J Biol Macromol 2023; 252:126529. [PMID: 37633557 DOI: 10.1016/j.ijbiomac.2023.126529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Although latex fluids are found in >20,000 plant species, the biochemical composition and biological function of their proteins are still poorly explored. Thus, this work aimed to conduct a proteomic analysis of Cryptostegia grandiflora latex (CgLP) for subsequent purification and characterization of an antifungal protein. After 2D-SDS-PAGE and mass spectrometry, 27 proteins were identified in CgLP, including a polygalacturonase inhibitor, cysteine peptidases, pathogenesis-related proteins (PR-4), and osmotins. Then, two osmotin isoforms (CgOsm) were purified, and a unique N-terminal sequence was determined (1ATFDIRSNCPYTVWAAAVPGGGRRLDRGQTWTINVAPGTA40). The PCR products revealed a cDNA sequence of 609 nucleotides for CgOsm, which encoded a polypeptide with 203 amino acid residues. The structure of CgOsm has features of typical osmotin or thaumatin-like proteins (TLPs), such as 16 conserved Cys residues, REDDD and FF motifs, an acidic cleft, and three main domains. Atomic force microscopy (AFM) and bioinformatics suggested that CgOsm is associated with three chain units. This result was interesting since the literature describes osmotins and TLPs as monomers. AFM also showed that Fusarium falciforme spores treated with CgOsm were drastically damaged. Therefore, it is speculated that CgOsm forms pores in the membrane of these cells, causing the leakage of cytoplasmic content.
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Affiliation(s)
- Cleverson D T Freitas
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Bloco 907, Fortaleza, Ceará CEP 60451-970, Brazil.
| | - Diego P Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Bloco 907, Fortaleza, Ceará CEP 60451-970, Brazil
| | - Thalles B Grangeiro
- Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, Bloco 906, Fortaleza, Ceará, Brazil
| | - Jeanlex S Sousa
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, Ceará, Brazil
| | - Isis V M Lima
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, Ceará, Brazil
| | - Pedro Filho N Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Bloco 907, Fortaleza, Ceará CEP 60451-970, Brazil
| | - Cristiano S Lima
- Departamento de Fitotecnia, Universidade Federal do Ceará, , Campus do Pici, Bloco 805, Fortaleza, Ceará, Brazil
| | - Alexandre D'Emery S Gomes
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Bloco 907, Fortaleza, Ceará CEP 60451-970, Brazil
| | - Ana C O Monteiro-Moreira
- Centro de Biologia Experimental (NUBEX), Universidade de Fortaleza (UNIFOR), Fortaleza, Ceará, Brazil
| | - Tawanny K B Aguiar
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Bloco 907, Fortaleza, Ceará CEP 60451-970, Brazil
| | - Márcio V Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, Bloco 907, Fortaleza, Ceará CEP 60451-970, Brazil.
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10
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Panda C, Sharma LG, Pandey LM. Experimental procedures to investigate fibrillation of proteins. MethodsX 2023; 11:102445. [PMID: 37928109 PMCID: PMC10622682 DOI: 10.1016/j.mex.2023.102445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023] Open
Abstract
The unwanted phenomenon of protein fibrillation is observed in vivo and during therapeutic protein development in the industry. Protein aggregation is associated with various degenerative disorders and might induce immune-related challenges post-administration of biopharmaceutics. A pipeline for early detection, identification, and removal of pre-formed fibrils is needed to improve the quality, efficacy, and effectiveness of the formulation. Protein fibril formation is accompanied by unfolding, secondary structural changes and the formation of larger aggregates. However, most detection processes come with extensive sample preparation steps and inefficient repeatability, incurring a financial burden on research. The current article summarizes and critically discusses six simple yet powerful methods to detect aggregation phenomena in the line of detecting fibrillar aggregates in heat-induced bovine serum albumin protein. Comparing the native and heat-induced protein samples would provide insights about aggregates. Easy, inexpensive and optimized protocols for detecting the fibrillation of proteins are explained. The procedures mentioned here detected the appearance of β-sheet-rich fibrils in the heat-induced protein sample. The aggregation is characterized by enhanced thioflavin-T fluorescence, alteration in the intrinsic fluorescence, decrease in helicity and subsequent increase in β-sheet and appearance of particles with larger hydrodynamic diameters. •This article summarizes various analytical techniques to easily characterize the fibrillation of proteins.•Various techniques to detect the formation of β-sheet rich structures, changes in the secondary structures and size of aggregates have been discussed.•The stated methodologies are validated on a model protein, albumin.
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Affiliation(s)
- Chinmaya Panda
- Bio-interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Laipubam Gayatri Sharma
- Bio-interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Lalit M Pandey
- Bio-interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India
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11
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Rodriguez A, Ali A, Holman AP, Dou T, Zhaliazka K, Kurouski D. Nanoscale structural characterization of transthyretin aggregates formed at different time points of protein aggregation using atomic force microscopy-infrared spectroscopy. Protein Sci 2023; 32:e4838. [PMID: 37967043 PMCID: PMC10683371 DOI: 10.1002/pro.4838] [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: 08/28/2023] [Revised: 10/25/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023]
Abstract
Transthyretin (TTR) amyloidosis is a progressive disease characterized by an abrupt aggregation of misfolded protein in multiple organs and tissues TTR is a tetrameric protein expressed in the liver and choroid plexus. Protein misfolding triggers monomerization of TTR tetramers. Next, monomers assemble forming oligomers and fibrils. Although the secondary structure of TTR fibrils is well understood, there is very little if anything is known about the structural organization of TTR oligomers. To end this, we used nano-infrared spectroscopy, also known as atomic force microscopy infrared (AFM-IR) spectroscopy. This emerging technique can be used to determine the secondary structure of individual amyloid oligomers and fibrils. Using AFM-IR, we examined the secondary structure of TTR oligomers formed at the early (3-6 h), middle (9-12 h), and late (28 h) of protein aggregation. We found that aggregating, TTR formed oligomers (Type 1) that were dominated by α-helix (40%) and β-sheet (~30%) together with unordered protein (30%). Our results showed that fibril formation was triggered by another type of TTR oligomers (Type 2) that appeared at 9 h. These new oligomers were primarily composed of parallel β-sheet (55%), with a small amount of antiparallel β-sheet, α-helix, and unordered protein. We also found that Type 1 oligomers were not toxic to cells, whereas TTR fibrils formed at the late stages of protein aggregation were highly cytotoxic. These results show the complexity of protein aggregation and highlight the drastic difference in the protein oligomers that can be formed during such processes.
