1
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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] [MESH Headings] [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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2
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Bowman SEJ, Byrnes J, Russi S, Zimanyi CM. Preparing research samples for safe arrival at centers and facilities: recipes for successful experiments. Acta Crystallogr F Struct Biol Commun 2024; 80:165-172. [PMID: 38990054 DOI: 10.1107/s2053230x24006174] [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: 04/19/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024] Open
Abstract
Preparation of biomacromolecules for structural biology studies is a complex and time-consuming process. The goal is to produce a highly concentrated, highly pure product that is often shipped to large facilities with tools to prepare the samples for crystallization trials or for measurements at synchrotrons and cryoEM centers. The aim of this article is to provide guidance and to discuss general considerations for shipping biomacromolecular samples. Details are also provided about shipping samples for specific experiment types, including solution- and cryogenic-based techniques. These guidelines are provided with the hope that the time and energy invested in sample preparation is not lost due to shipping logistics.
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Affiliation(s)
- Sarah E J Bowman
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christina M Zimanyi
- National Center for CryoEM Access and Training, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
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3
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Anitas EM. Integrating machine learning with α -SAS for enhanced structural analysis in small-angle scattering: applications in biological and artificial macromolecular complexes. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:39. [PMID: 38831117 DOI: 10.1140/epje/s10189-024-00435-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
Small-Angle Scattering (SAS), encompassing both X-ray (SAXS) and Neutron (SANS) techniques, is a crucial tool for structural analysis at the nanoscale, particularly in the realm of biological macromolecules. This paper explores the intricacies of SAS, emphasizing its application in studying complex biological systems and the challenges associated with sample preparation and data analysis. We highlight the use of neutron-scattering properties of hydrogen isotopes and isotopic labeling in SANS for probing structures within multi-subunit complexes, employing techniques like contrast variation (CV) for detailed structural analysis. However, traditional SAS analysis methods, such as Guinier and Kratky plots, are limited by their partial use of available data and inability to operate without substantial a priori knowledge of the sample's chemical composition. To overcome these limitations, we introduce a novel approach integrating α -SAS, a computational method for simulating SANS with CV, with machine learning (ML). This approach enables the accurate prediction of scattering contrast in multicomponent macromolecular complexes, reducing the need for extensive sample preparation and computational resources. α -SAS, utilizing Monte Carlo methods, generates comprehensive datasets from which structural invariants can be extracted, enhancing our understanding of the macromolecular form factor in dilute systems. The paper demonstrates the effectiveness of this integrated approach through its application to two case studies: Janus particles, an artificial structure with a known SAS intensity and contrast, and a biological system involving RNA polymerase II in complex with Rtt103. These examples illustrate the method's capability to provide detailed structural insights, showcasing its potential as a powerful tool for advanced SAS analysis in structural biology.
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Affiliation(s)
- Eugen Mircea Anitas
- Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region, Russian Federation, 141980.
- Department of Nuclear Physics, "Horia Hulubei" National R &D Institute for Physics and Nuclear Engineering, Reactorului 30, 077125, Magurele, Ilfov, Romania.
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4
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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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5
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Matsui T, Rajkovic I, Mooers BHM, Liu P, Weiss TM. Adaptable SEC-SAXS data collection for higher quality structure analysis in solution. Protein Sci 2024; 33:e4946. [PMID: 38501481 PMCID: PMC10949327 DOI: 10.1002/pro.4946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
The two major challenges in synchrotron size-exclusion chromatography coupled in-line with small-angle x-ray scattering (SEC-SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation-damaged materials on the walls of the sample cell. In recent years, many post-experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC-SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4-2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4-2). The first mode, the High-Resolution mode, enables SEC-SAXS data collection with excellent sample separation and virtually no additional peak broadening from the UHPLC UV detector to the x-ray position by taking advantage of the low system dispersion of the UHPLC. The small bed volume of the analytical SEC column minimizes sample dilution in the column and facilitates data collection at higher sample concentrations with excellent sample economy equal to or even less than that of the conventional equilibrium SAXS method. Radiation damage problems during SEC-SAXS data collection are evaded by additional cleaning of the sample cell after buffer data collection and avoidance of unnecessary exposures through the use of the x-ray shutter control options, allowing sample data collection with a clean sample cell. Therefore, accurate background subtraction can be performed at a level equivalent to the conventional equilibrium SAXS method without requiring baseline correction, thereby leading to more reliable downstream structural analysis and quicker access to new science. The two other data collection modes, the High-Throughput mode and the Co-Flow mode, add agility to the planning and execution of experiments to efficiently achieve the user's scientific objectives at the SSRL BL4-2.
