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Halder K, Sabnam K, Das A, Goswami DK, Dasgupta S. Thin Film Formation of HSA in the Presence of CTAB-Capped Gold Nanorods through Phase Separation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38952216 DOI: 10.1021/acs.langmuir.4c00694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Phase behavior in protein-nanoparticle systems in light of protein corona formation has been investigated. We report the formation of HSA thin films following the addition of a solid protein to a solution of CTAB-capped gold nanorods (AuNRs) via phase separation. The phase separation behavior was observed through UV-vis spectroscopy, turbidity assays, and DLS studies. UV-vis spectra for the protein-AuNR solution indicated a possible self-assembly formation by CTAB-HSA complexes and AuNR-HSA conjugates. The turbidity was found to increase linearly up to 30-50% v/v for each component. The growth phase slope is proportional to the concentration of the components, AuNRs, and HSA, with no lag phase. Dynamic light scattering (DLS) shows the formation of larger aggregates with time, implying a segregated phase of AuNR-HSA and a CTAB-HSA-AuNR network. ζ-potential values confirm surface modification, implying protein corona formation on nanorods. The thin films were also characterized using SEM, AFM, SAXS, XPS, FTIR, and TGA studies. SEM images show a smooth surface with a reduced number of pores, indicating the compactness of the deposited structure. AFM shows two different structural pattern formations with the deposition, indicating possible self-assembly of the protein-conjugated nanoparticles. FTIR studies indicate a change in the hydrogen bonding network and confirm the CTAB-HSA-AuNR complex network formation. The XPS studies indicate Au-S bond formation, along with Au-S-S-Au interactions. SAXS studies indicate the formation of aggregates (oligomers), as well as the presence of dominant attractive intermolecular interactions in the thin films.
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Affiliation(s)
- Krishna Halder
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Kabira Sabnam
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Abhirup Das
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Dipak K Goswami
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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2
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Nakada M, Kanda J, Uchiyama H, Matsumura K. Nanoscale intracellular ultrastructures affected by osmotic pressure using small-angle X-ray scattering. Biophys Chem 2024; 312:107287. [PMID: 38981174 DOI: 10.1016/j.bpc.2024.107287] [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: 05/12/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Although intracellular ultrastructures have typically been studied using microscopic techniques, it is difficult to observe ultrastructures at the submicron scale of living cells due to spatial resolution (fluorescence microscopy) or high vacuum environment (electron microscopy). We investigate the nanometer scale intracellular ultrastructures of living CHO cells in various osmolality using small-angle X-ray scattering (SAXS), and especially the structures of ribosomes, DNA double helix, and plasma membranes in-cell environment are observed. Ribosomes expand and contract in response to osmotic pressure, and the inter-ribosomal correlation occurs under isotonic and hyperosmolality. The DNA double helix is not dependent on the osmotic pressure. Under high osmotic pressure, the plasma membrane folds into form a multilamellar structure with a periodic length of about 6 nm. We also study the ultrastructural changes caused by formaldehyde fixation, freezing and heating.
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Affiliation(s)
- Masaru Nakada
- Toray Research Center, Inc., 2-11 Sonoyama 3-chome, Otsu, Shiga 520-8567, Japan.
| | - Junko Kanda
- Toray Research Center, Inc., 2-11 Sonoyama 3-chome, Otsu, Shiga 520-8567, Japan
| | - Hironobu Uchiyama
- Toray Research Center, Inc., 2-11 Sonoyama 3-chome, Otsu, Shiga 520-8567, Japan
| | - Kazuaki Matsumura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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3
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Han Q, Veríssimo NVP, Bryant SJ, Martin AV, Huang Y, Pereira JFB, Santos-Ebinuma VC, Zhai J, Bryant G, Drummond CJ, Greaves TL. Scattering approaches to unravel protein solution behaviors in ionic liquids and deep eutectic solvents: From basic principles to recent developments. Adv Colloid Interface Sci 2024; 331:103242. [PMID: 38964196 DOI: 10.1016/j.cis.2024.103242] [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: 10/22/2023] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
Proteins in ionic liquids (ILs) and deep eutectic solvents (DESs) have gained significant attention due to their potential applications in various fields, including biocatalysis, bioseparation, biomolecular delivery, and structural biology. Scattering approaches including dynamic light scattering (DLS) and small-angle X-ray and neutron scattering (SAXS and SANS) have been used to understand the solution behavior of proteins at the nanoscale and microscale. This review provides a thorough exploration of the application of these scattering techniques to elucidate protein properties in ILs and DESs. Specifically, the review begins with the theoretical foundations of the relevant scattering approaches and describes the essential solvent properties of ILs and DESs linked to scattering such as refractive index, scattering length density, ion-pairs, liquid nanostructure, solvent aggregation, and specific ion effects. Next, a detailed introduction is provided on protein properties such as type, concentration, size, flexibility and structure as observed through scattering methodologies. This is followed by a review of the literature on the use of scattering for proteins in ILs and DESs. It is highlighted that enhanced data analysis and modeling tools are necessary for assessing protein flexibility and structure, and for understanding protein hydration, aggregation and specific ion effects. It is also noted that complementary approaches are recommended for comprehensively understanding the behavior of proteins in solution due to the complex interplay of factors, including ion-binding, dynamic hydration, intermolecular interactions, and specific ion effects. Finally, the challenges and potential research directions for this field are proposed, including experimental design, data analysis approaches, and supporting methods to obtain fundamental understandings of complex protein behavior and protein systems in solution. We envisage that this review will support further studies of protein interface science, and in particular studies on solvent and ion effects on proteins.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Nathalia V P Veríssimo
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto 14040-020, Brazil
| | - Saffron J Bryant
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Andrew V Martin
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Yuhong Huang
- Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Jorge F B Pereira
- Univ Coimbra, CERES, Department of Chemical Engineering, Pólo II - Pinhal de Marrocos, Coimbra 3030-790, Portugal
| | - Valéria C Santos-Ebinuma
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto 14040-020, Brazil
| | - Jiali Zhai
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Gary Bryant
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
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4
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Zhang J, Song P, Zhu Z, Li Y, Liu G, Henderson MJ, Li J, Wang W, Tian Q, Li N. Evaporation-induced self-assembly of Janus pyramid molecules from fractal network to core-shell nanoclusters evidenced by small-angle X-ray scattering. J Colloid Interface Sci 2024; 674:437-444. [PMID: 38941936 DOI: 10.1016/j.jcis.2024.06.156] [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: 03/27/2024] [Revised: 06/13/2024] [Accepted: 06/22/2024] [Indexed: 06/30/2024]
Abstract
Self-assembly of nanoclusters (NCs) is an effective synthetic method for preparing functionalized nanomaterials. However, the assembly process and mechanisms in solutions still remain ambiguous owing to the limited strategies to monitor intermediate assembled states. Herein, the self-assembly process of amphiphilic molecule 4POSS-DL-POM (consisting of four polyhedral oligomeric silsesquioxanes, a dendritic linker, and one polyoxometalate) by evaporation of acetone in a mixed acetone/n-decane solution is monitored by time-resolved synchrotron small-angle X-ray scattering (SAXS). Scattering data assessments, including Kratky analysis, pair distance distribution function, and model fitting, track the self-assembly process of 4POSS-DL-POM from a fractal network to compact NCs, then to core-shell NCs, and finally to superlattice structure. The calculated average aggregation number of a core-shell NC is 11 according to the parameters obtained from core-shell model fitting, in agreement with electron microscopy. The fundamental understanding of the self-assembly dynamics from heterocluster into NCs provides principles to control building block shape and guide target aggregation, which can further promote the design and construction of highly ordered cluster-assembled functional nanomaterials.
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Affiliation(s)
- Jianqiao Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Panqi Song
- Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai 201210, China
| | - Zhongjie Zhu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai 201210, China
| | - Yiwen Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai 201210, China
| | - Guangfeng Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai 201210, China
| | - Mark Julian Henderson
- State Key Laboratory of Environment-friendly Energy Materials, Southwest University of Science and Technology, Mianyang 621010, China
| | - Jixiang Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Centre for Synthetic Soft Materials, Key Laboratory of Functional Polymer Materials of Ministry of Education and Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Qiang Tian
- State Key Laboratory of Environment-friendly Energy Materials, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Na Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai 201210, China.
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5
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Ren H, Chen H, Kang Y, Liu W, Liu Y, Tao F, Miao S, Zhang Y, Liu Q, Dong M, Liu Y, Liu B, Yang P. Non-fibril amyloid aggregation at the air/water interface: self-adaptive pathway resulting in a 2D Janus nanofilm. Chem Sci 2024; 15:8946-8958. [PMID: 38873054 PMCID: PMC11168098 DOI: 10.1039/d4sc00560k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/27/2024] [Indexed: 06/15/2024] Open
Abstract
The amyloid states of proteins are implicated in several neurodegenerative diseases and bioadhesion processes. However, the classical amyloid fibrillization mechanism fails to adequately explain the formation of polymorphic aggregates and their adhesion to various surfaces. Herein, we report a non-fibril amyloid aggregation pathway, with disulfide-bond-reduced lysozyme (R-Lyz) as a model protein under quasi-physiological conditions. Very different from classical fibrillization, this pathway begins with the air-water interface (AWI) accelerated oligomerization of unfolded full-length protein, resulting in unique plate-like oligomers with self-adaptive ability, which can adjust their conformations to match various interfaces such as the asymmetric AWI and amyloid-protein film surface. The pathway enables a stepwise packing of the plate-like oligomers into a 2D Janus nanofilm, exhibiting a divergent distribution of hydrophilic/hydrophobic residues on opposite sides of the nanofilm. The resulting Janus nanofilm possesses a top-level Young's modulus (8.3 ± 0.6 GPa) among amyloid-based materials and exhibits adhesive strength two times higher (145 ± 81 kPa) than that of barnacle cement. Furthermore, we found that such an interface-directed pathway exists in several amyloidogenic proteins with a similar self-adaptive 2D-aggregation process, including bovine serum albumin, insulin, fibrinogen, hemoglobin, lactoferrin, and ovalbumin. Thus, our findings on the non-fibril self-adaptive mechanism for amyloid aggregation may shed light on polymorphic amyloid assembly and their adhesions through an alternative pathway.