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Affiliation(s)
- Axell Rodriguez
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Abid Ali
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Aidan P. Holman
- Department of EntomologyTexas A&M UniversityCollege StationTexasUSA
| | - Tianyi Dou
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Kiryl Zhaliazka
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Dmitry Kurouski
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUSA
- Department of Biomedical EngineeringTexas A&M UniversityCollege StationTexasUSA
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12
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Boulos I, Jabbour J, Khoury S, Mikhael N, Tishkova V, Candoni N, Ghadieh HE, Veesler S, Bassim Y, Azar S, Harb F. Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics. Molecules 2023; 28:7176. [PMID: 37894653 PMCID: PMC10608922 DOI: 10.3390/molecules28207176] [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: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.
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Affiliation(s)
- Imad Boulos
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Joy Jabbour
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Serena Khoury
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Nehme Mikhael
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Victoria Tishkova
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Nadine Candoni
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Stéphane Veesler
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Youssef Bassim
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Frédéric Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
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13
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Liu Y, Bu Y, Zhu W, Li J, Li X. Effects of divalent mercury on myosin structure of large yellow croaker and its binding mechanism: Multi-spectroscopies and molecular docking. Food Chem 2023; 418:135972. [PMID: 36965387 DOI: 10.1016/j.foodchem.2023.135972] [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: 11/02/2022] [Revised: 03/02/2023] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Heavy metals have long biological half-lives and are therefore a major threat to aquatic organisms, especially fish. Divalent mercury (Hg(II)) is an important form from a toxicological viewpoint. In this paper, we studied the interaction mechanism between large yellow croaker myosin and Hg(II) by multi-spectroscopies and molecular docking. Hg(II) had a positive effect on improving the elasticity of myosin gel, and the constant increase of charge would destroy the gel. Hg(II) caused myosin to aggregate, and the protein's apparent structure rapidly increased in length. The content of α-helix obviously decreased, β-turns and β-sheet increased. The myosin and Hg(II) quenching type was static quenching. Thermodynamic analysis suggested hydrogen bonding and van der Waals forces were the main forces for the combination. The molecular docking further confirmed the mechanism of action. This study provides a theoretical guidance for the preventions and control of marine heavy metals.
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Affiliation(s)
- Yingnan Liu
- College of Food Science and Engineering, Bohai University. National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Ying Bu
- College of Food Science and Engineering, Bohai University. National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Wenhui Zhu
- College of Food Science and Engineering, Bohai University. National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University. National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Xuepeng Li
- College of Food Science and Engineering, Bohai University. National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
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14
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Nirmalraj PN, Schneider T, Lüder L, Felbecker A. Protein fibril length in cerebrospinal fluid is increased in Alzheimer's disease. Commun Biol 2023; 6:251. [PMID: 36890343 PMCID: PMC9995532 DOI: 10.1038/s42003-023-04606-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/16/2023] [Indexed: 03/10/2023] Open
Abstract
Alzheimer's disease (AD) associated proteins exist in cerebrospinal fluid (CSF). This paper evidences that protein aggregate morphology distinctly differs in CSF of patients with AD dementia (ADD), mild cognitive impairment due to AD (MCI AD), with subjective cognitive decline without amyloid pathology (SCD) and with non-AD MCI using liquid-based atomic force microscopy (AFM). Spherical-shaped particles and nodular-shaped protofibrils were present in the CSF of SCD patients, whereas CSF of ADD patients abundantly contained elongated mature fibrils. Quantitative analysis of AFM topographs confirms fibril length is higher in CSF of ADD than in MCI AD and lowest in SCD and non-AD dementia patients. CSF fibril length is inversely correlated with CSF amyloid beta (Aβ) 42/40 ratio and CSF p-tau protein levels (obtained from biochemical assays) to predict amyloid and tau pathology with an accuracy of 94% and 82%, respectively, thus identifying ultralong protein fibrils in CSF as a possible signature of AD pathology.
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Affiliation(s)
- Peter Niraj Nirmalraj
- Transport at Nanoscale Interfaces Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, CH-8600, Switzerland.
| | - Thomas Schneider
- Department of Neurology, Cantonal Hospital St. Gallen, St. Gallen, CH-9007, Switzerland
| | - Lars Lüder
- Transport at Nanoscale Interfaces Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, CH-8600, Switzerland
| | - Ansgar Felbecker
- Department of Neurology, Cantonal Hospital St. Gallen, St. Gallen, CH-9007, Switzerland.
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15
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Sun H, Wang J. Novel perspective for protein-drug interaction analysis: atomic force microscope. Analyst 2023; 148:454-474. [PMID: 36398684 DOI: 10.1039/d2an01591a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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16
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End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images. Sci Rep 2023; 13:129. [PMID: 36599879 DOI: 10.1038/s41598-022-27057-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
Observing the structural dynamics of biomolecules is vital to deepening our understanding of biomolecular functions. High-speed (HS) atomic force microscopy (AFM) is a powerful method to measure biomolecular behavior at near physiological conditions. In the AFM, measured image profiles on a molecular surface are distorted by the tip shape through the interactions between the tip and molecule. Once the tip shape is known, AFM images can be approximately deconvolved to reconstruct the surface geometry of the sample molecule. Thus, knowing the correct tip shape is an important issue in the AFM image analysis. The blind tip reconstruction (BTR) method developed by Villarrubia (J Res Natl Inst Stand Technol 102:425, 1997) is an algorithm that estimates tip shape only from AFM images using mathematical morphology operators. While the BTR works perfectly for noise-free AFM images, the algorithm is susceptible to noise. To overcome this issue, we here propose an alternative BTR method, called end-to-end differentiable BTR, based on a modern machine learning approach. In the method, we introduce a loss function including a regularization term to prevent overfitting to noise, and the tip shape is optimized with automatic differentiation and backpropagations developed in deep learning frameworks. Using noisy pseudo-AFM images of myosin V motor domain as test cases, we show that our end-to-end differentiable BTR is robust against noise in AFM images. The method can also detect a double-tip shape and deconvolve doubled molecular images. Finally, application to real HS-AFM data of myosin V walking on an actin filament shows that the method can reconstruct the accurate surface geometry of actomyosin consistent with the structural model. Our method serves as a general post-processing for reconstructing hidden molecular surfaces from any AFM images. Codes are available at https://github.com/matsunagalab/differentiable_BTR .