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Affiliation(s)
- Tsutomu Matsui
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Ivan Rajkovic
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Blaine H. M. Mooers
- Department of Biochemistry and PhysiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Stephenson Cancer CenterUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Laboratory of Biomolecular Structure and FunctionUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
| | - Ping Liu
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
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6
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Cai G, Li Y, Fu Y, Yang H, Mei L, Nie Z, Li T, Liu H, Ke Y, Wang XL, Brédas JL, Tang MC, Chen X, Zhan X, Lu X. Deuteration-enhanced neutron contrasts to probe amorphous domain sizes in organic photovoltaic bulk heterojunction films. Nat Commun 2024; 15:2784. [PMID: 38555349 PMCID: PMC10981694 DOI: 10.1038/s41467-024-47052-7] [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: 08/16/2023] [Accepted: 03/17/2024] [Indexed: 04/02/2024] Open
Abstract
An organic photovoltaic bulk heterojunction comprises of a mixture of donor and acceptor materials, forming a semi-crystalline thin film with both crystalline and amorphous domains. Domain sizes critically impact the device performance; however, conventional X-ray scattering techniques cannot detect the contrast between donor and acceptor materials within the amorphous intermixing regions. In this study, we employ neutron scattering and targeted deuteration of acceptor materials to enhance the scattering contrast by nearly one order of magnitude. Remarkably, the PM6:deuterated Y6 system reveals a new length scale, indicating short-range aggregation of Y6 molecules in the amorphous intermixing regions. All-atom molecular dynamics simulations confirm that this short-range aggregation is an inherent morphological advantage of Y6 which effectively assists charge extraction and suppresses charge recombination as shown by capacitance spectroscopy. Our findings uncover the amorphous nanomorphology of organic photovoltaic thin films, providing crucial insights into the morphology-driven device performance.
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Affiliation(s)
- Guilong Cai
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China
- Beijing Key Laboratory of Ionic Liquids Clean Process, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Yuhao Li
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China.
- Spallation Neutron Source Science Center, Dongguan, 523803, China.
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 10049, China.
| | - Yuang Fu
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China
| | - Hua Yang
- Spallation Neutron Source Science Center, Dongguan, 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 10049, China
| | - Le Mei
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Zhaoyang Nie
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Tengfei Li
- School of Materials Science and Engineering, Peking University, Beijing, China
| | - Heng Liu
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China
| | - Yubin Ke
- Spallation Neutron Source Science Center, Dongguan, 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 10049, China
| | - Xun-Li Wang
- Department of Physics and Center for Neutron Scattering, City University of Hong Kong, Hong Kong, China
- Hong Kong Institute for Advanced Study, City University of Hong Kong, Hong Kong, China
| | - Jean-Luc Brédas
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona, 85721-0041, USA
| | - Man-Chung Tang
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xiankai Chen
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Xiaowei Zhan
- School of Materials Science and Engineering, Peking University, Beijing, China.
| | - Xinhui Lu
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China.
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7
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Colijn I, Postma E, Fix R, van der Kooij HM, Schroën K. Particle dispersion governs nano to bulk dynamics for tailored nanocomposite design. J Colloid Interface Sci 2024; 658:354-361. [PMID: 38113544 DOI: 10.1016/j.jcis.2023.12.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/10/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Nanoparticle addition can expand bioplastic use, as the resultant nanocomposite features e.g., improved mechanical properties. HYPOTHESIS It is generally hypothesised that the nanoparticle-polymer interaction strength is pivotal to reduce polymer dynamics within the interphasial region and beyond. EXPERIMENTS Translating nanoscale phenomena to bulk properties is challenging, as traditional techniques that probe interphasial dynamics are limited to well-dispersed systems. Laser speckle imaging (LSI) enabled us to probe interphasial nanoscale dynamics of samples containing aggregated nanoparticles. We relate these LSI-derived relaxation times to bulk rheological properties at a micro scale. FINDINGS Nanocomposites with well-dispersed PDMS-coated titanium dioxide nanoparticles of ∼100 nm showed higher viscosities than nanocomposites containing aggregated PVP- and PAA-coated nanoparticles of 200-2000 nm. Within the interphasial region, nanoparticle addition increased relaxation times by a factor 101-102, reaching ultraslow relaxations of ∼103 s. While the viscosity increased upon nanoparticle loading, interphasial relaxation times plateaued at 5 wt% for nanocomposites containing well-dispersed nanoparticles and 10 wt% for nanocomposites containing aggregated nanoparticles. Likely, interphasial regions between nanoparticles interact, which is more prominent in systems with well-dispersed nanoparticles and at higher loadings. Our results highlight that, contrary to general belief, nanoparticle dispersion seems of greater importance for mechanical reinforcement than the interaction between polymer and particle.