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Affiliation(s)
- Hao Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Huan Chen
- First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University Xi'an 710061 China
| | - Yu Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 China
| | - Wei Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Yongchun Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Fei Tao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Shuting Miao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Yingying Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Qian Liu
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus C Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Aarhus C Denmark
| | - Yonggang Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 China
| | - Bing Liu
- First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University Xi'an 710061 China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an Key Laboratory of Polymeric Soft Matter, International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
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6
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Chen LX, Yano J. Deciphering Photoinduced Catalytic Reaction Mechanisms in Natural and Artificial Photosynthetic Systems on Multiple Temporal and Spatial Scales Using X-ray Probes. Chem Rev 2024; 124:5421-5469. [PMID: 38663009 DOI: 10.1021/acs.chemrev.3c00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Utilization of renewable energies for catalytically generating value-added chemicals is highly desirable in this era of rising energy demands and climate change impacts. Artificial photosynthetic systems or photocatalysts utilize light to convert abundant CO2, H2O, and O2 to fuels, such as carbohydrates and hydrogen, thus converting light energy to storable chemical resources. The emergence of intense X-ray pulses from synchrotrons, ultrafast X-ray pulses from X-ray free electron lasers, and table-top laser-driven sources over the past decades opens new frontiers in deciphering photoinduced catalytic reaction mechanisms on the multiple temporal and spatial scales. Operando X-ray spectroscopic methods offer a new set of electronic transitions in probing the oxidation states, coordinating geometry, and spin states of the metal catalytic center and photosensitizers with unprecedented energy and time resolution. Operando X-ray scattering methods enable previously elusive reaction steps to be characterized on different length scales and time scales. The methodological progress and their application examples collected in this review will offer a glimpse into the accomplishments and current state in deciphering reaction mechanisms for both natural and synthetic systems. Looking forward, there are still many challenges and opportunities at the frontier of catalytic research that will require further advancement of the characterization techniques.
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Affiliation(s)
- Lin X Chen
- Chemical Science and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Junko Yano
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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7
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Buckland B, Sanyal G, Ranheim T, Pollard D, Searles JA, Behrens S, Pluschkell S, Josefsberg J, Roberts CJ. Vaccine process technology-A decade of progress. Biotechnol Bioeng 2024. [PMID: 38711222 DOI: 10.1002/bit.28703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 05/08/2024]
Abstract
In the past decade, new approaches to the discovery and development of vaccines have transformed the field. Advances during the COVID-19 pandemic allowed the production of billions of vaccine doses per year using novel platforms such as messenger RNA and viral vectors. Improvements in the analytical toolbox, equipment, and bioprocess technology have made it possible to achieve both unprecedented speed in vaccine development and scale of vaccine manufacturing. Macromolecular structure-function characterization technologies, combined with improved modeling and data analysis, enable quantitative evaluation of vaccine formulations at single-particle resolution and guided design of vaccine drug substances and drug products. These advances play a major role in precise assessment of critical quality attributes of vaccines delivered by newer platforms. Innovations in label-free and immunoassay technologies aid in the characterization of antigenic sites and the development of robust in vitro potency assays. These methods, along with molecular techniques such as next-generation sequencing, will accelerate characterization and release of vaccines delivered by all platforms. Process analytical technologies for real-time monitoring and optimization of process steps enable the implementation of quality-by-design principles and faster release of vaccine products. In the next decade, the field of vaccine discovery and development will continue to advance, bringing together new technologies, methods, and platforms to improve human health.
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Affiliation(s)
- Barry Buckland
- National Institute for Innovation in Manufacturing Biopharmaceuticals, University of Delaware, Newark, Delaware, USA
| | - Gautam Sanyal
- Vaccine Analytics, LLC, Kendall Park, New Jersey, USA
| | - Todd Ranheim
- Advanced Analytics Core, Resilience, Chapel Hill, North Carolina, USA
| | - David Pollard
- Sartorius, Corporate Research, Marlborough, Massachusetts, USA
| | | | - Sue Behrens
- Engineering and Biopharmaceutical Processing, Keck Graduate Institute, Claremont, California, USA
| | - Stefanie Pluschkell
- National Institute for Innovation in Manufacturing Biopharmaceuticals, University of Delaware, Newark, Delaware, USA
| | - Jessica Josefsberg
- Merck & Co., Inc., Process Research & Development, Rahway, New Jersey, USA
| | - Christopher J Roberts
- National Institute for Innovation in Manufacturing Biopharmaceuticals, University of Delaware, Newark, Delaware, USA
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8
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Li L, Wang J, Zhong X, Jiang Y, Pei G, Yang X, Zhang K, Shen S, Jin X, Sun G, Su C, Chen S, Yin H. ADP-Hep-Induced Liquid Phase Condensation of TIFA-TRAF6 Activates ALPK1/TIFA-Dependent Innate Immune Responses. RESEARCH (WASHINGTON, D.C.) 2024; 7:0315. [PMID: 38357697 PMCID: PMC10865109 DOI: 10.34133/research.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
The ALPK1 (alpha-kinase 1)-TIFA (TRAF-interacting protein with fork head-associated domain)-TRAF6 signaling pathway plays a pivotal role in regulating inflammatory processes, with TIFA and TRAF6 serving as key molecules in this cascade. Despite its significance, the functional mechanism of TIFA-TRAF6 remains incompletely understood. In this study, we unveil that TIFA undergoes liquid-liquid phase separation (LLPS) induced by ALPK1 in response to adenosine diphosphate (ADP)-β-D-manno-heptose (ADP-Hep) recognition. The phase separation of TIFA is primarily driven by ALPK1, the pT9-FHA domain, and the intrinsically disordered region segment. Simultaneously, TRAF6 exhibits phase separation during ADP-Hep-induced inflammation, a phenomenon observed consistently across various inflammatory signal pathways. Moreover, TRAF6 is recruited within the TIFA condensates, facilitating lysine (K) 63-linked polyubiquitin chain synthesis. The subsequent recruitment, enrichment, and activation of downstream effectors within these condensates contribute to robust inflammatory signal transduction. Utilizing a novel chemical probe (compound 22), our analysis demonstrates that the activation of the ALPK1-TIFA-TRAF6 signaling pathway in response to small molecules necessitates the phase separation of TIFA. In summary, our findings reveal TIFA as a sensor for upstream signals, initiating the LLPS of itself and downstream proteins. This process results in the formation of membraneless condensates within the ALPK1-TIFA-TRAF6 pathway, suggesting potential applications in therapeutic biotechnology development.
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Affiliation(s)
- Liping Li
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology,
Peking University, Beijing, China
| | - Xincheng Zhong
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yaoyao Jiang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- School of Life Sciences,
Tsinghua University, Beijing, 100084, China
| | - Xikang Yang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Siqi Shen
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Xue Jin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaoge Sun
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Chaofei Su
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Shuzhen Chen
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hang Yin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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9
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Ujfalusi-Pozsonyi K, Bódis E, Nyitrai M, Kengyel A, Telek E, Pécsi I, Fekete Z, Varnyuné Kis-Bicskei N, Mas C, Moussaoui D, Pernot P, Tully MD, Weik M, Schirò G, Kapetanaki SM, Lukács A. ATP-dependent conformational dynamics in a photoactivated adenylate cyclase revealed by fluorescence spectroscopy and small-angle X-ray scattering. Commun Biol 2024; 7:147. [PMID: 38307988 PMCID: PMC10837130 DOI: 10.1038/s42003-024-05842-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Structural insights into the photoactivated adenylate cyclases can be used to develop new ways of controlling cellular cyclic adenosine monophosphate (cAMP) levels for optogenetic and other applications. In this work, we use an integrative approach that combines biophysical and structural biology methods to provide insight on the interaction of adenosine triphosphate (ATP) with the dark-adapted state of the photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata (OaPAC). A moderate affinity of the nucleotide for the enzyme was calculated and the thermodynamic parameters of the interaction have been obtained. Stopped-flow fluorescence spectroscopy and small-angle solution scattering have revealed significant conformational changes in the enzyme, presumably in the adenylate cyclase (AC) domain during the allosteric mechanism of ATP binding to OaPAC with small and large-scale movements observed to the best of our knowledge for the first time in the enzyme in solution upon ATP binding. These results are in line with previously reported drastic conformational changes taking place in several class III AC domains upon nucleotide binding.
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Affiliation(s)
- K Ujfalusi-Pozsonyi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Bódis
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - M Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - A Kengyel
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Telek
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - I Pécsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Z Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | | | - C Mas
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, ISBG, F-38000, Grenoble, France
| | - D Moussaoui
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - P Pernot
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M D Tully
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M Weik
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - G Schirò
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - S M Kapetanaki
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
| | - A Lukács
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
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10
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Prokhorov NS, Davis C, Maruthi K, Yang Q, Sherman M, Woodson M, White M, Miller LM, Jarrold M, Catalano C, Morais M. Biophysical and structural characterization of a multifunctional viral genome packaging motor. Nucleic Acids Res 2024; 52:831-843. [PMID: 38084901 PMCID: PMC10810279 DOI: 10.1093/nar/gkad1135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 01/26/2024] Open
Abstract
The large dsDNA viruses replicate their DNA as concatemers consisting of multiple covalently linked genomes. Genome packaging is catalyzed by a terminase enzyme that excises individual genomes from concatemers and packages them into preassembled procapsids. These disparate tasks are catalyzed by terminase alternating between two distinct states-a stable nuclease that excises individual genomes and a dynamic motor that translocates DNA into the procapsid. It was proposed that bacteriophage λ terminase assembles as an anti-parallel dimer-of-dimers nuclease complex at the packaging initiation site. In contrast, all characterized packaging motors are composed of five terminase subunits bound to the procapsid in a parallel orientation. Here, we describe biophysical and structural characterization of the λ holoenzyme complex assembled in solution. Analytical ultracentrifugation, small angle X-ray scattering, and native mass spectrometry indicate that 5 subunits assemble a cone-shaped terminase complex. Classification of cryoEM images reveals starfish-like rings with skewed pentameric symmetry and one special subunit. We propose a model wherein nuclease domains of two subunits alternate between a dimeric head-to-head arrangement for genome maturation and a fully parallel arrangement during genome packaging. Given that genome packaging is strongly conserved in both prokaryotic and eukaryotic viruses, the results have broad biological implications.