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17
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Vekilov PG, Wolynes PG. Time-Resolved In Situ AFM Measurement of Growth Rates of Aβ40 Fibrils. Methods Mol Biol 2023; 2551:63-77. [PMID: 36310197 DOI: 10.1007/978-1-0716-2597-2_6] [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
We employ time-resolved in situ atomic force microcopy to monitor the growth of individual Aβ40 fibrils and thereby directly measure the fibril growth rates. We describe procedures to express and purify the Aβ peptide and verify its identity, prepare solutions and seeds, quantify the displacements of the growing tips of individual fibrils, and determine their respective growth rates. We discuss approaches to evaluate and minimize the impact of the scanning tip on the monitored processes. We use the distribution of fibril thickness to characterize approximately the fibril structure. The ability to quantify faithfully the growth kinetics of amyloid fibrils empowers exploration of the molecular-level processes of fibril growth that relate to behaviors of amyloid species of laboratory and clinical interest.
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
- Department of Chemistry, University of Houston, Houston, TX, USA.
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
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18
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Wojciechowski JW, Tekoglu E, Gąsior-Głogowska M, Coustou V, Szulc N, Szefczyk M, Kopaczyńska M, Saupe SJ, Dyrka W. Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins. PLoS Comput Biol 2022; 18:e1010787. [PMID: 36542665 PMCID: PMC9815663 DOI: 10.1371/journal.pcbi.1010787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 01/05/2023] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of cellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here, we explore the diverse world of effector and signaling domains of fungal NLRs using state-of-the-art bioinformatic methods including MMseqs2 for fast clustering, probabilistic context-free grammars for sequence analysis, and AlphaFold2 deep neural networks for structure prediction. In addition to substantially improving the overall annotation, especially in basidiomycetes, the study identifies novel domains and reveals the structural similarity of MLKL-related HeLo- and Goodbye-like domains forming the most abundant superfamily of fungal NLR effectors. Moreover, compared to previous studies, we found several times more amyloid motif instances, including novel families, and validated aggregating and prion-forming properties of the most abundant of them in vitro and in vivo. Also, through an extensive in silico search, the NLR-associated amyloid signaling was identified in basidiomycetes. The emerging picture highlights similarities and differences in the NLR architectures and amyloid signaling in ascomycetes, basidiomycetes and other branches of life.
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Affiliation(s)
- Jakub W. Wojciechowski
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Emirhan Tekoglu
- Biyomühendislik Bölümü, Yıldız Teknik Üniversitesi, İstanbul, Turkey
- Wydział Chemiczny, Politechnika Wrocławska, Poland
| | - Marlena Gąsior-Głogowska
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Virginie Coustou
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux, France
| | - Natalia Szulc
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Monika Szefczyk
- Katedra Chemii Bioorganicznej, Wydział Chemiczny, Politechnika Wrocławska, Wrocław, Poland
| | - Marta Kopaczyńska
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
| | - Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux, France
- * E-mail: (SJS); (WD)
| | - Witold Dyrka
- Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland
- * E-mail: (SJS); (WD)
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19
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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [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: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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20
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Tiwari K, Singh G, Singh SK. Purification and Structural Characterization of N-Terminal 190 Amino Acid Deleted Essential Mammalian Protein; Transcription Termination Factor 1. ACS OMEGA 2022; 7:45165-45173. [PMID: 36530226 PMCID: PMC9753541 DOI: 10.1021/acsomega.2c05603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
The mammalian transcription termination factor 1 (TTF1) is an essential protein that plays diverse cellular physiological functions like transcription regulation (both initiation and termination), replication fork blockage, chromatin remodeling, and DNA damage repair. Hence, understanding the structure and mechanism conferred by its variable conformations is important. However, so far, almost nothing is known about the structure of either the full-length protein or any of its domains in isolation. Since the full-length protein even after multiple attempts could not be purified in soluble form, we have codon optimized, expressed, and purified the N-terminal 190 amino acid deleted TTF1 (ΔN190TTF1) protein. In this study, we characterized this essential protein by studying its homogeneity, molecular size, and secondary structure using tools like dynamic light scattering (DLS), circular dichroism (CD) spectroscopy, Raman spectroscopy, and atomic force microscopy (AFM). By CD spectroscopy and DLS, we confirmed that the purified protein is homogeneous and soluble. CD spectroscopy also revealed that ΔN190TTF1 is a helical protein, which was further established by analysis of Raman spectra and amide I region deconvolution studies. The DLS study estimated the size of a single protein molecule to be 17.2 nm (in aqueous solution). Our structural and biophysical characterization of this essential protein will open avenues toward solving the structure to atomic resolution and will also encourage researchers to investigate the mechanism behind its diverse functions attributed to its various domains.
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21
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Infrared nanospectroscopic imaging of DNA molecules on mica surface. Sci Rep 2022; 12:18972. [PMID: 36348038 PMCID: PMC9643503 DOI: 10.1038/s41598-022-23637-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying IR-AFM technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the AFM-IR investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of AFM-IR mapping modalities with corresponding absorption spectra based on two different DNA deposition protocols on spermidine and Ni2+ pretreated mica surface. The nanoscale IR absorbance of distinctly formed DNA morphologies on mica are demonstrated through series of AFM-IR absorption maps with corresponding IR spectrum. Our results thus demonstrate the sensitivity of AFM-IR nanospectroscopy for a nucleic acid research with an open potential to be employed in further investigation of nucleoprotein complexes.
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22
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Microplastics and nanoplastics in food, water, and beverages, part II. Methods. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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23
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Quantitative super-resolution imaging of pathological aggregates reveals distinct toxicity profiles in different synucleinopathies. Proc Natl Acad Sci U S A 2022; 119:e2205591119. [PMID: 36206368 PMCID: PMC9573094 DOI: 10.1073/pnas.2205591119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Protein aggregation is a hallmark of major neurodegenerative disorders. Increasing data suggest that smaller aggregates cause higher toxic response than filamentous aggregates (fibrils). However, the size of small aggregates has challenged their detection within biologically relevant environments. Here, we report approaches to quantitatively super-resolve aggregates in live cells and ex vivo brain tissues. We show that Amytracker 630 (AT630), a commercial aggregate-activated fluorophore, has outstanding photophysical properties that enable super-resolution imaging of α-synuclein, tau, and amyloid-β aggregates, achieving ∼4 nm precision. Applying AT630 to AppNL-G-F mouse brain tissues or aggregates extracted from a Parkinson's disease donor, we demonstrate excellent agreement with antibodies specific for amyloid-β or α-synuclein, respectively, confirming the specificity of AT630. Subsequently, we use AT630 to reveal a linear relationship between α-synuclein aggregate size and cellular toxicity and discovered that aggregates smaller than 450 ± 60 nm (aggregate450nm) readily penetrated the plasma membrane. We determine aggregate450nm concentrations in six Parkinson's disease and dementia with Lewy bodies donor samples and show that aggregates in different synucleinopathies demonstrate distinct potency in toxicity. We further show that cell-penetrating aggregates are surrounded by proteasomes, which assemble into foci to gradually process aggregates. Our results suggest that the plasma membrane effectively filters out fibrils but is vulnerable to penetration by aggregates of 450 ± 60 nm. Together, our findings present an exciting strategy to determine specificity of aggregate toxicity within heterogeneous samples. Our approach to quantitatively measure these toxic aggregates in biological environments opens possibilities to molecular examinations of disease mechanisms under physiological conditions.