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Affiliation(s)
- Ivanna Colijn
- Wageningen University and Research, Food Process Engineering Group, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Erik Postma
- Wageningen University and Research, Food Process Engineering Group, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands; Wageningen University and Research, Physical Chemistry and Soft Matter, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Raoul Fix
- Wageningen University and Research, Physical Chemistry and Soft Matter, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Hanne M van der Kooij
- Wageningen University and Research, Physical Chemistry and Soft Matter, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Karin Schroën
- Wageningen University and Research, Food Process Engineering Group, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
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8
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Kawamukai H, Takishita S, Shimizu K, Kohda D, Ishimori K, Saio T. Conformational Distribution of a Multidomain Protein Measured by Single-Pair Small-Angle X-ray Scattering. J Phys Chem Lett 2024; 15:744-750. [PMID: 38221741 PMCID: PMC10823528 DOI: 10.1021/acs.jpclett.3c02600] [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: 09/15/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
The difficulty in evaluating the conformational distribution of proteins in solution often hinders mechanistic insights. One possible strategy for visualizing conformational distribution is distance distribution measurement by single-pair small-angle X-ray scattering (SAXS), in which the scattering interference from only a specific pair of atoms in the target molecule is extracted. Despite this promising concept, with few applications in synthetic small molecules and DNA, technical difficulties have prevented its application in protein conformational studies. This study used a synthetic tag to fix the lanthanide ion at desired sites on the protein and used single-pair SAXS with contrast matching to evaluate the conformational distribution of the multidomain protein enzyme MurD. These data highlighted the broad conformational and ligand-driven distribution shifts of MurD in solution. This study proposes an important strategy in solution structural biology that targets dynamic proteins, including multidomain and intrinsically disordered proteins.
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Affiliation(s)
- Honoka Kawamukai
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
- Graduate
School of Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Shumpei Takishita
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Kazumi Shimizu
- Faculty
of Education and Integrated Arts and Sciences, Waseda University, Tokyo 169-8050, Japan
| | - Daisuke Kohda
- Division
of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Koichiro Ishimori
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido
University, Sapporo 060-0810, Japan
| | - Tomohide Saio
- Graduate
School of Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
- Institute
of Advanced Medical Sciences, Tokushima
University, Tokushima 770-8503, Japan
- Fujii
Memorial Institute of Medical Sciences, Institute of Advanced Medical
Sciences, Tokushima University, Tokushima 770-8503, Japan
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9
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Han Q, Darmanin C, Rosado CJ, Veríssimo NV, Pereira JFB, Bryant G, Drummond CJ, Greaves TL. Structure, aggregation dynamics and crystallization of superfolder green fluorescent protein: Effect of long alkyl chain imidazolium ionic liquids. Int J Biol Macromol 2023; 253:127456. [PMID: 37844813 DOI: 10.1016/j.ijbiomac.2023.127456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/26/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Green fluorescent protein (GFP) and its variants are widely used in medical and biological research, especially acting as indicators of protein structural integrity, protein-protein interactions and as biosensors. This study employs superfolder GFP (sfGFP) to investigate the impact of varying alkyl chain length of 1-Cn-3-methylimidazolium chloride ionic liquid (IL) series ([Cnmim]Cl, n = 2, 4, 6, 8, 10, 12) on the protein fluorescence, structure, hydration, aggregation dynamics and crystallization behaviour. The results revealed a concentration-dependent decrease in the sfGFP chromophore fluorescence, particularly in long alkyl chain ILs ([C10mim]Cl and [C12mim]Cl). Tryptophan (Trp) fluorescence showed the quenching rate increased with longer alkyl chains indicating a nonpolar interaction between Trp57 and the alkyl chain. Secondary structural changes were observed at the high IL concentration of 1.5 M in [C10mim]Cl and [C12mim]Cl. Small-angle X-ray scattering (SAXS) indicated relatively stable protein sizes, but with IL aggregates present in [C10mim]Cl and [C12mim]Cl solutions. Dynamic light scattering (DLS) data showed increased protein size and aggregation with longer alkyl chain ILs. Notably, ILs and salts, excluding [C2mim]Cl, promoted sfGFP crystallization. This study emphasizes the influence of the cation alkyl chain length and concentration on protein stability and aggregation, providing insights into utilizing IL solvents for protein stabilization and crystallization purposes.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Carlos J Rosado
- Department of Diabetes, Central Clinical School, Monash University, VIC 3004, Australia; Department of Biochemistry, Monash University, VIC 3800, Australia
| | - Nathalia Vieira Veríssimo
- School of Pharmaceutical Sciences, São Paulo University (USP), Av. Prof. Lineu Prestes, no. 580, B16, 05508-000, Cidade de Universitária, São Paulo, SP, Brazil
| | - Jorge F B Pereira
- University of Coimbra, CIEPQPF, Department of Chemical Engineering, Rua Sílvio Lima, Pólo II - Pinhal de Marrocos, 3030-790 Coimbra, Portugal
| | - 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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10