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Affiliation(s)
- Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Christal R Davis
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kashyap Maruthi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Qin Yang
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Michael Woodson
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Lohra M Miller
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carlos E Catalano
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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11
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Britton D, Christians LF, Liu C, Legocki J, Xiao Y, Meleties M, Yang L, Cammer M, Jia S, Zhang Z, Mahmoudinobar F, Kowalski Z, Renfrew PD, Bonneau R, Pochan DJ, Pak AJ, Montclare JK. Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure. Biomacromolecules 2024; 25:258-271. [PMID: 38110299 PMCID: PMC10777397 DOI: 10.1021/acs.biomac.3c00968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled-coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled-coil hydrogel design. Using Rosetta energy scores and Poisson-Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled-coil proteins while simultaneously exploring five new coiled-coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled-coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled-coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled-coil fiber formation.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Luc F. Christians
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Chengliang Liu
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Yingxin Xiao
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Michael Meleties
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Lin Yang
- National
Synchrotron Light Source-II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Michael Cammer
- Microscopy
Laboratory, New York University Langone
Health, New York, New York 10016, United States
| | - Sihan Jia
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Zihan Zhang
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Farbod Mahmoudinobar
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center for
Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, United States
| | - Zuzanna Kowalski
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - P. Douglas Renfrew
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Richard Bonneau
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center
for Genomics and Systems Biology, New York
University, New York, New York 10003, United States
- Courant
Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10009, United States
| | - Darrin J. Pochan
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Alexander J. Pak
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative
Biosciences and Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomedical Engineering, New
York University, New York, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department
of Radiology, New York University School
of Medicine, New York, New York 10016, United States
- Department of Biomaterials, New York University
College of Dentistry, New York, New York 10010, United States
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12
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Kotev M, Diaz Gonzalez C. Molecular Dynamics and Other HPC Simulations for Drug Discovery. Methods Mol Biol 2024; 2716:265-291. [PMID: 37702944 DOI: 10.1007/978-1-0716-3449-3_12] [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: 09/14/2023]
Abstract
High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical systems with high precision in a short time, thanks to the use of sophisticated algorithms. It promotes the advancement of knowledge in fields that are inaccessible or difficult to access through experimentation and it contributes to accelerating the discovery of drugs for unmet medical needs while reducing costs. Herein, we report how computational performance has evolved over the past years, and then we detail three domains where HPC is essential. Molecular dynamics (MD) is commonly used to explore the flexibility of proteins, thus generating a better understanding of different possible approaches to modulate their activity. Modeling and simulation of biopolymer complexes enables the study of protein-protein interactions (PPI) in healthy and disease states, thus helping the identification of targets of pharmacological interest. Virtual screening (VS) also benefits from HPC to predict in a short time, among millions or billions of virtual chemical compounds, the best potential ligands that will be tested in relevant assays to start a rational drug design process.
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Affiliation(s)
- Martin Kotev
- Evotec SE, Integrated Drug Discovery, Molecular Architects, Campus Curie, Toulouse, France
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13
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Sen S, Sharma P, Pal VK, Roy S. Designing Cardin-Motif Peptide and Heparin-Based Multicomponent Advanced Bioactive Hydrogel Scaffolds to Control Cellular Behavior. Biomacromolecules 2023; 24:4923-4938. [PMID: 37909341 DOI: 10.1021/acs.biomac.3c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Recently, peptide and sugar-based multicomponent systems have gained much interest in attaining the sophisticated structure and biofunctional complexity of the extracellular matrix (ECM). To this direction, we have designed for the first time a biologically relevant minimalist Cardin-motif peptide capable of binding ECM-derived glycosaminoglycans. Herein, we explored Cardin-motif peptide and heparin-based biomolecular matrix by employing simple noncovalent interactions at the molecular level. Interestingly, this peptide was inadequate to induce hydrogelation at ambient pH due to the presence of basic amino acids. However, addition of heparin successfully triggered its gelation at physiological pH following favorable electrostatic interactions with heparin. Importantly, the newly developed scaffolds displayed tunable nanofibrous morphology and superior mechanical properties as controlled simply by the differential mixing ratio of both biomolecular entities. Additionally, these composite scaffolds could closely mimic the complexity of ECM as they demonstrated superior biocompatibility and enhanced growth and proliferation of neural cells as compared to the peptide scaffold.
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Affiliation(s)
- Sourav Sen
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, 140306 Mohali, Punjab India
| | - Pooja Sharma
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, 140306 Mohali, Punjab India
| | - Vijay Kumar Pal
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, 140306 Mohali, Punjab India
| | - Sangita Roy
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, 140306 Mohali, Punjab India
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14
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Cho Y, Choi YJ, Kaser SJ, Meacham R, Christoff-Tempesta T, Wu S, Zuo X, Ortony JH. Geometric Transformations Afforded by Rotational Freedom in Aramid Amphiphile Nanostructures. J Am Chem Soc 2023; 145:22954-22963. [PMID: 37819710 DOI: 10.1021/jacs.3c04598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Molecular self-assembly in water leads to nanostructure geometries that can be tuned owing to the highly dynamic nature of amphiphiles. There is growing interest in strongly interacting amphiphiles with suppressed dynamics, as they exhibit ultrastability in extreme environments. However, such amphiphiles tend to assume a limited range of geometries upon self-assembly due to the specific spatial packing induced by their strong intermolecular interactions. To overcome this limitation while maintaining structural robustness, we incorporate rotational freedom into the aramid amphiphile molecular design by introducing a diacetylene moiety between two aramid units, resulting in diacetylene aramid amphiphiles (D-AAs). This design strategy enables rotations along the carbon-carbon sp hybridized bonds of an otherwise fixed aramid domain. We show that varying concentrations and equilibration temperatures of D-AA in water lead to self-assembly into four different nanoribbon geometries: short, extended, helical, and twisted nanoribbons, all while maintaining robust structure with thermodynamic stability. We use advanced microscopy, X-ray scattering, spectroscopic techniques, and two-dimensional (2D) NMR to understand the relationship between conformational freedom within strongly interacting amphiphiles and their self-assembly pathways.
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Affiliation(s)
- Yukio Cho
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yu-Jin Choi
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Samuel J Kaser
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rebecca Meacham
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ty Christoff-Tempesta
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Siyu Wu
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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15
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Motycka B, Csarman F, Tscheliessnig R, Hammel M, Ludwig R. Resolving domain positions of cellobiose dehydrogenase by small angle X-ray scattering. FEBS J 2023; 290:4726-4743. [PMID: 37287434 PMCID: PMC10592539 DOI: 10.1111/febs.16885] [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] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023]
Abstract
The interdomain electron transfer (IET) between the catalytic flavodehydrogenase domain and the electron-transferring cytochrome domain of cellobiose dehydrogenase (CDH) plays an essential role in biocatalysis, biosensors and biofuel cells, as well as in its natural function as an auxiliary enzyme of lytic polysaccharide monooxygenase. We investigated the mobility of the cytochrome and dehydrogenase domains of CDH, which is hypothesised to limit IET in solution by small angle X-ray scattering (SAXS). CDH from Myriococcum thermophilum (syn. Crassicarpon hotsonii, syn. Thermothelomyces myriococcoides) was probed by SAXS to study the CDH mobility at different pH and in the presence of divalent cations. By comparison of the experimental SAXS data, using pair-distance distribution functions and Kratky plots, we show an increase in CDH mobility at higher pH, indicating alterations of domain mobility. To further visualise CDH movement in solution, we performed SAXS-based multistate modelling. Glycan structures present on CDH partially masked the resulting SAXS shapes, we diminished these effects by deglycosylation and studied the effect of glycoforms by modelling. The modelling shows that with increasing pH, the cytochrome domain adopts a more flexible state with significant separation from the dehydrogenase domain. On the contrary, the presence of calcium ions decreases the mobility of the cytochrome domain. Experimental SAXS data, multistate modelling and previously reported kinetic data show how pH and divalent ions impact the closed state necessary for the IET governed by the movement of the CDH cytochrome domain.
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Affiliation(s)
- Bettina Motycka
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Technology, Muthgasse 18, 1190 Vienna, Austria
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190 Vienna, Austria
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkely, California, USA
| | - Florian Csarman
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Technology, Muthgasse 18, 1190 Vienna, Austria
| | - Rupert Tscheliessnig
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190 Vienna, Austria
- Division of Biophysics, Gottfried-Schatz-Research-Center, Medical University of Graz, Graz, Austria
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkely, California, USA
| | - Roland Ludwig
- University of Natural Resources and Life Sciences, Vienna, Department of Food Science and Technology, Institute of Food Technology, Muthgasse 18, 1190 Vienna, Austria
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16
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Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [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: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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17
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Pesce F, Lindorff-Larsen K. Combining Experiments and Simulations to Examine the Temperature-Dependent Behavior of a Disordered Protein. J Phys Chem B 2023. [PMID: 37433228 DOI: 10.1021/acs.jpcb.3c01862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Intrinsically disordered proteins are a class of proteins that lack stable folded conformations and instead adopt a range of conformations that determine their biochemical functions. The temperature-dependent behavior of such disordered proteins is complex and can vary depending on the specific protein and environment. Here, we have used molecular dynamics simulations and previously published experimental data to investigate the temperature-dependent behavior of histatin 5, a 24-residue-long polypeptide. We examined the hypothesis that histatin 5 undergoes a loss of polyproline II (PPII) structure with increasing temperature, leading to more compact conformations. We found that the conformational ensembles generated by the simulations generally agree with small-angle X-ray scattering data for histatin 5, but show some discrepancies with the hydrodynamic radius as probed by pulsed-field gradient NMR spectroscopy, and with the secondary structure information derived from circular dichroism. We attempted to reconcile these differences by reweighting the conformational ensembles against the scattering and NMR data. By doing so, we were in part able to capture the temperature-dependent behavior of histatin 5 and to link the observed decrease in hydrodynamic radius with increasing temperature to a loss of PPII structure. We were, however, unable to achieve agreement with both the scattering and NMR data within experimental errors. We discuss different possible reasons for this including inaccuracies in the force field, differences in conditions of the NMR and scattering experiments, and issues related to the calculation of the hydrodynamic radius from conformational ensembles. Our study highlights the importance of integrating multiple types of experimental data when modeling conformational ensembles of disordered proteins and how environmental factors such as the temperature influence them.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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18
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Lourenço TC, de Mello LR, Icimoto MY, Bicev RN, Hamley IW, Castelletto V, Nakaie CR, da Silva ER. DNA-templated self-assembly of bradykinin into bioactive nanofibrils. SOFT MATTER 2023. [PMID: 37334565 DOI: 10.1039/d3sm00431g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Bradykinin (BK) is a peptide hormone that plays a crucial role in blood pressure control, regulates inflammation in the human body, and has recently been implicated in the pathophysiology of COVID-19. In this study, we report a strategy for fabricating highly ordered 1D nanostructures of BK using DNA fragments as a template for self-assembly. We have combined synchrotron small-angle X-ray scattering and high-resolution microscopy to provide insights into the nanoscale structure of BK-DNA complexes, unveiling the formation of ordered nanofibrils. Fluorescence assays hint that BK is more efficient at displacing minor-groove binders in comparison with base-intercalant dyes, thus, suggesting that interaction with DNA strands is mediated by electrostatic attraction between cationic groups at BK and the high negative electron density of minor-grooves. Our data also revealed an intriguing finding that BK-DNA complexes can induce a limited uptake of nucleotides by HEK-293t cells, which is a feature that has not been previously reported for BK. Moreover, we observed that the complexes retained the native bioactivity of BK, including the ability to modulate Ca2+ response into endothelial HUVEC cells. Overall, the findings presented here demonstrate a promising strategy for the fabrication of fibrillar structures of BK using DNA as a template, which keep bioactivity features of the native peptide and may have implications in the development of nanotherapeutics for hypertension and related disorders.
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Affiliation(s)
- Thiago C Lourenço
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04062-000, Brazil.
| | - Lucas R de Mello
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04062-000, Brazil.
| | - Marcelo Y Icimoto
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04062-000, Brazil.
| | - Renata N Bicev
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04062-000, Brazil.
| | - Ian W Hamley
- Department of Chemistry, University of Reading, Reading RG6 6AD, UK
| | | | - Clovis R Nakaie
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04062-000, Brazil.
| | - Emerson R da Silva
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04062-000, Brazil.