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24
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Bridstrup J, Yuan J, Schreck JS. Stochastic kinetic study of protein aggregation and molecular crowding effects of
Aβ40
and
Aβ42. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- John Bridstrup
- Department of Physics Drexel University Philadelphia Pennsylvania USA
| | - Jian‐Min Yuan
- Department of Physics Drexel University Philadelphia Pennsylvania USA
| | - John S. Schreck
- Computational and Information Systems Lab National Center for Atmospheric Research (NCAR) Boulder Colorado USA
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25
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Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [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: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
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Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
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Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196448. [PMID: 36234985 PMCID: PMC9573641 DOI: 10.3390/molecules27196448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.
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27
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Small soluble α-synuclein aggregates are the toxic species in Parkinson's disease. Nat Commun 2022; 13:5512. [PMID: 36127374 PMCID: PMC9489799 DOI: 10.1038/s41467-022-33252-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
Soluble α-synuclein aggregates varying in size, structure, and morphology have been closely linked to neuronal death in Parkinson's disease. However, the heterogeneity of different co-existing aggregate species makes it hard to isolate and study their individual toxic properties. Here, we show a reliable non-perturbative method to separate a heterogeneous mixture of protein aggregates by size. We find that aggregates of wild-type α-synuclein smaller than 200 nm in length, formed during an in vitro aggregation reaction, cause inflammation and permeabilization of single-liposome membranes and that larger aggregates are less toxic. Studying soluble aggregates extracted from post-mortem human brains also reveals that these aggregates are similar in size and structure to the smaller aggregates formed in aggregation reactions in the test tube. Furthermore, we find that the soluble aggregates present in Parkinson's disease brains are smaller, largely less than 100 nm, and more inflammatory compared to the larger aggregates present in control brains. This study suggests that the small non-fibrillar α-synuclein aggregates are the critical species driving neuroinflammation and disease progression.
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Cheung E, Xia Y, Caporini MA, Gilmore JL. Tools shaping drug discovery and development. BIOPHYSICS REVIEWS 2022; 3:031301. [PMID: 38505278 PMCID: PMC10903431 DOI: 10.1063/5.0087583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/21/2022] [Indexed: 03/21/2024]
Abstract
Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.
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Affiliation(s)
- Eugene Cheung
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Yan Xia
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Marc A. Caporini
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jamie L. Gilmore
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
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29
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Zhao GM, Zhang GY, Bai XY, Yin F, Ru A, Yu XL, Zhao LJ, Zhu CZ. Effects of NaCl-assisted regulation on the emulsifying properties of heat-induced type I collagen. Food Res Int 2022; 159:111599. [DOI: 10.1016/j.foodres.2022.111599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/02/2022] [Accepted: 06/28/2022] [Indexed: 11/04/2022]
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Suleman M, Lee S, Kim M, Nguyen VH, Riaz M, Nasir N, Kumar S, Park HM, Jung J, Seo Y. NaCl-Assisted Temperature-Dependent Controllable Growth of Large-Area MoS 2 Crystals Using Confined-Space CVD. ACS OMEGA 2022; 7:30074-30086. [PMID: 36061644 PMCID: PMC9434612 DOI: 10.1021/acsomega.2c03108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Due to its semiconducting nature, controlled growth of large-area chemical vapor deposition (CVD)-grown two-dimensional (2D) molybdenum disulfide (MoS2) has a lot of potential applications in photodetectors, sensors, and optoelectronics. Yet the controllable, large-area, and cost-effective growth of highly crystalline MoS2 remains a challenge. Confined-space CVD is a very promising method for the growth of highly crystalline MoS2 in a controlled manner. Herein, we report the large-scale growth of MoS2 with different morphologies using NaCl as a seeding promoter for confined-space CVD. Changes in the morphologies of MoS2 are reported by variation in the amount of seeding promoter, precursor ratio, and the growth temperature. Furthermore, the properties of the grown MoS2 are analyzed using optical microscopy, scanning electron microscopy (SEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), energy-dispersive X-ray spectroscopy (EDX), and atomic force microscopy (AFM). The electrical properties of the CVD-grown MoS2 show promising performance from fabricated field-effect transistors. This work provides new insight into the growth of large-area MoS2 and opens the way for its various optoelectronic and electronic applications.
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31
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Okamoto Y, Hamaguchi K, Watanabe M, Watanabe N, Umakoshi H. Characterization of Phase Separated Planar Lipid Bilayer Membrane by Fluorescence Ratio Imaging and Scanning Probe Microscope. MEMBRANES 2022; 12:770. [PMID: 36005685 PMCID: PMC9415343 DOI: 10.3390/membranes12080770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
The lipid membrane forms nanodomains (rafts) and shows heterogeneous properties. These nanodomains relate to significant roles in various cell functions, and thus the analysis of the nanodomains in phase-separated lipid membranes is important to clarify the function and role of the nanodomains. However, the lipid membrane possesses small-sized nanodomains and shows a small height difference between the nanodomains and their surroundings at certain lipid compositions. In addition, nanodomain analysis sometimes requires highly sensitive and expensive apparatus, such as a two-photon microscope. These have prevented the analysis by the conventional fluorescence microscope and by the topography of the scanning probe microscope (SPM), even though these are promising methods in macroscale and microscale analysis, respectively. Therefore, this study aimed to overcome these problems in nanodomain analysis. We successfully demonstrated that solvatochromic dye, LipiORDER, could analyze the phase state of the lipid membrane at the macroscale with low magnification lenses. Furthermore, we could prove that the phase mode of SPM was effective in the visualization of specific nanodomains by properties difference as well as topographic images of SPM. Hence, this combination method successfully gave much information on the phase state at the micro/macro scale, and thus this would be applied to the analysis of heterogeneous lipid membranes.