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Li Y, Li Q, Gillilan RE, Abbaspourrad A. Reversible disassembly-reassembly of C-phycocyanin in pressurization-depressurization cycles of high hydrostatic pressure. Int J Biol Macromol 2023; 253:127623. [PMID: 37879586 PMCID: PMC10842036 DOI: 10.1016/j.ijbiomac.2023.127623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
Hydrostatic pressure can reversibly modulate protein-protein and protein-chromophore interactions of C-phycocyanin (C-PC) from Spirulina platensis. Small-angle X-ray scattering combined with UV-Vis spectrophotometry and protein modeling was used to explore the color and structural changes of C-PC under high pressure conditions at different pH levels. It was revealed that pressures up to 350 MPa were enough to fully disassemble C-PC from trimers to monomers at pH 7.0, or from monomers to detached subunits at pH 9.0. These disassemblies were accompanied by protein unfolding that caused these high-pressure induced structures to be more extended. These changes were reversible following depressurization. The trimer-to-monomer transition proceeded through a collection of previously unrecognized, L-shaped intermediates resembling C-PC dimers. Additionally, pressurized C-PC showed decayed Q-band absorption and fortified Soret-band absorption. This was evidence that the folded tetrapyrroles, which had folded at ambient pressure, formed semicyclic unfolded conformations at a high pressure. Upon depressurization, the peak intensity and shift all recovered stepwise, showing pressure can precisely manipulate C-PC's structure as well as its color. Overall, a protein-chromophore regulatory theory of C-PC was unveiled. The pressure-tunability could be harnessed to modify and stabilize C-PC's structure and photochemical properties for designing new delivery and optical materials.
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Affiliation(s)
- Ying Li
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Qike Li
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Richard E Gillilan
- Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, Ithaca, NY, USA
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.
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11
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Ferrero DS, Tomás Gilabert O, Verdaguer N. Structural insights on the nucleoprotein C-terminal domain of Měnglà virus. Microbiol Spectr 2023; 11:e0237323. [PMID: 37888996 PMCID: PMC10714759 DOI: 10.1128/spectrum.02373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Filoviruses are the causative agents of severe and often fatal hemorrhagic disease in humans. Měnglà virus (MLAV) is a recently reported filovirus, isolated from fruit bats that is capable to replicate in human cells, representing a potential risk for human health. An in-depth structural and functional knowledge of MLAV proteins is an essential step for antiviral research on this virus that can also be extended to other emerging filoviruses. In this study, we determined the first crystal structures of the C-terminal domain (CTD) of the MLAV nucleoprotein (NP), showing important similarities to the equivalent domain in MARV. The structural data also show that the NP CTD has the ability to form large helical oligomers that may participate in the control of cytoplasmic inclusion body formation during viral replication.
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Affiliation(s)
| | | | - Nuria Verdaguer
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
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12
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Hu X, Liao M, Ding K, Wang J, Xu H, Tao K, Zhou F, Lu JR. Neutron reflection and scattering in characterising peptide assemblies. Adv Colloid Interface Sci 2023; 322:103033. [PMID: 37931380 DOI: 10.1016/j.cis.2023.103033] [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: 08/04/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
Self-assemblies of de novo designed short peptides at interface and in bulk solution provide potential platforms for developing applications in many medical and technological areas. However, characterising how bioinspired supramolecular nanostructures evolve with dynamic self-assembling processes and respond to different stimuli remains challenging. Neutron scattering technologies including small angle neutron scattering (SANS) and neutron reflection (NR) can be advantageous and complementary to other state-of-the-art techniques in tracing structural changes under different conditions. With more neutron sources now available, SANS and NR are becoming increasingly popular in studying self-assembling processes of diverse peptide and protein systems, but the difficulty in experimental manipulation and data analysis can deter beginners. This review will introduce the basic theory, general experimental setup and data analysis of SANS and NR, followed by provision of their applications in characterising interfacial and solution self-assemblies of representative peptides and proteins. SANS and NR are remarkably effective in determining the morphological features self-assembled short peptides, especially size and shape transitions as a result of either sequence changes or in response to environmental stimuli, demonstrating the unique capability of NR and SANS in unravelling the interactive processes. These examples highlight the potential of NR and SANS in supporting the development of novel short peptides and proteins as biopharmaceutical candidates in the fight against many diseases and infections that share common features of membrane interactive processes.
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Affiliation(s)
- Xuzhi Hu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK.; Lanzhou Institute of Chemical Physics, Tianshui Middle Road, Lanzhou 730000, Gansu, China
| | - Mingrui Liao
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ke Ding
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jiqian Wang
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Kai Tao
- State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou 310058, China; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Zhejiang University, Hangzhou 311215, China
| | - Feng Zhou
- Lanzhou Institute of Chemical Physics, Tianshui Middle Road, Lanzhou 730000, Gansu, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK..