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19
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Baer A, Hoffmann I, Mahmoudi N, Poulhazan A, Harrington MJ, Mayer G, Schmidt S, Schneck E. The Internal Structure of the Velvet Worm Projectile Slime: A Small-Angle Scattering Study. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300516. [PMID: 36828797 DOI: 10.1002/smll.202300516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/03/2023] [Indexed: 06/02/2023]
Abstract
For prey capture and defense, velvet worms eject an adhesive slime which has been established as a model system for recyclable complex liquids. Triggered by mechanical agitation, the liquid bio-adhesive rapidly transitions into solid fibers. In order to understand this mechanoresponsive behavior, here, the nanostructural organization of slime components are studied using small-angle scattering with neutrons and X-rays. The scattering intensities are successfully described with a three-component model accounting for proteins of two dominant molecular weight fractions and nanoscale globules. In contrast to the previous assumption that high molecular weight proteins-the presumed building blocks of the fiber core-are contained in the nanoglobules, it is found that the majority of slime proteins exist freely in solution. Only less than 10% of the slime proteins are contained in the nanoglobules, necessitating a reassessment of their function in fiber formation. Comparing scattering data of slime re-hydrated with light and heavy water reveals that the majority of lipids in slime are contained in the nanoglobules with homogeneous distribution. Vibrating mechanical impact under exclusion of air neither leads to formation of fibers nor alters the bulk structure of slime significantly, suggesting that interfacial phenomena and directional shearing are required for fiber formation.
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Affiliation(s)
- Alexander Baer
- Department of Zoology, Institute of Biology, University of Kassel, D-34132, Kassel, Germany
| | - Ingo Hoffmann
- Spectroscopy Group, Institut Laue-Langevin, 38000, Grenoble, France
| | - Najet Mahmoudi
- Small-Angle Neutron Scattering Group, ISIS Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Alexandre Poulhazan
- Department of Chemistry, University of Quebec at Montreal, Montreal, QC, H2X 2J6, Canada
| | | | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, D-34132, Kassel, Germany
| | - Stephan Schmidt
- Chemistry Department, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Emanuel Schneck
- Physics Department, Technische Universität Darmstadt, D-64289, Darmstadt, Germany
- Biomaterials Department, Max Planck Institute of Colloids and Interfaces, D-14476, Potsdam, Germany
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20
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Vermeire PJ, Lilina AV, Hashim HM, Dlabolová L, Fiala J, Beelen S, Kukačka Z, Harvey JN, Novák P, Strelkov SV. Molecular structure of soluble vimentin tetramers. Sci Rep 2023; 13:8841. [PMID: 37258554 DOI: 10.1038/s41598-023-34814-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Intermediate filaments (IFs) are essential constituents of the metazoan cytoskeleton. A vast family of cytoplasmic IF proteins are capable of self-assembly from soluble tetrameric species into typical 10-12 nm wide filaments. The primary structure of these proteins includes the signature central 'rod' domain of ~ 300 residues which forms a dimeric α-helical coiled coil composed of three segments (coil1A, coil1B and coil2) interconnected by non-helical, flexible linkers (L1 and L12). The rod is flanked by flexible terminal head and tail domains. At present, the molecular architecture of mature IFs is only poorly known, limiting our capacity to rationalize the effect of numerous disease-related mutations found in IF proteins. Here we addressed the molecular structure of soluble vimentin tetramers which are formed by two antiparallel, staggered dimers with coil1B domains aligned (A11 tetramers). By examining a series of progressive truncations, we show that the presence of the coil1A domain is essential for the tetramer formation. In addition, we employed a novel chemical cross-linking pipeline including isotope labelling to identify intra- and interdimeric cross-links within the tetramer. We conclude that the tetramer is synergistically stabilized by the interactions of the aligned coil1B domains, the interactions between coil1A and the N-terminal portion of coil2, and the electrostatic attraction between the oppositely charged head and rod domains. Our cross-linking data indicate that, starting with a straight A11 tetramer, flexibility of linkers L1 and L12 enables 'backfolding' of both the coil1A and coil2 domains onto the tetrameric core formed by the coil1B domains. Through additional small-angle X-ray scattering experiments we show that the elongated A11 tetramers dominate in low ionic strength solutions, while there is also a significant structural flexibility especially in the terminal domains.
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Affiliation(s)
| | | | - Hani M Hashim
- Laboratory for Biocrystallography, KU Leuven, 3000, Leuven, Belgium
- Department of Chemistry, KU Leuven, 3000, Leuven, Belgium
| | - Lada Dlabolová
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Jan Fiala
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Steven Beelen
- Laboratory for Biocrystallography, KU Leuven, 3000, Leuven, Belgium
| | - Zdeněk Kukačka
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | | | - Petr Novák
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, KU Leuven, 3000, Leuven, Belgium.
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21
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Han Q, El Mohamad M, Brown S, Zhai J, Rosado CJ, Shen Y, Blanch EW, Drummond CJ, Greaves TL. Small angle X-ray scattering investigation of ionic liquid effect on the aggregation behavior of globular proteins. J Colloid Interface Sci 2023; 648:376-388. [PMID: 37302221 DOI: 10.1016/j.jcis.2023.05.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Globular proteins are well-folded model proteins, where ions can substantially influence their structure and aggregation. Ionic liquids (ILs) are salts in the liquid state with versatile ion combinations. Understanding the IL effect on protein behavior remains a major challenge. Here, we employed small angle X-ray scattering to investigate the effect of aqueous ILs on the structure and aggregation of globular proteins, namely, hen egg white lysozyme (Lys), human lysozyme (HLys), myoglobin (Mb), β-lactoglobulin (βLg), trypsin (Tryp) and superfolder green fluorescent protein (sfGFP). The ILs contain ammonium-based cations paired with the mesylate, acetate or nitrate anion. Results showed that only Lys was monomeric, whereas the other proteins formed small or large aggregates in buffer. Solutions with over 17 mol% IL resulted in significant changes in the protein structure and aggregation. The Lys structure was expanded at 1 mol% but compact at 17 mol% with structural changes in loop regions. HLys formed small aggregates, with the IL effect similar to Lys. Mb and βLg mostly had distinct monomer and dimer distributions depending on IL type and IL concentration. Complex aggregation was noted for Tryp and sfGFP. While the anion had the largest ion effect, changing the cation also induced the structural expansion and protein aggregation.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Mohamad El Mohamad
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Stuart Brown
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Jiali Zhai
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Carlos J Rosado
- Department of Diabetes, Central Clinical School, Monash University, VIC 3004, Australia; Department of Biochemistry, Monash University, VIC 3800, Australia
| | - Yi Shen
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia; The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ewan W Blanch
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
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22
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Murty R, Bera MK, Walton IM, Whetzel C, Prausnitz MR, Walton KS. Interrogating Encapsulated Protein Structure within Metal-Organic Frameworks at Elevated Temperature. J Am Chem Soc 2023; 145:7323-7330. [PMID: 36961883 PMCID: PMC10080685 DOI: 10.1021/jacs.2c13525] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Encapsulating biomacromolecules within metal-organic frameworks (MOFs) can confer thermostability to entrapped guests. It has been hypothesized that the confinement of guest molecules within a rigid MOF scaffold results in heightened stability of the guests, but no direct evidence of this mechanism has been shown. Here, we present a novel analytical method using small-angle X-ray scattering (SAXS) to solve the structure of bovine serum albumin (BSA) while encapsulated within two zeolitic imidazolate frameworks (ZIF-67 and ZIF-8). Our approach comprises subtracting the scaled SAXS spectrum of the ZIF from that of the biocomposite BSA@ZIF to determine the radius of gyration of encapsulated BSA through Guinier, Kratky, and pair distance distribution function analyses. While native BSA exposed to 70 °C became denatured, in situ SAXS analysis showed that encapsulated BSA retained its size and folded state at 70 °C when encapsulated within a ZIF scaffold, suggesting that entrapment within MOF cavities inhibited protein unfolding and thus denaturation. This method of SAXS analysis not only provides insight into biomolecular stabilization in MOFs but may also offer a new approach to study the structure of other conformationally labile molecules in rigid matrices.
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Affiliation(s)
- Rohan Murty
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mrinal K Bera
- NSF's ChemMatCARS, Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Ian M Walton
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Christina Whetzel
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mark R Prausnitz
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Krista S Walton
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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23
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Hiew SH, Lu Y, Han H, Gonçalves RA, Alfarano SR, Mezzenga R, Parikh AN, Mu Y, Miserez A. Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations. J Am Chem Soc 2023; 145:3382-3393. [PMID: 36730942 DOI: 10.1021/jacs.2c09853] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.
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Affiliation(s)
- Shu Hui Hiew
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yang Lu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Hao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Rui A Gonçalves
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Serena Rosa Alfarano
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Atul N Parikh
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,Departments of Biomedical Engineering and Materials Science & Engineering, University of California, Davis, California 95616, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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24
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Dispersion Performances and Fluorescent Behaviors of Naphthalic Anhydride Doped in Poly(acrylic acid) Frameworks for pH-Sensitive Ibuprofen Delivery via Fractal Evolution. Polymers (Basel) 2023; 15:polym15030596. [PMID: 36771896 PMCID: PMC9921450 DOI: 10.3390/polym15030596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The pH-responsive fluorescent P(1,8-naphthalic anhydride (NA)-acrylic acid (AA)) matrix was successfully prepared by a doping method using poly(acrylic acid) (PAA) as a pH-sensitive polymer and NA as a fluorescent tracer. The fluorescent behaviors of the used NA dispersed in PAA frameworks were demonstrated based on fractal features combined with various characterizations, such as small-angle X-ray scattering (SAXS) patterns, photoluminescence (PL) spectra, scanning electron microscope (SEM) images, thermogravimetry (TG) profiles, Fourier transform infrared (FT-IR) spectroscopy, and time-resolved decays. The effects of NA-doping on the representative fluorescent P(NA-AA) were investigated, in which the fluorescent performance of the doped NA was emphasized. The results indicated that aggregated clusters of the doped NA were gradually serious with an increase in NA doping amount or extension of NA doping time, accompanied by an increase in mass fractal dimension (Dm) values. Meanwhile, the doped NA presented stable fluorescent properties during the swelling-shrinking process of PAA. Ibuprofen (IBU) was used as a model drug, and fractal evolutions of the obtained P(NA-AA) along with the drug loading and releasing behaviors were evaluated via SAXS patterns, in which the drug-loaded P(NA-AA) presented surface fractal (Ds) characteristics, while the Dm value varied from 2.94 to 2.58 during sustained drug-release in pH 2.0, indicating occurrences of its structural transformation from dense to loose with extension of IBU-releasing time. Finally, the cytotoxicity and cellular uptake behaviors of the obtained P(NA-AA) were preliminarily explored. These demonstrations revealed that the resultant P(NA-AA) should be a potential intelligent-responsive drug carrier for targeted delivery.