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Optical Fiber Probe Microcantilever Sensor Based on Fabry–Perot Interferometer. SENSORS 2022; 22:s22155748. [PMID: 35957304 PMCID: PMC9370988 DOI: 10.3390/s22155748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023]
Abstract
Optical fiber Fabry–Perot sensors have long been the focus of researchers in sensing applications because of their unique advantages, including highly effective, simple light path, low cost, compact size, and easy fabrication. Microcantilever-based devices have been extensively explored in chemical and biological fields while the interrogation methods are still a challenge. The optical fiber probe microcantilever sensor is constructed with a microcantilever beam on an optical fiber, which opens the door for highly sensitive, as well as convenient readout. In this review, we summarize a wide variety of optical fiber probe microcantilever sensors based on Fabry–Perot interferometer. The operation principle of the optical fiber probe microcantilever sensor is introduced. The fabrication methods, materials, and sensing applications of an optical fiber probe microcantilever sensor with different structures are discussed in detail. The performances of different kinds of fiber probe microcantilever sensors are compared. We also prospect the possible development direction of optical fiber microcantilever sensors.
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33
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Xu Y, Zhu H, Denduluri A, Ou Y, Erkamp NA, Qi R, Shen Y, Knowles TPJ. Recent Advances in Microgels: From Biomolecules to Functionality. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200180. [PMID: 35790106 DOI: 10.1002/smll.202200180] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The emerging applications of hydrogel materials at different length scales, in areas ranging from sustainability to health, have driven the progress in the design and manufacturing of microgels. Microgels can provide miniaturized, monodisperse, and regulatable compartments, which can be spatially separated or interconnected. These microscopic materials provide novel opportunities for generating biomimetic cell culture environments and are thus key to the advances of modern biomedical research. The evolution of the physical and chemical properties has, furthermore, highlighted the potentials of microgels in the context of materials science and bioengineering. This review describes the recent research progress in the fabrication, characterization, and applications of microgels generated from biomolecular building blocks. A key enabling technology allowing the tailoring of the properties of microgels is their synthesis through microfluidic technologies, and this paper highlights recent advances in these areas and their impact on expanding the physicochemical parameter space accessible using microgels. This review finally discusses the emerging roles that microgels play in liquid-liquid phase separation, micromechanics, biosensors, and regenerative medicine.
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Affiliation(s)
- Yufan Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Hongjia Zhu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Akhila Denduluri
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Yangteng Ou
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Nadia A Erkamp
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Runzhang Qi
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Yi Shen
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
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34
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Schaefer A, Naser D, Siebeneichler B, Tarasca MV, Meiering EM. Methodological advances and strategies for high resolution structure determination of cellular protein aggregates. J Biol Chem 2022; 298:102197. [PMID: 35760099 PMCID: PMC9396402 DOI: 10.1016/j.jbc.2022.102197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 01/14/2023] Open
Abstract
Aggregation of proteins is at the nexus of molecular processes crucial to aging, disease, and employing proteins for biotechnology and medical applications. There has been much recent progress in determining the structural features of protein aggregates that form in cells; yet, owing to prevalent heterogeneity in aggregation, many aspects remain obscure and often experimentally intractable to define. Here we review recent results of structural studies for cell-derived aggregates of normally globular proteins, with a focus on high resolution methods for their analysis and prediction. Complementary results obtained by solid-state NMR spectroscopy, Fourier transform infrared (FTIR) spectroscopy and microspectroscopy, cryo-electron microscopy, and amide hydrogen/deuterium exchange measured by NMR and mass spectrometry (MS), applied to bacterial inclusion bodies and disease inclusions, are uncovering novel information on in-cell aggregation patterns as well as great diversity in the structural features of useful and aberrant protein aggregates. Using these advances as a guide, this review aims to advise the reader on which combination of approaches may be the most appropriate to apply to their unique system.
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Affiliation(s)
- Anna Schaefer
- Department of Chemistry, University of Waterloo Waterloo ON Canada
| | - Dalia Naser
- Department of Chemistry, University of Waterloo Waterloo ON Canada
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35
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Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy. Int J Mol Sci 2022; 23:ijms23126781. [PMID: 35743221 PMCID: PMC9224231 DOI: 10.3390/ijms23126781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/14/2022] Open
Abstract
S100A9 is a pro-inflammatory protein that co-aggregates with other proteins in amyloid fibril plaques. S100A9 can influence the aggregation kinetics and amyloid fibril structure of alpha-synuclein (α-syn), which is involved in Parkinson's disease. Currently, there are limited data regarding their cross-interaction and how it influences the aggregation process. In this work, we analyzed this interaction using solution 19F and 2D 15N-1H HSQC NMR spectroscopy and studied the aggregation properties of these two proteins. Here, we show that α-syn interacts with S100A9 at specific regions, which are also essential in the first step of aggregation. We also demonstrate that the 4-fluorophenylalanine label in alpha-synuclein is a sensitive probe to study interaction and aggregation using 19F NMR spectroscopy.
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36
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Du J, Dang M, Jia Y, Xu Y, Li C. Persimmon tannin unevenly changes the physical properties, morphology, subunits composition and cross-linking types of gliadin and glutenin. Food Chem 2022; 387:132913. [PMID: 35421646 DOI: 10.1016/j.foodchem.2022.132913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 11/18/2022]
Abstract
To answer which is the key component caused the alterations of gluten in the presence of persimmon tannin (PT), the changes on physical properties, morphology, subunits coposition and cross-linking types of glutenin and gliadin were investigated. The results showed that compared with gliadin, glutenin was more sensitive to PT due to the greater changes in the thermal stability, network structure and aggregation behavior. This might be explained by the remarkable decreases in soluble subunits content, free sulfhydryl groups (SH), disulfide bonds (SS) and free amino groups (-NH2) cross-linking of glutenin after 8% of PT addition, as well as the varying degree in subunits composition. Therefore, glutenin played a more important role in the changes in the properties and network structure of gluten induced by PT than gliadin. Our work provided a guidance for the incorporation of phenolic compounds in wheat flour-based products.