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13
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Raviv U, Asor R, Shemesh A, Ginsburg A, Ben-Nun T, Schilt Y, Levartovsky Y, Ringel I. Insight into structural biophysics from solution X-ray scattering. J Struct Biol 2023; 215:108029. [PMID: 37741561 DOI: 10.1016/j.jsb.2023.108029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
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Affiliation(s)
- Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yaelle Schilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
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14
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Żyła A, Martel A, Jurczak P, Moliński A, Szymańska A, Kozak M. Human cystatin C induces the disaggregation process of selected amyloid beta peptides: a structural and kinetic view. Sci Rep 2023; 13:20833. [PMID: 38012338 PMCID: PMC10682421 DOI: 10.1038/s41598-023-47514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD) and various types of amyloidosis, are incurable; therefore, understanding the mechanisms of amyloid decomposition is crucial to develop an effective drug against them for future therapies. It has been reported that one out of three people over the age of 85 are suffering from dementia as a comorbidity to AD. Amyloid beta (Aβ), the hallmark of AD, transforms structurally from monomers into β-stranded aggregates (fibrils) via multiple oligomeric states. Astrocytes in the central nervous system secrete the human cystatin C protein (HCC) in response to various proteases and cytokines. The codeposition of Aβ and HCC in the brains of patients with AD led to the hypothesis that cystatin C is implicated in the disease process. In this study, we investigate the intermolecular interactions between different atomic structures of fibrils formed by Aβ peptides and HCC to understand the pathological aggregation of these polypeptides into neurotoxic oligomers and then amyloid plaques. To characterize the interactions between Aβ and HCC, we used a complementary approach based on the combination of small-angle neutron scattering analysis, atomic force microscopy and computational modelling, allowing the exploration of the structures of multicomponent protein complexes. We report here an optimized protocol to study that interaction. The results show a dependency of the sequence length of the Aβ peptide on the ability of the associated HCC to disaggregate it.
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Affiliation(s)
- Adriana Żyła
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
- NanoBioMedical Centre, Adam Mickiewicz University, Poznań, Poland
| | - Anne Martel
- Large Scale Structures, ILL Neutrons for Society, Institute Laue-Langevin, Grenoble, France
| | - Przemysław Jurczak
- Laboratory of Medical Chemistry, Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Augustyn Moliński
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
- NanoBioMedical Centre, Adam Mickiewicz University, Poznań, Poland
| | - Aneta Szymańska
- Laboratory of Medical Chemistry, Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland.
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Kraków, Poland.
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15
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Han Q, Su Y, Smith KM, Binns J, Drummond CJ, Darmanin C, Greaves TL. Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids. J Colloid Interface Sci 2023; 650:1393-1405. [PMID: 37480654 DOI: 10.1016/j.jcis.2023.07.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/24/2023]
Abstract
Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Yuyu Su
- School of Engineering, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Kate M Smith
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC 3168, Australia; Swiss Light Source, Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232 Villigen, Switzerland
| | - Jack Binns
- 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.
| | - Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
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16
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Blanchet CE, Round A, Mertens HDT, Ayyer K, Graewert M, Awel S, Franke D, Dörner K, Bajt S, Bean R, Custódio TF, de Wijn R, Juncheng E, Henkel A, Gruzinov A, Jeffries CM, Kim Y, Kirkwood H, Kloos M, Knoška J, Koliyadu J, Letrun R, Löw C, Makroczyova J, Mall A, Meijers R, Pena Murillo GE, Oberthür D, Round E, Seuring C, Sikorski M, Vagovic P, Valerio J, Wollweber T, Zhuang Y, Schulz J, Haas H, Chapman HN, Mancuso AP, Svergun D. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Commun Biol 2023; 6:1057. [PMID: 37853181 PMCID: PMC10585004 DOI: 10.1038/s42003-023-05416-7] [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: 01/30/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment. In solution, chemical and biophysical parameters that have an influence on the structure and dynamics of molecules can be varied and their effect on conformational changes can be monitored in time-resolved XFEL and SAXS experiments. We report here the collection of scattering form factors of proteins in solution using FEL X-rays. The form factors correspond to the scattering signal of the protein ensemble alone; the scattering contributions from the solvent and the instrument are separately measured and accurately subtracted. The experiment was done using a liquid jet for sample delivery. These results pave the way for time-resolved studies and measurements from dilute samples, capitalizing on the intense and short FEL X-ray pulses.
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Affiliation(s)
- Clement E Blanchet
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Kartik Ayyer
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - E Juncheng
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | | | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Christian Löw
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | | | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Rob Meijers
- Institute for Protein Innovation (IPI), 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Gisel Esperanza Pena Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Ekaterina Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tamme Wollweber
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yulong Zhuang
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Dmitri Svergun
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany.