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25
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Pesce F, Newcombe EA, Seiffert P, Tranchant EE, Olsen JG, Grace CR, Kragelund BB, Lindorff-Larsen K. Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins. Biophys J 2023; 122:310-321. [PMID: 36518077 PMCID: PMC9892621 DOI: 10.1016/j.bpj.2022.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Diffusion measurements by pulsed-field gradient NMR and fluorescence correlation spectroscopy can be used to probe the hydrodynamic radius of proteins, which contains information about the overall dimension of a protein in solution. The comparison of this value with structural models of intrinsically disordered proteins is nonetheless impaired by the uncertainty of the accuracy of the methods for computing the hydrodynamic radius from atomic coordinates. To tackle this issue, we here build conformational ensembles of 11 intrinsically disordered proteins that we ensure are in agreement with measurements of compaction by small-angle x-ray scattering. We then use these ensembles to identify the forward model that more closely fits the radii derived from pulsed-field gradient NMR diffusion experiments. Of the models we examined, we find that the Kirkwood-Riseman equation provides the best description of the hydrodynamic radius probed by pulsed-field gradient NMR experiments. While some minor discrepancies remain, our results enable better use of measurements of the hydrodynamic radius in integrative modeling and for force field benchmarking and parameterization.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Estella A Newcombe
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Pernille Seiffert
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Emil E Tranchant
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christy R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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26
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Sarker M, Watts S, Salentinig S, Lim S. Protein Cage-Stabilized Emulsions: Formulation and Characterization. Methods Mol Biol 2023; 2671:219-239. [PMID: 37308648 DOI: 10.1007/978-1-0716-3222-2_13] [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: 06/14/2023]
Abstract
The formulation of Pickering emulsions using protein cages is gaining interest for applications in molecular delivery. Despite the growing interest, methods to investigate the at the liquid-liquid interface are limited. This chapter describes standard methods to formulate and protocols to characterize protein cage-stabilized emulsions. The characterization methods are dynamic light scattering (DLS), intrinsic fluorescence spectroscopy (TF), circular dichroism (CD), and small angle X-ray scattering (SAXS). Combining these methods allows understanding of the protein cage nanostructure at the oil/water interface.
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Affiliation(s)
- Mridul Sarker
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Samuel Watts
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Department of Chemistry, University of Fribourg, Fribourg, Switzerland
| | - Stefan Salentinig
- Department of Chemistry, University of Fribourg, Fribourg, Switzerland.
| | - Sierin Lim
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore.
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27
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Li Y, Zhang C, Liang Y, Wang L, Xiong W. Solubility and conformational characterization of rice glutelin after high temperature treatment. Int J Biol Macromol 2022; 223:1720-1726. [PMID: 36252633 DOI: 10.1016/j.ijbiomac.2022.10.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/01/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
Enhancing the solubility of rice glutelin in neutral aqueous solution is the prerequisite for the development of rice protein drinks and ingredients. Herein, glutelin was first dissolved in an aqueous solution of pH 12, and then heated at 121 °C for 20 min. The results showed that the solubility of glutelin increased from 2.55 mg/mL to 20.7 mg/mL at pH 7. The size of glutelin aggregates at pH 7 decreased from 900 nm to 400 nm after high temperature treatment (HTT), which was confirmed by atomic force microscopy. The results of small angle X-ray scattering showed that HTT induced the conformational unfolding of glutelin, and the protein in the aggregate was rod like shape as well as the mean square rotation radius decreased from 64.9 to 54.8 Å. Furthermore, Raman spectrum results also agree with the unfolding of glutelin conformation, which was mainly reflected in the changes of tyrosine and tryptophan residues, as well as the decreasing of α-helix content and increasing of β-sheet content. After being freeze-dried, HTT glutelin has a re-solubilization capacity of 15.48 mg/mL in pH 7 aqueous solution, which was superior to that of spray dried glutelin powder (pH 7, 9.19 mg/mL).
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Affiliation(s)
- Ya Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Chunlan Zhang
- College of Food Science and Engineering, Tarim University, Alar, 843300, China
| | - Yuxing Liang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Lifeng Wang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Wenfei Xiong
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, 570228, China.
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28
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Deng N, Zuo X, Stack AG, Lee SS, Zhou Z, Weber J, Hu Y. Selenite and Selenate Sequestration during Coprecipitation with Barite: Insights from Mineralization Processes of Adsorption, Nucleation, and Growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15518-15527. [PMID: 36322394 DOI: 10.1021/acs.est.2c03292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Coprecipitation of selenium oxyanions with barite is a facile way to sequester Se in the environments. However, the chemical composition of Se-barite coprecipitates usually deviates from that predicted from thermodynamic calculations. This discrepancy was resolved by considering variations in nucleation and growth rates controlled by ion-mineral interactions, solubility, and interfacial energy. For homogeneous precipitation, ∼10% of sulfate, higher than thermodynamic predictions (<0.3%), was substituted by Se(IV) or Se(VI) oxyanion, which was attributed to adsorption-induced entrapment during crystal growth. For heterogeneous precipitation, thiol- and carboxylic-based organic films, utilized as model interfaces to mimic the natural organic-abundant environments, further enhanced the sequestration of Se(VI) oxyanions (up to 41-92%) with barite. Such enhancement was kinetically driven by increased nucleation rates of selenate-rich barite having a lower interfacial energy than pure barite. In contrast, only small amounts of Se(IV) oxyanions (∼1%) were detected in heterogeneous coprecipitates mainly due to a lower saturation index of BaSeO3 and deprotonation degree of Se(IV) oxyanion at pH 5.6. These roles of nanoscale mineralization mechanisms observed during composition selection of Se-barite could mark important steps toward the remediation of contaminants through coprecipitation.
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Affiliation(s)
- Ning Deng
- Department of Civil and Environmental Engineering, University of Houston, Houston, Texas77004, United States
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai200444, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - Andrew G Stack
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Sang Soo Lee
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - Zehao Zhou
- The Key Laboratory of Water and Sediment Sciences, College of Environmental Sciences and Engineering, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing100871, China
| | - Juliane Weber
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Yandi Hu
- Department of Civil and Environmental Engineering, University of Houston, Houston, Texas77004, United States
- The Key Laboratory of Water and Sediment Sciences, College of Environmental Sciences and Engineering, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing100871, China
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29
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Delhommel F, Martínez-Lumbreras S, Sattler M. Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes. Methods Enzymol 2022; 678:263-297. [PMID: 36641211 DOI: 10.1016/bs.mie.2022.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Understanding the structure and dynamics of biological macromolecules is essential to decipher the molecular mechanisms that underlie cellular functions. The description of structure and conformational dynamics often requires the integration of complementary techniques. In this review, we highlight the utility of combining nuclear magnetic resonance (NMR) spectroscopy with small angle scattering (SAS) to characterize these challenging biomolecular systems. NMR can assess the structure and conformational dynamics of multidomain proteins, RNAs and biomolecular complexes. It can efficiently provide information on interaction surfaces, long-distance restraints and relative domain orientations at residue-level resolution. Such information can be readily combined with high-resolution structural data available on subcomponents of biomolecular assemblies. Moreover, NMR is a powerful tool to characterize the dynamics of biomolecules on a wide range of timescales, from nanoseconds to seconds. On the other hand, SAS approaches provide global information on the size and shape of biomolecules and on the ensemble of all conformations present in solution. Therefore, NMR and SAS provide complementary data that are uniquely suited to investigate dynamic biomolecular assemblies. Here, we briefly review the type of data that can be obtained by both techniques and describe different approaches that can be used to combine them to characterize biomolecular assemblies. We then provide guidelines on which experiments are best suited depending on the type of system studied, ranging from fully rigid complexes, dynamic structures that interconvert between defined conformations and systems with very high structural heterogeneity.
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Affiliation(s)
- Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany.
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30
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Rongpipi S, Del Mundo JT, Gomez ED, Gomez EW. Extracting structural insights from soft X-ray scattering of biological assemblies. Methods Enzymol 2022; 678:121-144. [PMID: 36641206 DOI: 10.1016/bs.mie.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Resonant soft X-ray scattering (RSoXS), a technique that combines X-ray absorption spectroscopy and X-ray scattering, can probe the nano- and meso-scale structure of biological assemblies with chemical specificity. RSoXS experiments yield scattering data collected at several photon energies, for example across an elemental absorption edge of interest. Collecting a near-edge X-ray absorption fine structure (NEXAFS) spectrum complements RSoXS experiments and determines X-ray energies that are best suited for RSoXS measurements. The analysis of RSoXS data is similar in many ways to analysis of small angle X-ray scattering using hard X-rays, with an added dimension that includes an X-ray energy dependence. This chapter discusses procedures for predicting scattering contrast and thereby identifying energies suitable for RSoXS measurements using NEXAFS spectra, analyses of 2D RSoXS images through integration into 1D profiles, and strategies for elucidating the origin of RSoXS scattering features. It also discusses existing and potential methods for interpretation of RSoXS data to gain detailed structural insights into biological systems.
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Affiliation(s)
- Sintu Rongpipi
- Advanced Light Source and Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Joshua T Del Mundo
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Enrique D Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States; Department of Materials Science and Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA, United States.
| | - Esther W Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States; Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, United States.
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31
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Marciano S, Dey D, Listov D, Fleishman SJ, Sonn-Segev A, Mertens H, Busch F, Kim Y, Harvey SR, Wysocki VH, Schreiber G. Protein quaternary structures in solution are a mixture of multiple forms. Chem Sci 2022; 13:11680-11695. [PMID: 36320402 PMCID: PMC9555727 DOI: 10.1039/d2sc02794a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Over half the proteins in the E. coli cytoplasm form homo or hetero-oligomeric structures. Experimentally determined structures are often considered in determining a protein's oligomeric state, but static structures miss the dynamic equilibrium between different quaternary forms. The problem is exacerbated in homo-oligomers, where the oligomeric states are challenging to characterize. Here, we re-evaluated the oligomeric state of 17 different bacterial proteins across a broad range of protein concentrations and solutions by native mass spectrometry (MS), mass photometry (MP), size exclusion chromatography (SEC), and small-angle X-ray scattering (SAXS), finding that most exhibit several oligomeric states. Surprisingly, some proteins did not show mass-action driven equilibrium between the oligomeric states. For approximately half the proteins, the predicted oligomeric forms described in publicly available databases underestimated the complexity of protein quaternary structures in solution. Conversely, AlphaFold multimer provided an accurate description of the potential multimeric states for most proteins, suggesting that it could help resolve uncertainties on the solution state of many proteins.