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Affiliation(s)
- Jing Du
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Meizhu Dang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Henan University of Animal Husbandry and Economy, Henan 477100, China
| | - Yangyang Jia
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yujuan Xu
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Products, Ministry of Agriculture, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China.
| | - Chunmei Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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37
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Mukhopadhyay S, Bera SC, Ramola K. Observation of two-step aggregation kinetics of Amyloid- βproteins from fractal analysis. Phys Biol 2022; 19. [PMID: 35381581 DOI: 10.1088/1478-3975/ac6478] [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: 01/24/2022] [Accepted: 04/05/2022] [Indexed: 11/12/2022]
Abstract
Self-aggregation in proteins has long been studied and modeled due to its ubiquity and importance in many biological contexts. Several models propose a two step aggregation mechanism, consisting of linear growth of fibrils and secondary growth involving branch formation. Single molecule imaging techniques such as total internal reflection fluorescence (TIRF) microscopy can provide direct evidence of such mechanisms, however, analyzing such large data-sets is challenging. In this paper, we analyze for the first time, images of growing amyloid fibrils obtained from TIRF microscopy using the techniques of fractal geometry, which provides a natural framework to disentangle the two types of growth mechanisms at play. We find that after an initial linear growth phase, identified by a plateau in the average fractal dimension with time, the occurrence of branching events leads to a further increase in the fractal dimension, with a final saturation value ≈ 2. This provides direct evidence of the two-step nature of the aggregation kinetics of Amyloid-βproteins, with an initial linear elongation phase followed by branching at later times.
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Affiliation(s)
- Soham Mukhopadhyay
- Tata Institute of Fundamental Research Centre for Interdisciplinary Sciences, 36/P, Gopanpally Tanda, Serilingampally Mandal, Hyderabad, Telangana, 500046, INDIA
| | - Subhas C Bera
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, Erlangen, Bayern, 91058, GERMANY
| | - Kabir Ramola
- Tata Institute of Fundamental Research Centre for Interdisciplinary Sciences, 36/P, Gopanpally Tanda, Serilingampally Mandal, Hyderabad, Telangana, 500046, INDIA
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38
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Zhang P, Tan C. Cross-Reactive Fluorescent Sensor Array for Discrimination of Amyloid Beta Aggregates. Anal Chem 2022; 94:5469-5473. [PMID: 35362962 DOI: 10.1021/acs.analchem.2c00579] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It has been hypothesized that misfolding and misassembly of proteins into various aggregation states contribute to several neurodegenerative diseases. For instance, amyloid beta (Aβ) aggregation is considered a major factor in Alzheimer's disease pathogenesis. Herein, a fluorescent sensor array for detecting Aβ aggregates was fabricated using two probe pairs of conjugated polyelectrolytes and organic dye molecules, PPE1-Thioflavin T (ThT) and PPESO3-Nile Red (NR). Pattern recognition was achieved by linear discriminant analysis and hierarchical clustering analysis algorithms. As a result of distinguishing among monomers and three pure aggregate species, namely oligomers, protofibrils, and fibrils, the cross-reactive sensor array was also able to monitor aggregation kinetics in various aggregate forms and distinguish between on- and off- aggregate pathways. Our study provides a convenient approach for simultaneous detection of Aβ aggregates in mixtures, which may also be applied to the analysis of other disease-related proteins that are prone to aggregates.
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Affiliation(s)
- Pangmiaomiao Zhang
- State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, People's Republic of China
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39
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Mebus-Antunes NC, Ferreira WS, Barbosa GM, Neves-Martins TC, Weissmuller G, Almeida FCL, Da Poian AT. The interaction of dengue virus capsid protein with negatively charged interfaces drives the in vitro assembly of nucleocapsid-like particles. PLoS One 2022; 17:e0264643. [PMID: 35231063 PMCID: PMC8887749 DOI: 10.1371/journal.pone.0264643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/15/2022] [Indexed: 01/06/2023] Open
Abstract
Dengue virus (DENV) causes a major arthropod-borne viral disease, with 2.5 billion people living in risk areas. DENV consists in a 50 nm-diameter enveloped particle in which the surface proteins are arranged with icosahedral symmetry, while information about nucleocapsid (NC) structural organization is lacking. DENV NC is composed of the viral genome, a positive-sense single-stranded RNA, packaged by the capsid (C) protein. Here, we established the conditions for a reproducible in vitro assembly of DENV nucleocapsid-like particles (NCLPs) using recombinant DENVC. We analyzed NCLP formation in the absence or presence of oligonucleotides in solution using small angle X-ray scattering, Rayleigh light scattering as well as fluorescence anisotropy, and characterized particle structural properties using atomic force and transmission electron microscopy imaging. The experiments in solution comparing 2-, 5- and 25-mer oligonucleotides established that 2-mer is too small and 5-mer is sufficient for the formation of NCLPs. The assembly process was concentration-dependent and showed a saturation profile, with a stoichiometry of 1:1 (DENVC:oligonucleotide) molar ratio, suggesting an equilibrium involving DENVC dimer and an organized structure compatible with NCLPs. Imaging methods proved that the decrease in concentration to sub-nanomolar concentrations of DENVC allows the formation of regular spherical NCLPs after protein deposition on mica or carbon surfaces, in the presence as well as in the absence of oligonucleotides, in this latter case being surface driven. Altogether, the results suggest that in vitro assembly of DENV NCLPs depends on DENVC charge neutralization, which must be a very coordinated process to avoid unspecific aggregation. Our hypothesis is that a specific highly positive spot in DENVC α4-α4' is the main DENVC-RNA binding site, which is required to be firstly neutralized to allow NC formation.
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Affiliation(s)
- Nathane C. Mebus-Antunes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wellington S. Ferreira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Glauce M. Barbosa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thais C. Neves-Martins
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto Weissmuller
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C. L. Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrea T. Da Poian
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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40
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Kurisaki I, Tanaka S. Remarked suppression of Aβ 42 protomer-protomer dissociation reaction elucidated by molecular dynamics simulation. Proteins 2022; 90:1367-1375. [PMID: 35137442 DOI: 10.1002/prot.26319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/24/2022] [Accepted: 02/02/2022] [Indexed: 01/27/2023]
Abstract
Multimeric protein complexes are molecular apparatuses to regulate biological systems and often determine their fate. Among proteins forming such molecular assemblies, amyloid proteins have drawn attention over a half-century since amyloid fibril formation of these proteins is supposed to be a common pathogenic cause for neurodegenerative diseases. This process is triggered by the accumulation of fibril-like aggregates, while the microscopic mechanisms are mostly elusive due to technical limitation of experimental methodologies in individually observing each of diverse aggregate species in the aqueous solution. We then addressed this problem by employing atomistic molecular dynamics simulations for the paradigmatic amyloid protein, amyloid-β (Aβ42 ). Seven different dimeric forms of oligomeric Aβ42 fibril-like aggregate in aqueous solution, ranging from tetramer to decamer, were considered. We found additive effects of the size of these fibril-like aggregates on their thermodynamic stability and have clarified kinetic suppression of protomer-protomer dissociation reactions at and beyond the point of pentamer dimer formation. This observation was obtained from the specific combination of the Aβ42 protomer structure and the physicochemical condition that we here examined, while it is worthwhile to recall that several amyloid fibrils take dimeric forms of their protomers. We could thus conclude that the stable formation of fibril-like protomer dimer should be involved in a turning point where rapid growth of amyloid fibrils is triggered.