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17
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Bolinsson H, Söderberg C, Herranz-Trillo F, Wahlgren M, Nilsson L. Realizing the AF4-UV-SAXS on-line coupling on protein and antibodies using high flux synchrotron radiation at the CoSAXS beamline, MAX IV. Anal Bioanal Chem 2023; 415:6237-6246. [PMID: 37572213 PMCID: PMC10558385 DOI: 10.1007/s00216-023-04900-7] [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: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
In this paper, we demonstrate the coupling of synchrotron small angle X-ray scattering (SAXS) to asymmetrical flow-field flow fractionation (AF4) for protein characterization. To the best of our knowledge, this is the first time AF4 is successfully coupled to a synchrotron for on-line measurements on proteins. This coupling has potentially high impact, as it opens the possibility to characterize individual constituents of sensitive and/or complex samples, not suited for separation using other techniques, and for low electron density samples where high X-ray flux is required, e.g., biomolecules and biologics. AF4 fractionates complex samples in native or close to native environment, with low shear forces and system surface area. Many orders of magnitude in size can be fractionated in one measurement, without having to reconfigure the experimental setup. We report AF4 fractionations with correlated UV and statistically adequate SAXS data of bovine serum albumin and a monoclonal antibody and evaluate SAXS data recorded for the two protein systems.
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Affiliation(s)
- Hans Bolinsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden.
| | - Christopher Söderberg
- RISE Research Institutes of Sweden, Division Bioeconomy and Health, Chemical Process and Pharmaceutical Development, Lund, Sweden
| | | | - Marie Wahlgren
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Lars Nilsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
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18
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Graewert MA, Wilhelmy C, Bacic T, Schumacher J, Blanchet C, Meier F, Drexel R, Welz R, Kolb B, Bartels K, Nawroth T, Klein T, Svergun D, Langguth P, Haas H. Quantitative size-resolved characterization of mRNA nanoparticles by in-line coupling of asymmetrical-flow field-flow fractionation with small angle X-ray scattering. Sci Rep 2023; 13:15764. [PMID: 37737457 PMCID: PMC10516866 DOI: 10.1038/s41598-023-42274-z] [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: 07/08/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
We present a generically applicable approach to determine an extensive set of size-dependent critical quality attributes inside nanoparticulate pharmaceutical products. By coupling asymmetrical-flow field-flow fractionation (AF4) measurements directly in-line with solution small angle X-ray scattering (SAXS), vital information such as (i) quantitative, absolute size distribution profiles, (ii) drug loading, (iii) size-dependent internal structures, and (iv) quantitative information on free drug is obtained. Here the validity of the method was demonstrated by characterizing complex mRNA-based lipid nanoparticle products. The approach is particularly applicable to particles in the size range of 100 nm and below, which is highly relevant for pharmaceutical products-both biologics and nanoparticles. The method can be applied as well in other fields, including structural biology and environmental sciences.
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Affiliation(s)
| | - Christoph Wilhelmy
- Department of Biopharmaceutics and Pharmaceutical Technology, Johannes Gutenberg-University, Mainz, Germany
| | | | | | - Clement Blanchet
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | - Roland Welz
- Postnova Analytics GmbH, Landsberg am Lech, Germany
| | - Bastian Kolb
- Department of Biopharmaceutics and Pharmaceutical Technology, Johannes Gutenberg-University, Mainz, Germany
| | - Kim Bartels
- Department of Biopharmaceutics and Pharmaceutical Technology, Johannes Gutenberg-University, Mainz, Germany
| | - Thomas Nawroth
- Department of Biopharmaceutics and Pharmaceutical Technology, Johannes Gutenberg-University, Mainz, Germany
| | | | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
- BIOSAXS GmbH, Hamburg, Germany
| | - Peter Langguth
- Department of Biopharmaceutics and Pharmaceutical Technology, Johannes Gutenberg-University, Mainz, Germany
| | - Heinrich Haas
- Department of Biopharmaceutics and Pharmaceutical Technology, Johannes Gutenberg-University, Mainz, Germany.
- BioNTech SE, Mainz, Germany.