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Affiliation(s)
- Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Debabrata Dey
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Adar Sonn-Segev
- Refeyn Ltd 1 Electric Avenue, Ferry Hinksey Road Oxford OX2 0BY UK
| | - Haydyn Mertens
- Hamburg Outstation, European Molecular Biology Laboratory Notkestrasse 85 Hamburg 22607 Germany
| | - Florian Busch
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Yongseok Kim
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
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Ehm T, Philipp J, Barkey M, Ober M, Brinkop AT, Simml D, von Westphalen M, Nickel B, Beck R, Rädler JO. 3D-printed SAXS chamber for controlled in situ dialysis and optical characterization. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1014-1019. [PMID: 35787568 PMCID: PMC9255564 DOI: 10.1107/s1600577522005136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
3D printing changes the scope of how samples can be mounted for small-angle X-ray scattering (SAXS). In this paper a 3D-printed X-ray chamber, which allows for in situ exchange of buffer and in situ optical transmission spectroscopy, is presented. The chamber is made of cyclic olefin copolymers (COC), including COC X-ray windows providing ultra-low SAXS background. The design integrates a membrane insert for in situ dialysis of the 100 µl sample volume against a reservoir, which enables measurements of the same sample under multiple conditions using an in-house X-ray setup equipped with a 17.4 keV molybdenum source. The design's capabilities are demonstrated by measuring reversible structural changes in lipid and polymer systems as a function of salt concentration and pH. In the same chambers optical light transmission spectroscopy was carried out measuring the optical turbidity of the mesophases and local pH values using pH-responsive dyes. Microfluidic exchange and optical spectroscopy combined with in situ X-ray scattering enables vast applications for the study of responsive materials.
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Affiliation(s)
- Tamara Ehm
- School of Physics and Astronomy, Center for Physics and Chemistry of Living Systems, and Center for Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Israel
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Julian Philipp
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Martin Barkey
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Martina Ober
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Achim Theo Brinkop
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - David Simml
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Miriam von Westphalen
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Bert Nickel
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Roy Beck
- School of Physics and Astronomy, Center for Physics and Chemistry of Living Systems, and Center for Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Joachim O. Rädler
- Faculty of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, Munich, Germany
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Covaceuszach S, Peche LY, Konarev PV, Grdadolnik J, Cattaneo A, Lamba D. Untangling the Conformational Plasticity of V66M Human proBDNF Polymorphism as a Modifier of Psychiatric Disorder Susceptibility. Int J Mol Sci 2022; 23:ijms23126596. [PMID: 35743044 PMCID: PMC9224406 DOI: 10.3390/ijms23126596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 01/27/2023] Open
Abstract
The human genetic variant BDNF (V66M) represents the first example of neurotrophin family member that has been linked to psychiatric disorders. In order to elucidate structural differences that account for the effects in cognitive function, this hproBDNF polymorph was expressed, refolded, purified, and compared directly to the WT variant for the first time for differences in their 3D structures by DSF, limited proteolysis, FT-IR, and SAXS measurements in solution. Our complementary studies revealed a deep impact of V66M polymorphism on hproBDNF conformations in solution. Although the mean conformation in solution appears to be more compact in the V66M variant, overall, we demonstrated a large increase in flexibility in solution upon V66M mutation. Thus, considering that plasticity in IDR is crucial for protein function, the observed alterations may be related to the functional alterations in hproBDNF binding to its receptors p75NTR, sortilin, HAP1, and SorCS2. These effects can provoke altered intracellular neuronal trafficking and/or affect proBDNF physiological functions, leading to many brain-associated diseases and conditions such as cognitive impairment and anxiety. The structural alterations highlighted in the present study may pave the way to the development of drug discovery strategies to provide greater therapeutic responses and of novel pharmacologic strategy in human populations with this common polymorphism, ultimately guiding personalized medicine for neuropsychiatric disorders.
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Affiliation(s)
- Sonia Covaceuszach
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, 34149 Trieste, Italy;
- Correspondence: (S.C.); (D.L.)
| | - Leticia Yamila Peche
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, 34149 Trieste, Italy;
| | - Petr Valeryevich Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, 119333 Moscow, Russia;
| | - Joze Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia;
| | - Antonino Cattaneo
- European Brain Research Institute, 00161 Roma, Italy;
- Scuola Normale Superiore, 56126 Pisa, Italy
| | - Doriano Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, 34149 Trieste, Italy;
- Consorzio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi”, 00136 Roma, Italy
- Correspondence: (S.C.); (D.L.)
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Li M, Yin P. Model2SAS: software for small-angle scattering data calculation from custom shapes. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576722003600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
To meet the challenges in resolving the complex morphologies of emergent nanoparticles, a program with a user-friendly graphical user interface has been developed for calculating small-angle scattering curves from custom shapes. The software allows STL-format 3D models, models defined by mathematical functions or combinations of the two as initial input. As a transitional stage, lattice models are generated and the orientation-averaged small-angle scattering data can be calculated using typical spherical harmonics expansion. The validity of the protocol is verified by demonstration models with Protein Data Bank structures and known scattering functions. The software is applied to successfully calculate the scattering curves of a porous spherical shell model where traditional mathematical derivation fails.
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Zhao B, Bian X, Zhuang X, Liu S, Liu Z, Song F. Screening apo-SOD1 conformation stabilizers from natural flavanones using native ion mobility mass spectrometry and fluorescence spectroscopy methods. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9251. [PMID: 34978114 DOI: 10.1002/rcm.9251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
RATIONALE A large number of studies have shown that the production of aberrant and deleterious copper zinc superoxide dismutase (SOD1) species is closely related to amyotrophic lateral sclerosis (ALS). Therefore, it is of great significance to screen effective inhibitors of misfolding and aggregation of SOD1 for treating ALS disease. METHODS The interaction between flavanone compounds with apo-SOD1was investigated using native electrospray ion mobility mass spectrometry (native ESI-IM-MS). Binding affinities of ligands were compared using native MS, ESI-MS/MS, collision-induced unfolding, and competitive experiments. The effect of ligands on apo-SOD1 aggregation was investigated using the fluorescence spectroscopy method. RESULTS The results of MS showed that the binding affinity of liquiritin apioside was the strongest, better than the corresponding monosaccharide and aglycone, indicating that the presence and the number of glycosyl group are beneficial to enhance ligand affinity to protein. The results of fluorescence spectroscopy for inhibiting protein aggregation in vitro were consistent with the binding affinity. In addition, the results of the collision-induced unfolding indicated that liquiritin apioside can slow down the unfolding of the protein. Meanwhile, the results of competition experiment suggested that liquiritin apiosides share different binding sites with naringin and 5-fluorouridine, which are significant for the structural stability of SOD1. CONCLUSIONS This study revealed that the binding of liquiritin apioside can stabilize apo-SOD1 dimer and inhibit the aggregation of apo-SOD1, and illustrated that native ESI-IM-MS is a powerful tool for providing insight into investigating the structure-activity relationship between small molecules and protein, and screening protein conformation stabilizers.
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Affiliation(s)
- Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Muti-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Xinyu Bian
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Xiaoyu Zhuang
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shu Liu
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Zhiqiang Liu
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Fengrui Song
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
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36
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Jiang Y, Zheng T, Jin W, Shi Y, Huang Q. Enhancing Intestinal Permeability of Theaflavin-3,3'-digallate by Chitosan-Caseinophosphopeptides Nanocomplexes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2029-2041. [PMID: 35108002 DOI: 10.1021/acs.jafc.1c07382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Low intestinal permeability is an unfavorable feature that limits the bioavailability of many hydrophilic polyphenols. In this study, chitosan (CS) was used to complex with caseinophosphopeptides (CPPs), aiming to improve the intestinal permeability of theaflavin-3,3'-digallate (TF-3), a characteristic polyphenol in black tea with poor intestinal permeability. Complexation between CS and CPPs was systemically investigated by turbidimetric titration under various conditions, revealing that electrostatic interaction was the dominant force. The sizes, PDIs, and ζ potentials of CS-CPP nanocomplexes varied with their compositions. The optimized CS-CPP nanocomplex was subsequently used to encapsulate TF-3, which showed high encapsulation efficiency and low cytotoxicity. Microstructural studies showed strong intermolecular associations between CS, CPPs, and TF-3. Encapsulation of TF-3 maintained the globular unit structure of CS-CPP nanocomplexes, but high concentrations of TF-3 resulted in aggregation. Importantly, as proved using the Caco-2 monolayer model, the intestinal permeability of TF-3 was significantly enhanced by the CS-CPP nanocomplexes.
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Affiliation(s)
- Yike Jiang
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Ting Zheng
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Weiping Jin
- College of Food Science and Engineering, Wuhan Polytechnic University, 68 Xuefu Road, Wuhan 430023, China
| | - Yuxin Shi
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Qingrong Huang
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, New Jersey 08901, United States
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37
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Sun Y, Li X, Zhao M, Chen Y, Xu Y, Wang K, Bian S, Jiang Q, Fan Y, Zhang X. Bioinspired supramolecular nanofiber hydrogel through self-assembly of biphenyl-tripeptide for tissue engineering. Bioact Mater 2022; 8:396-408. [PMID: 34541409 PMCID: PMC8429915 DOI: 10.1016/j.bioactmat.2021.05.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/12/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Supramolecular nanofiber peptide assemblies had been used to construct functional hydrogel biomaterials and achieved great progress. Here, a new class of biphenyl-tripeptides with different C-terminal amino acids sequences transposition were developed, which could self-assemble to form robust supramolecular nanofiber hydrogels from 0.7 to 13.8 kPa at ultra-low weight percent (about 0.27 wt%). Using molecular dynamics simulations to interrogate the physicochemical properties of designed biphenyl-tripeptide sequences in atomic detail, reasonable hydrogen bond interactions and "FF" brick (phenylalanine-phenylalanine) promoted the formation of supramolecular fibrous hydrogels. The biomechanical properties and intermolecular interactions were also analyzed by rheology and spectroscopy analysis to optimize amino acid sequence. Enhanced L929 cells adhesion and proliferation demonstrated good biocompatibility of the hydrogels. The storage modulus of BPAA-AFF with 10 nm nanofibers self-assembling was around 13.8 kPa, and the morphology was similar to natural extracellular matrix. These supramolecular nanofiber hydrogels could effectively support chondrocytes spreading and proliferation, and specifically enhance chondrogenic related genes expression and chondrogenic matrix secretion. Such biomimetic supramolecular short peptide biomaterials hold great potential in regenerative medicine as promising innovative matrices because of their simple and regular molecular structure and excellent biological performance.