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Affiliation(s)
- Ikuo Kurisaki
- Department of Computational Science, Graduate School of System Informatics, Kobe University, Kobe, Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University, Kobe, Japan
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41
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Cho DH, Xie T, Mulcahey PJ, Kelleher NP, Hahm JI. Distinctive Adsorption Mechanism and Kinetics of Immunoglobulin G on a Nanoscale Polymer Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1458-1470. [PMID: 35037456 DOI: 10.1021/acs.langmuir.1c02710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Elucidation of protein adsorption beyond simple polymer surfaces to those presenting greater chemical complexity and nanoscopic features is critical to developing well-controlled nanobiomaterials and nanobiosensors. In this study, we repeatedly and faithfully track individual proteins on the same nanodomain areas of a block copolymer (BCP) surface and monitor the adsorption and assembly behavior of a model protein, immunoglobulin G (IgG), over time into a tight surface-packed structure. With discrete protein adsorption events unambiguously visualized at the biomolecular level, the detailed assembly and packing states of IgG on the BCP nanodomain surface are subsequently correlated to various regimes of IgG adsorption kinetic plots. Intriguing features, entirely different from those observed from macroscopic homopolymer templates, are identified from the IgG adsorption isotherms on the nanoscale, chemically varying BCP surface. They include the presence of two Langmuir-like adsorption segments and a nonmonotonic regime in the adsorption plot. Via correlation to time-corresponding topographic data, the unique isotherm features are explained with single biomolecule level details of the IgG adsorption pathway on the BCP. This work not only provides much needed, direct experimental evidence for time-resolved, single protein level, adsorption events on nanoscale polymer surfaces but also signifies mutual linking between specific topographic states of protein adsorption and assembly to particular segments of adsorption isotherms. From the fundamental research viewpoint, the correlative ability to examine the nanoscopic surface organizations of individual proteins and their local as well as global adsorption kinetic profiles will be highly valuable for accurately determining protein assembly mechanisms and interpreting protein adsorption kinetics on nanoscale surfaces. Application-wise, such knowledge will also be important for fundamentally guiding the design and development of biomaterials and biomedical devices that exploit nanoscale polymer architectures.
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Affiliation(s)
- David H Cho
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Tian Xie
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Patrick J Mulcahey
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Noah P Kelleher
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Jong-In Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
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Haghighijoo Z, Zamani L, Moosavi F, Emami S. Therapeutic potential of quinazoline derivatives for Alzheimer's disease: A comprehensive review. Eur J Med Chem 2022; 227:113949. [PMID: 34742016 DOI: 10.1016/j.ejmech.2021.113949] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/02/2021] [Accepted: 10/22/2021] [Indexed: 12/24/2022]
Abstract
Quinazolines are considered as a promising class of bioactive heterocyclic compounds with broad properties. Particularly, the quinazoline scaffold has an impressive role in the design and synthesis of new CNS-active drugs. The drug-like properties and pharmacological characteristics of quinazoline could lead to different drugs with various targets. Among CNS disorders, Alzheimer's disease (AD) is a progressive neurodegenerative disorder with memory loss, cognitive decline and language dysfunction. AD is a complex and multifactorial disease therefore, the need for finding multi-target drugs against this devastative disease is urgent. A literature survey revealed that quinazoline derivatives have diverse therapeutic potential for AD as modulators/inhibitors of β-amyloid, tau protein, cholinesterases, monoamine oxidases, and phosphodiesterases as well as other protective effects. Thus, we describe here the most relevant and recent studies about anti-AD agents with quinazoline structure which can further aid the development and discovery of new anti-AD agents.
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Affiliation(s)
- Zahra Haghighijoo
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA
| | - Leila Zamani
- Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - Fatemeh Moosavi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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Asadi V, Li X, Ruggeri FS, Zuilhof H, van der Gucht J, Kodger TE. Synthesis of well-defined linear–bottlebrush–linear triblock copolymer towards architecturally-tunable soft materials. Polym Chem 2022; 13:4666-4674. [PMID: 36092984 PMCID: PMC9379773 DOI: 10.1039/d2py00841f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Linear–bottlebrush–linear (LBBL) triblock copolymers are emerging systems for topologically-tunable elastic materials. In this paper, a new synthetic methodology is presented to synthesize LBBL polystyrene-block-bottlebrushpolydimethylsiloxane-block-polystyrene (PS-b-bbPDMS-b-PS) triblock copolymer via the “grafting onto” approach where the precursors are individually synthesized through living anionic polymerization and selective coupling reaction. In this two-step approach, polystyrene-block-polymethylvinylsiloxane (PS-b-PMVS) diblock copolymer with a low dispersity couples with another living PS block to form PS-b-PMVS-b-PS triblock copolymer. Secondly, this is followed by grafting of separately prepared monohydride-terminated PDMS chains with controllable grafting density through a hydrosilylation reaction. In addition to fully tunable architectural parameters, this approach permits a quantitative determination of the ratio of diblock and triblock bottlebrush copolymers and consistency between batches, highlighting the feasibility for scaled-up production. These LBBL triblock copolymers self-assemble into soft, low-modulus thermoplastic elastomers, and the precise knowledge of the composition is crucial for correlating microstructure to mechanical properties. A new method is discussed to synthesize linear–bottlebrush–linear polystyrene-block-polydimethylsiloxane-block-polystyrene triblock copolymer via “grafting onto” approach with well-defined and tunable architectural parameters.![]()
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Affiliation(s)
- Vahid Asadi
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Xuecong Li
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Francesco Simone Ruggeri
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Thomas E. Kodger
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Abstract
Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.