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19
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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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20
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Triolo A, Lo Celso F, Fourmentin S, Russina O. Liquid Structure Scenario of the Archetypal Supramolecular Deep Eutectic Solvent: Heptakis(2,6-di- O-methyl)-β-cyclodextrin/levulinic Acid. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:9103-9110. [PMID: 37351462 PMCID: PMC10283020 DOI: 10.1021/acssuschemeng.3c01858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/24/2023] [Indexed: 06/24/2023]
Abstract
The concept of supramolecular solvents has been recently introduced, and the extended liquid-state window accessible for mixtures of functionalized cyclodextrins (CDs) with hydrogen bond (HB) donor species, e.g., levulinic acid, led to the debut of supramolecular deep eutectic solvents (SUPRA-DES). These solvents retain CD's inclusion ability and complement it with enhanced solvation effectiveness due to an extended HB network. However, so far, these promising features were not rationalized in terms of a microscopic description, thus hindering a more complete capitalization. This is the first joint experimental and computational study on the archetypal SUPRA-DES: heptakis(2,6-di-O-methyl)-β-CD/levulinic acid (1:27). We used X-ray scattering to probe CD's aggregation level and molecular dynamics simulation to determine the nature of interactions between SUPRA-DES components. We discover that CDs are homogeneously distributed in bulk and that HB interactions, together with the electrostatic ones, play a major role in determining mutual interaction between components. However, dispersive forces act in synergy with HB to accomplish a fundamental task in hindering hydrophobic interactions between neighbor CDs and maintaining the system homogeneity. The mechanism of mutual solvation of CD and levulinic acid is fully described, providing fundamental indications on how to extend the spectrum of SUPRA-DES combinations. Overall, this study provides the key to interpreting structural organization and solvation tunability in SUPRA-DES to extend the range of sustainable applications for these new, unique solvents.
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Affiliation(s)
- Alessandro Triolo
- Laboratorio
Liquidi Ionici, Istituto Struttura della
Materia-Consiglio Nazionale delle Ricerche (ISM-CNR), Rome 00133, Italy
| | - Fabrizio Lo Celso
- Laboratorio
Liquidi Ionici, Istituto Struttura della
Materia-Consiglio Nazionale delle Ricerche (ISM-CNR), Rome 00133, Italy
- Department
of Physics and Chemistry, Università
di Palermo, Palermo 90133, Italy
| | - Sophie Fourmentin
- Unité
de Chimie Environnementale et Interactions sur le Vivant (UCEIV, UR
4492), Université du Littoral Côte
d’Opale (ULCO), 59140 Dunkerque, France
| | - Olga Russina
- Laboratorio
Liquidi Ionici, Istituto Struttura della
Materia-Consiglio Nazionale delle Ricerche (ISM-CNR), Rome 00133, Italy
- Department
of Chemistry, Sapienza University of Rome, Rome 00185, Italy
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21
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Sonje J, Thakral S, Krueger S, Suryanarayanan R. Enabling Efficient Design of Biological Formulations Through Advanced Characterization. Pharm Res 2023; 40:1459-1477. [PMID: 36959413 DOI: 10.1007/s11095-023-03495-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/01/2023] [Indexed: 03/25/2023]
Abstract
The present review summarizes the use of differential scanning calorimetry (DSC) and scattering techniques in the context of protein formulation design and characterization. The scattering techniques include wide angle X-ray diffractometry (XRD), small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS). While DSC is valuable for understanding thermal behavior of the excipients, XRD provides critical information about physical state of solutes during freezing, annealing and in the final lyophile. However, as these techniques lack the sensitivity to detect biomolecule-related transitions, complementary characterization techniques such as small-angle scattering can provide valuable insights.
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Affiliation(s)
- Jayesh Sonje
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
- BioTherapeutics, Pharmaceutical Sciences, Pfizer Inc., 1 Burtt Road, Andover, USA
| | - Seema Thakral
- Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Susan Krueger
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Raj Suryanarayanan
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA.
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22
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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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23
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Barclay A, Kragelund BB, Arleth L, Pedersen MC. Modeling of flexible membrane-bound biomolecular complexes for solution small-angle scattering. J Colloid Interface Sci 2023; 635:611-621. [PMID: 36634513 DOI: 10.1016/j.jcis.2022.12.024] [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: 08/25/2022] [Revised: 11/18/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Recent advances in protein expression protocols, sample handling, and experimental set up of small-angle scattering experiments have allowed users of the technique to structurally investigate biomolecules of growing complexity and structural disorder. Notable examples include intrinsically disordered proteins, multi-domain proteins and membrane proteins in suitable carrier systems. Here, we outline a modeling scheme for calculating the scattering profiles from such complex samples. This kind of modeling is necessary for structural information to be refined from the corresponding data. The scheme bases itself on a hybrid of classical form factor based modeling and the well-known spherical harmonics-based formulation of small-angle scattering amplitudes. Our framework can account for flexible domains alongside other structurally elaborate components of the molecular system in question. We demonstrate the utility of this modeling scheme through a recent example of a structural model of the growth hormone receptor membrane protein in a phospholipid bilayer nanodisc which is refined against experimental SAXS data. Additionally we investigate how the scattering profiles from the complex would appear under different scattering contrasts. For each contrast situation we discuss what structural information is contained and the related consequences for modeling of the data.
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Affiliation(s)
- Abigail Barclay
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark.