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Affiliation(s)
- Yong Sun
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Xing Li
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Mingda Zhao
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Yafang Chen
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Yang Xu
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Kefeng Wang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Shaoquan Bian
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Qing Jiang
- College of Materials Science and Engineering, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Yujiang Fan
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
| | - Xingdong Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, PR China
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Lin D, Zhang W, Yin H, Hu H, Li Y, Zhang H, Wang L, Xie X, Hu H, Yan Y, Ling H, Liu J, Qian Y, Tang L, Wang Y, Dong C, Xie L, Zhang H, Wang S, Wei Y, Guo X, Lu D, Huang W. Cross-Scale Synthesis of Organic High- k Semiconductors Based on Spiro-Gridized Nanopolymers. Research (Wash D C) 2022; 2022:9820585. [PMID: 35098138 PMCID: PMC8777471 DOI: 10.34133/2022/9820585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/06/2021] [Indexed: 11/06/2022] Open
Abstract
High dielectric constants in organic semiconductors have been identified as a central challenge for the improvement in not only piezoelectric, pyroelectric, and ferroelectric effects but also photoelectric conversion efficiency in OPVs, carrier mobility in OFETs, and charge density in charge-trapping memories. Herein, we report an ultralong persistence length (l p ≈ 41 nm) effect of spiro-fused organic nanopolymers on dielectric properties, together with excitonic and charge carrier behaviors. The state-of-the-art nanopolymers, namely, nanopolyspirogrids (NPSGs), are synthesized via the simple cross-scale Friedel-Crafts polygridization of A2B2-type nanomonomers. The high dielectric constant (k = 8.43) of NPSG is firstly achieved by locking spiro-polygridization effect that results in the enhancement of dipole polarization. When doping into a polystyrene-based dielectric layer, such a high-k feature of NPSG increases the field-effect carrier mobility from 0.20 to 0.90 cm2 V-1 s-1 in pentacene OFET devices. Meanwhile, amorphous NPSG film exhibits an ultralow energy disorder (<50 meV) for an excellent zero-field hole mobility of 3.94 × 10-3 cm2 V-1 s-1, surpassing most of the amorphous π-conjugated polymers. Organic nanopolymers with high dielectric constants open a new way to break through the bottleneck of efficiency and multifunctionality in the blueprint of the fourth-generation semiconductors.
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Affiliation(s)
- Dongqing Lin
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Wenhua Zhang
- National Synchrotron Radiation Laboratory, Anhui Provincial Engineering Laboratory of Advanced Functional Polymer Film, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Hang Yin
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Haixia Hu
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Yang Li
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - He Zhang
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Le Wang
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Xinmiao Xie
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.,Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hongkai Hu
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yongxia Yan
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Haifeng Ling
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jin'an Liu
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yue Qian
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lei Tang
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yongxia Wang
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Chaoyang Dong
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Linghai Xie
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.,Frontiers Science Center for Flexible Electronics (FSCFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Northwestern Polytechnical University, Xi'an 710072, China
| | - Hao Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Avenue, Changchun 130012, China
| | - Shasha Wang
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Ying Wei
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dan Lu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Avenue, Changchun 130012, China
| | - Wei Huang
- Centre for Molecular Systems and Organic Devices (CMSOD), State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.,Frontiers Science Center for Flexible Electronics (FSCFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Northwestern Polytechnical University, Xi'an 710072, China
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Structural basis for effector recognition by an antibacterial type IV secretion system. Proc Natl Acad Sci U S A 2022; 119:2112529119. [PMID: 34983846 PMCID: PMC8740702 DOI: 10.1073/pnas.2112529119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 11/19/2022] Open
Abstract
Type IV secretion systems (T4SSs) have been studied for more than 70 y because of their roles in mediating horizontal DNA transfer, responsible for the spread of antibiotic resistance, and the injection of virulence factors into animal and plant hosts. Another important function is the contact-dependent injection of toxic effectors into competing bacteria of different species during bacterial warfare. The present study reveals how T4SSs use a specific domain of the VirD4 coupling protein to recruit antibacterial toxins for secretion by recognizing conserved carboxyl-terminal secretion signal domains. The molecular structure of the secretion signal domain described in this work will serve as a model for thousands of homologs encountered in several hundred distinct bacterial species. Many soil-, water-, and plant-associated bacterial species from the orders Xanthomonadales, Burkholderales, and Neisseriales carry a type IV secretion system (T4SS) specialized in translocating effector proteins into other gram-negative species, leading to target cell death. These effectors, known as X-Tfes, carry a carboxyl-terminal domain of ∼120 residues, termed XVIPCD, characterized by several conserved motifs and a glutamine-rich tail. Previous studies showed that the XVIPCD is required for interaction with the T4SS coupling protein VirD4 and for T4SS-dependent translocation. However, the structural basis of the XVIPCD–VirD4 interaction is unknown. Here, we show that the XVIPCD interacts with the central all-alpha domain of VirD4 (VirD4AAD). We used solution NMR spectroscopy to solve the structure of the XVIPCD of X-TfeXAC2609 from Xanthomonas citri and to map its interaction surface with VirD4AAD. Isothermal titration calorimetry and in vivo Xanthomonas citri versus Escherichia coli competition assays using wild-type and mutant X-TfeXAC2609 and X-TfeXAC3634 indicate that XVIPCDs can be divided into two regions with distinct functions: the well-folded N-terminal region contains specific conserved motifs that are responsible for interactions with VirD4AAD, while both N- and carboxyl-terminal regions are required for effective X-Tfe translocation into the target cell. The conformational stability of the N-terminal region is reduced at and below pH 7.0, a property that may facilitate X-Tfe unfolding and translocation through the more acidic environment of the periplasm.
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40
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Munier P, Hadi SE, Segad M, Bergström L. Rheo-SAXS study of shear-induced orientation and relaxation of cellulose nanocrystal and montmorillonite nanoplatelet dispersions. SOFT MATTER 2022; 18:390-396. [PMID: 34901987 DOI: 10.1039/d1sm00837d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The development of robust production processes is essential for the introduction of advanced materials based on renewable and Earth-abundant resources. Cellulose nanomaterials have been combined with other highly available nanoparticles, in particular clays, to generate multifunctional films and foams. Here, the structure of dispersions of rod-like cellulose nanocrystals (CNC) and montmorillonite nanoplatelets (MNT) was probed using small-angle X-ray scattering within a rheological cell (Rheo-SAXS). Shear induced a high degree of particle orientation in both the CNC-only and CNC:MNT composite dispersions. Relaxation of the shear-induced orientation in the CNC-only dispersion decayed exponentially and reached a steady-state within 20 seconds, while the relaxation of the CNC:MNT composite dispersion was found to be strongly retarded and partially inhibited. Viscoelastic measurements and Guinier analysis of dispersions at the shear rate of 0.1 s-1 showed that the addition of MNT promotes gel formation of the CNC:MNT composite dispersions. A better understanding of shear-dependent assembly and orientation of multi-component nanoparticle dispersions can be used to process materials with improved mechanical and functional properties.
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Affiliation(s)
- Pierre Munier
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 10691, Sweden.
| | - Seyed Ehsan Hadi
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 10691, Sweden.
- Wallenberg Wood Science Center, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 10691, Sweden
| | - Mo Segad
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 10691, Sweden.
| | - Lennart Bergström
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 10691, Sweden.
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Matsuo T, Arluison V, Wien F, Peters J. Structural Information on Bacterial Amyloid and Amyloid-DNA Complex Obtained by Small-Angle Neutron or X-Ray Scattering. Methods Mol Biol 2022; 2538:75-93. [PMID: 35951294 DOI: 10.1007/978-1-0716-2529-3_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: 06/15/2023]
Abstract
Small-angle scattering is a powerful technique to obtain structural information on biomacromolecules in aqueous solution at the sub-nanometer and nanometer length scales. It provides the sizes and overall shapes of the scattering particles. While small-angle X-ray scattering (SAXS) has often been used for structural analysis of a single-component system, small-angle neutron scattering (SANS) has been used to reveal the internal organization of a multicomponent system such as protein-protein and protein-DNA complexes. This is due to the fact that the neutron scattering length is largely different between hydrogen and deuterium, and thus it allows to make a specific component in complexes "invisible" to neutrons by changing the H2O/D2O ratio in the solvent with or without molecular deuteration. In this chapter, we describe a method to characterize the biomolecular structures using SANS and SAXS, in particular, focusing on fibrillar proteins such as bacterial amyloids and their complexes with nucleic acids.
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Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France.
- Institut Laue-Langevin, Grenoble Cedex 9, France.
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki, Japan.
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France
- Université de Paris Cité, Paris, France
| | - Frank Wien
- DISCO Beamline, Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France.
- Institut Laue-Langevin, Grenoble Cedex 9, France.
- Institut Universitaire de France, Paris, France.
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Chinnam NB, Syed A, Burnett KH, Hura GL, Tainer JA, Tsutakawa SE. Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights. Methods Mol Biol 2022; 2444:43-68. [PMID: 35290631 PMCID: PMC9020468 DOI: 10.1007/978-1-0716-2063-2_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structures provide a critical breakthrough step for biological analyses, and small angle X-ray scattering (SAXS) is a powerful structural technique to study dynamic DNA repair proteins. As toxic and mutagenic repair intermediates need to be prevented from inadvertently harming the cell, DNA repair proteins often chaperone these intermediates through dynamic conformations, coordinated assemblies, and allosteric regulation. By measuring structural conformations in solution for both proteins, DNA, RNA, and their complexes, SAXS provides insight into initial DNA damage recognition, mechanisms for validation of their substrate, and pathway regulation. Here, we describe exemplary SAXS analyses of a DNA damage response protein spanning from what can be derived directly from the data to obtaining super resolution through the use of SAXS selection of atomic models. We outline strategies and tactics for practical SAXS data collection and analysis. Making these structural experiments in reach of any basic and clinical researchers who have protein, SAXS data can readily be collected at government-funded synchrotrons, typically at no cost for academic researchers. In addition to discussing how SAXS complements and enhances cryo-electron microscopy, X-ray crystallography, NMR, and computational modeling, we furthermore discuss taking advantage of recent advances in protein structure prediction in combination with SAXS analysis.
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Affiliation(s)
- Naga Babu Chinnam
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kathryn H Burnett
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Han Q, Binns J, Zhai J, Guo X, Ryan TM, Drummond CJ, Greaves TL. Insights on lysozyme aggregation in protic ionic liquid solvents by using small angle X-ray scattering and high throughput screening. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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44
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Zhang F, Richter G, Bourgeois B, Spreitzer E, Moser A, Keilbach A, Kotnik P, Madl T. A General Small-Angle X-ray Scattering-Based Screening Protocol for Studying Physical Stability of Protein Formulations. Pharmaceutics 2021; 14:69. [PMID: 35056965 PMCID: PMC8778066 DOI: 10.3390/pharmaceutics14010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
A fundamental step in developing a protein drug is the selection of a stable storage formulation that ensures efficacy of the drug and inhibits physiochemical degradation or aggregation. Here, we designed and evaluated a general workflow for screening of protein formulations based on small-angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling, temperature control, and fast data analysis and provides protein particle interaction information. SAXS, together with different methods including turbidity analysis, dynamic light scattering (DLS), and SDS-PAGE measurements, were used to obtain different parameters to provide high throughput screenings. Using a set of model proteins and biopharmaceuticals, we show that SAXS is complementary to dynamic light scattering (DLS), which is widely used in biopharmaceutical research and industry. We found that, compared to DLS, SAXS can provide a more sensitive measure for protein particle interactions, such as protein aggregation and repulsion. Moreover, we show that SAXS is compatible with a broader range of buffers, excipients, and protein concentrations and that in situ SAXS provides a sensitive measure for long-term protein stability. This workflow can enable future high-throughput analysis of proteins and biopharmaceuticals and can be integrated with well-established complementary physicochemical analysis pipelines in (biopharmaceutical) research and industry.