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Affiliation(s)
| | - Natalia Szulc
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland
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Particles in Biopharmaceutical Formulations, Part 2: An Update on Analytical Techniques and Applications for Therapeutic Proteins, Viruses, Vaccines and Cells. J Pharm Sci 2021; 111:933-950. [PMID: 34919969 DOI: 10.1016/j.xphs.2021.12.011] [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: 12/07/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022]
Abstract
Particles in biopharmaceutical formulations remain a hot topic in drug product development. With new product classes emerging it is crucial to discriminate particulate active pharmaceutical ingredients from particulate impurities. Technical improvements, new analytical developments and emerging tools (e.g., machine learning tools) increase the amount of information generated for particles. For a proper interpretation and judgment of the generated data a thorough understanding of the measurement principle, suitable application fields and potential limitations and pitfalls is required. Our review provides a comprehensive overview of novel particle analysis techniques emerging in the last decade for particulate impurities in therapeutic protein formulations (protein-related, excipient-related and primary packaging material-related), as well as particulate biopharmaceutical formulations (virus particles, virus-like particles, lipid nanoparticles and cell-based medicinal products). In addition, we review the literature on applications, describe specific analytical approaches and illustrate advantages and drawbacks of currently available techniques for particulate biopharmaceutical formulations.
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Matuszyk MM, Garwood CJ, Ferraiuolo L, Simpson JE, Staniforth RA, Wharton SB. Biological and methodological complexities of beta-amyloid peptide: Implications for Alzheimer's disease research. J Neurochem 2021; 160:434-453. [PMID: 34767256 DOI: 10.1111/jnc.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023]
Abstract
Although controversial, the amyloid cascade hypothesis remains central to the Alzheimer's disease (AD) field and posits amyloid-beta (Aβ) as the central factor initiating disease onset. In recent years, there has been an increase in emphasis on studying the role of low molecular weight aggregates, such as oligomers, which are suggested to be more neurotoxic than fibrillary Aβ. Other Aβ isoforms, such as truncated Aβ, have also been implicated in disease. However, developing a clear understanding of AD pathogenesis has been hampered by the complexity of Aβ biochemistry in vitro and in vivo. This review explores factors contributing to the lack of consistency in experimental approaches taken to model Aβ aggregation and toxicity and provides an overview of the different techniques available to analyse Aβ, such as electron and atomic force microscopy, nuclear magnetic resonance spectroscopy, dye-based assays, size exclusion chromatography, mass spectrometry and SDS-PAGE. The review also explores how different types of Aβ can influence Aβ aggregation and toxicity, leading to variation in experimental outcomes, further highlighting the need for standardisation in Aβ preparations and methods used in current research.
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Affiliation(s)
- Martyna M Matuszyk
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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47
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Integration of Fluorescent, NV-Rich Nanodiamond Particles with AFM Cantilevers by Focused Ion Beam for Hybrid Optical and Micromechanical Devices. COATINGS 2021. [DOI: 10.3390/coatings11111332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this paper, a novel fabrication technology of atomic force microscopy (AFM) probes integrating cantilever tips with an NV-rich diamond particle is presented. Nanomanipulation techniques combined with the focused electron beam-induced deposition (FEBID) procedure were applied to position the NV-rich diamond particle on an AFM cantilever tip. Ultrasonic treatment of nanodiamond suspension was applied to reduce the size of diamond particles for proper geometry and symmetry. The fabricated AFM probes were tested utilizing measurements of the electrical resistance at highly oriented pyrolytic graphite (HOPG) and compared with a standard AFM cantilever performance. The results showed novel perspectives arising from combining the functionalities of a scanning AFM with optically detected magnetic resonance (ODMR). In particular, it offers enhanced magnetometric sensitivity and the nanometric resolution.
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48
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Vieweg S, Mahul-Mellier AL, Ruggeri FS, Riguet N, DeGuire SM, Chiki A, Cendrowska U, Dietler G, Lashuel HA. The Nt17 Domain and its Helical Conformation Regulate the Aggregation, Cellular Properties and Neurotoxicity of Mutant Huntingtin Exon 1. J Mol Biol 2021; 433:167222. [PMID: 34492254 DOI: 10.1016/j.jmb.2021.167222] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022]
Abstract
Converging evidence points to the N-terminal domain comprising the first 17 amino acids of the Huntingtin protein (Nt17) as a key regulator of its aggregation, cellular properties and toxicity. In this study, we further investigated the interplay between Nt17 and the polyQ domain repeat length in regulating the aggregation and inclusion formation of exon 1 of the Huntingtin protein (Httex1). In addition, we investigated the effect of removing Nt17 or modulating its local structure on the membrane interactions, neuronal uptake, and toxicity of monomeric or fibrillar Httex1. Our results show that the polyQ and Nt17 domains synergistically modulate the aggregation propensity of Httex1 and that the Nt17 domain plays important roles in shaping the surface properties of mutant Httex1 fibrils and regulating their poly-Q-dependent growth, lateral association and neuronal uptake. Removal of Nt17 or disruption of its transient helical conformations slowed the aggregation of monomeric Httex1 in vitro, reduced inclusion formation in cells, enhanced the neuronal uptake and nuclear accumulation of monomeric Httex1 proteins, and was sufficient to prevent cell death induced by Httex1 72Q overexpression. Finally, we demonstrate that the uptake of Httex1 fibrils into primary neurons and the resulting toxicity are strongly influenced by mutations and phosphorylation events that influence the local helical propensity of Nt17. Altogether, our results demonstrate that the Nt17 domain serves as one of the key master regulators of Htt aggregation, internalization, and toxicity and represents an attractive target for inhibiting Htt aggregate formation, inclusion formation, and neuronal toxicity.
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Affiliation(s)
- Sophie Vieweg
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anne-Laure Mahul-Mellier
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Francesco S Ruggeri
- Laboratory of the Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Nathan Riguet
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sean M DeGuire
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Urszula Cendrowska
- Laboratory of the Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory of the Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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49
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Effects of high-pressure homogenization on structural and emulsifying properties of thermally soluble aggregated kidney bean (Phaseolus vulgaris L.) proteins. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106835] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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50
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van der Sleen LM, Tych KM. Bioconjugation Strategies for Connecting Proteins to DNA-Linkers for Single-Molecule Force-Based Experiments. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2424. [PMID: 34578744 PMCID: PMC8464727 DOI: 10.3390/nano11092424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/10/2023]
Abstract
The mechanical properties of proteins can be studied with single molecule force spectroscopy (SMFS) using optical tweezers, atomic force microscopy and magnetic tweezers. It is common to utilize a flexible linker between the protein and trapped probe to exclude short-range interactions in SMFS experiments. One of the most prevalent linkers is DNA due to its well-defined properties, although attachment strategies between the DNA linker and protein or probe may vary. We will therefore provide a general overview of the currently existing non-covalent and covalent bioconjugation strategies to site-specifically conjugate DNA-linkers to the protein of interest. In the search for a standardized conjugation strategy, considerations include their mechanical properties in the context of SMFS, feasibility of site-directed labeling, labeling efficiency, and costs.
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Affiliation(s)
| | - Katarzyna M. Tych
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands;
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