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Affiliation(s)
- Fangrong Zhang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China;
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Gesa Richter
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Armin Moser
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | | | - Petra Kotnik
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
- BioTechMed-Graz, 8010 Graz, Austria
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Wood DM, Dobson RC, Horne CR. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Biochem Soc Trans 2021; 49:2711-2726. [PMID: 34854920 PMCID: PMC8786299 DOI: 10.1042/bst20210674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022]
Abstract
Transcription is the principal control point for bacterial gene expression, and it enables a global cellular response to an intracellular or environmental trigger. Transcriptional regulation is orchestrated by transcription factors, which activate or repress transcription of target genes by modulating the activity of RNA polymerase. Dissecting the nature and precise choreography of these interactions is essential for developing a molecular understanding of transcriptional regulation. While the contribution of X-ray crystallography has been invaluable, the 'resolution revolution' of cryo-electron microscopy has transformed our structural investigations, enabling large, dynamic and often transient transcription complexes to be resolved that in many cases had resisted crystallisation. In this review, we highlight the impact cryo-electron microscopy has had in gaining a deeper understanding of transcriptional regulation in bacteria. We also provide readers working within the field with an overview of the recent innovations available for cryo-electron microscopy sample preparation and image reconstruction of transcription complexes.
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Affiliation(s)
- David M. Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R. Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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Ozerskaya AV, Zamay TN, Kolovskaya OS, Tokarev NA, Belugin KV, Chanchikova NG, Badmaev ON, Zamay GS, Shchugoreva IA, Moryachkov RV, Zabluda VN, Khorzhevskii VA, Shepelevich N, Gappoev SV, Karlova EA, Saveleva AS, Volzhentsev AA, Blagodatova AN, Lukyanenko KA, Veprintsev DV, Smolyarova TE, Tomilin FN, Zamay SS, Silnikov VN, Berezovski MV, Kichkailo AS. 11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography- computed tomography. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1159-1172. [PMID: 34853715 PMCID: PMC8601970 DOI: 10.1016/j.omtn.2021.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/30/2021] [Accepted: 10/19/2021] [Indexed: 11/25/2022]
Abstract
Identification of primary tumors and metastasis sites is an essential step in cancer diagnostics and the following treatment. Positron emission tomography-computed tomography (PET/CT) is one of the most reliable methods for scanning the whole organism for malignancies. In this work, we synthesized an 11C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer. The 11C-aptamer was applied for in vivo imaging of Ehrlich ascites carcinoma and its metastases in mice using PET/CT. The imaging experiments with the 11C-aptamer determined very small primary and secondary tumors of 3 mm2 and less. We also compared 11C imaging with the standard radiotracer, 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18F-FDG), and found better selectivity of the 11C-aptamer to metastatic lesions in the metabolically active organs than 18F-FDG. 11C radionuclide with an ultra-short (20.38 min) half-life is considered safest for PET/CT imaging and does not cause false-positive results in heart imaging. Its combination with aptamers gives us high-specificity and high-contrast imaging of cancer cells and can be applied for PET/CT-guided drug delivery in cancer therapies.
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Affiliation(s)
- Anastasia V. Ozerskaya
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Olga S. Kolovskaya
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Nikolay A. Tokarev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Kirill V. Belugin
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia G. Chanchikova
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Oleg N. Badmaev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Galina S. Zamay
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | | | - Roman V. Moryachkov
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
- Kirensky Institute of Physics, Krasnoyarsk, Russia
| | | | - Vladimir A. Khorzhevskii
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Nikolay Shepelevich
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Stanislav V. Gappoev
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Elena A. Karlova
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anastasia S. Saveleva
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexander A. Volzhentsev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anna N. Blagodatova
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
| | - Kirill A. Lukyanenko
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | | | - Tatyana E. Smolyarova
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
- Kirensky Institute of Physics, Krasnoyarsk, Russia
| | | | - Sergey S. Zamay
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Anna S. Kichkailo
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
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Vinnakota R, Dhingra S, Kumari J, Ansari MY, Shukla E, Nerkar MD, Kumar J. Role of Neto1 extracellular domain in modulation of kainate receptors. Int J Biol Macromol 2021; 192:525-536. [PMID: 34634333 DOI: 10.1016/j.ijbiomac.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 01/28/2023]
Abstract
Kainate receptors play fundamental roles in regulating synaptic transmission and plasticity in central nervous system and are regulated by their cognate auxiliary subunits Neuropilin and tolloid-like proteins 1 and 2 (Neto). While electrophysiology-based insights into functions of Neto proteins are known, biophysical and biochemical studies into Neto proteins have been largely missing till-date. Our biochemical, biophysical, and functional characterization of the purified extracellular domain (ECD) of Neto1 shows that Neto1-ECD exists as monomers in solution and has a micromolar affinity for GluK2 receptors in apo state or closed state. Remarkably, the affinity was ~2.8 fold lower for receptors trapped in the desensitized state, highlighting the conformation-dependent interaction of Neto proteins with kainate receptors. SAXS analysis of Neto1-ECD reveals that their dimensions are long enough to span the entire extracellular domain of kainate receptors. The shape and conformation of Neto1-ECD seems to be altered by calcium ions pointing towards its possible role in modulating Neto1 functions. Functional assays using GluK2 receptors and GluK2/GluA2 chimeric receptors reveal a differential role of Neto1 domains in modulating receptor functions. Although the desensitization rate was not affected by the Neto1-ECD, the recovery rates from the desensitized state are altered.
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Affiliation(s)
- Rajesh Vinnakota
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India
| | - Surbhi Dhingra
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India
| | - Jyoti Kumari
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India
| | - Mohammed Yousuf Ansari
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India
| | - Ekta Shukla
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India
| | - Mayuri Dattatray Nerkar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India
| | - Janesh Kumar
- Laboratory of Membrane Protein Biology, National Centre for Cell Science, NCCS Complex, S. P. Pune University, Pune, Maharashtra 411007, India.
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48
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Lattanzi V, André I, Gasser U, Dubackic M, Olsson U, Linse S. Amyloid β 42 fibril structure based on small-angle scattering. Proc Natl Acad Sci U S A 2021; 118:e2112783118. [PMID: 34815346 PMCID: PMC8640717 DOI: 10.1073/pnas.2112783118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Amyloid fibrils are associated with a number of neurodegenerative diseases, including fibrils of amyloid β42 peptide (Aβ42) in Alzheimer's disease. These fibrils are a source of toxicity to neuronal cells through surface-catalyzed generation of toxic oligomers. Detailed knowledge of the fibril structure may thus facilitate therapeutic development. We use small-angle scattering to provide information on the fibril cross-section dimension and shape for Aβ42 fibrils prepared in aqueous phosphate buffer at pH = 7.4 and pH 8.0 under quiescent conditions at 37 °C from pure recombinant Aβ42 peptide. Fitting the data using a continuum model reveals an elliptical cross-section and a peptide mass-per-unit length compatible with two filaments of two monomers, four monomers per plane. To provide a more detailed atomistic model, the data were fitted using as a starting state a high-resolution structure of the two-monomer arrangement in filaments from solid-state NMR (Protein Data Bank ID 5kk3). First, a twofold symmetric model including residues 11 to 42 of two monomers in the filament was optimized in terms of twist angle and local packing using Rosetta. A two-filament model was then built and optimized through fitting to the scattering data allowing the two N-termini in each filament to take different conformations, with the same conformation in each of the two filaments. This provides an atomistic model of the fibril with twofold rotation symmetry around the fibril axis. Intriguingly, no polydispersity as regards the number of filaments was observed in our system over separate samples, suggesting that the two-filament arrangement represents a free energy minimum for the Aβ42 fibril.
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Affiliation(s)
- Veronica Lattanzi
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden;
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ingemar André
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
| | - Urs Gasser
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Marija Dubackic
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ulf Olsson
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
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Radajewski D, Hunter L, He X, Nahi O, Galloway JM, Meldrum FC. An innovative data processing method for studying nanoparticle formation in droplet microfluidics using X-rays scattering. LAB ON A CHIP 2021; 21:4498-4506. [PMID: 34671784 DOI: 10.1039/d1lc00545f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
X-ray scattering techniques provide a powerful means of characterizing the formation of nanoparticles in solution. Coupling these techniques to segmented-flow microfluidic devices that offer well-defined environments gives access to in situ time-resolved analysis, excellent reproducibility, and eliminates potential radiation damage. However, analysis of the resulting datasets can be extremely time-consuming, where these comprise frames corresponding to the droplets alone, the continuous phase alone, and to both at their interface. We here describe a robust, low-cost, and versatile droplet microfluidics device and use it to study the formation of magnetite nanoparticles with simultaneous synchrotron SAXS and WAXS. Lateral outlet capillaries facilitate the X-ray analysis and reaction times of between a few seconds and minutes can be accommodated. A two-step data processing method is then described that exploits the unique WAXS signatures of the droplets, continuous phase, and interfacial region to identify the frames corresponding to the droplets. These are then sorted, and the background scattering is subtracted using an automated frame-by-frame approach, allowing the signal from the nanoparticles to be isolated from the raw data. Modeling these data gives quantitative information about the evolution of the sizes and structures of the nanoparticles, in agreement with TEM observations. This versatile platform can be readily employed to study a wide range of dynamic processes in heterogeneous systems.
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Affiliation(s)
- Dimitri Radajewski
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Liam Hunter
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Xuefeng He
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Ouassef Nahi
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Johanna M Galloway
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
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50
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Ecsédi P, Gógl G, Nyitray L. Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes. Front Mol Biosci 2021; 8:749052. [PMID: 34708078 PMCID: PMC8542695 DOI: 10.3389/fmolb.2021.749052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023] Open
Abstract
S100 proteins are small, dimeric, Ca2+-binding proteins of considerable interest due to their associations with cancer and rheumatic and neurodegenerative diseases. They control the functions of numerous proteins by forming protein–protein complexes with them. Several of these complexes were found to display “fuzzy” properties. Examining these highly flexible interactions, however, is a difficult task, especially from a structural biology point of view. Here, we summarize the available in vitro techniques that can be deployed to obtain structural information about these dynamic complexes. We also review the current state of knowledge about the structures of S100 complexes, focusing on their often-asymmetric nature.
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Affiliation(s)
- Péter Ecsédi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gergő Gógl
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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