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
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24
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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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25
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Liu G, Ekmen E, Jalalypour F, Mertens HDT, Jeffries CM, Svergun D, Atilgan AR, Atilgan C, Sayers Z. Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations. J Chem Phys 2023; 158:085101. [PMID: 36859088 DOI: 10.1063/5.0136558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations that can be adopted by a pH/ionic strength (IS) sensitive protein and to quantify its distinct populations in solution. To explore how the conformational distribution of proteins may be modified in the environmental niches of biological media, we focus on the periplasmic ferric binding protein A (FbpA) from Haemophilus influenzae involved in the mechanism by which bacteria capture iron from higher organisms. We examine iron-binding/release mechanisms of FbpA in varying conditions simulating its biological environment. While we show that these changes fall within the detectable range for SAXS as evidenced by differences observed in the theoretical scattering patterns calculated from the crystal structure models of apo and holo forms, detection of conformational changes due to the point mutation D52A and changes in ionic strength (IS) from SAXS scattering profiles have been challenging. Here, to reach conclusions, statistical analyses with SAXS profiles and results from different techniques were combined in a complementary fashion. The SAXS data complemented by size exclusion chromatography point to multiple and/or alternative conformations at physiological IS, whereas they are well-explained by single crystallographic structures in low IS buffers. By fitting the SAXS data with unique conformations sampled by a series of MD simulations under conditions mimicking the buffers, we quantify the populations of the occupied substates. We also find that the D52A mutant that we predicted by coarse-grained computational modeling to allosterically control the iron binding site in FbpA, responds to the environmental changes in our experiments with conformational selection scenarios that differ from those of the wild type.
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Affiliation(s)
- Goksin Liu
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Erhan Ekmen
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Farzaneh Jalalypour
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, 22603 Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, 22603 Hamburg, Germany
| | - Ali Rana Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Canan Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Zehra Sayers
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
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26
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Biniek-Antosiak K, Bejger M, Śliwiak J, Baranowski D, Mohammed ASA, Svergun DI, Rypniewski W. Structural, Thermodynamic and Enzymatic Characterization of N, N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus. Int J Mol Sci 2022; 23:ijms232415736. [PMID: 36555375 PMCID: PMC9779004 DOI: 10.3390/ijms232415736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Chitin is a major source of energy and macroelements for many organisms. An important step in its degradation is the deacetylation of chitin or its fragments. Deacetylase from the extremophile Pyrococcus chitonophagus has been analyzed by X-ray crystallography, small-angle X-ray scattering, differential scanning calorimetry, isothermal titration calorimetry and NMR to determine its structure, thermodynamics and enzymatic properties. It is a hexameric, zinc-containing metalloenzyme that retains its structural integrity up to temperatures slightly exceeding 100 °C. It removes the acetyl group specifically from the non-reducing end of the sugar substrate. Its main substrate is N,N-diacetylchitobiose but it also active, at a reduced level, toward N-acetyl-d-glucosamine or a trimer of N-acetyl-d-glucosamine units. Crystallographic analysis includes the structure of the enzyme with its main substrate approaching the active site in a monodentate manner, replacing the single water molecule that is bound at the Zn2+ cation when the ligand is absent. The Zn2+ cation remains tetrahedrally coordinated, with three of its ligands provided by the protein's conserved His-Asp-His triad. The crystal structures are consistent with the reaction mechanism proceeding via an anhydride intermediate. Hydrolysis as the first step cannot be ruled out in a hydrated environment but no defined 'hydrolytic water' site can be identified in the analyzed structures.
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Affiliation(s)
- Katarzyna Biniek-Antosiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Daniel Baranowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
| | - Ahmed S. A. Mohammed
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland
- Correspondence:
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27
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Miller RC, Cummings C, Huang Q, Ando N, Gillilan RE. Inline small-angle X-ray scattering-coupled chromatography under extreme hydrostatic pressure. Protein Sci 2022; 31:e4489. [PMID: 36320105 PMCID: PMC9669991 DOI: 10.1002/pro.4489] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
As continuing discoveries highlight the surprising abundance and resilience of deep ocean and subsurface microbial life, the effects of extreme hydrostatic pressure on biological structure and function have attracted renewed interest. Biological small-angle X-ray scattering (BioSAXS) is a widely used method of obtaining structural information from biomolecules in solution under a wide range of solution conditions. Due to its ability to reduce radiation damage, remove aggregates, and separate monodisperse components from complex mixtures, size-exclusion chromatography-coupled SAXS (SEC-SAXS) is now the dominant form of BioSAXS at many synchrotron beamlines. While BioSAXS can currently be performed with some difficulty under pressure with non-flowing samples, it has not been clear how, or even if, continuously flowing SEC-SAXS, with its fragile media-packed columns, might work in an extreme high-pressure environment. Here we show, for the first time, that reproducible chromatographic separations coupled directly to high-pressure BioSAXS can be achieved at pressures up to at least 100 MPa and that pressure-induced changes in folding and oligomeric state and other properties can be observed. The apparatus described here functions at a range of temperatures (0°C-50°C), expanding opportunities for understanding biomolecular rules of life in deep ocean and subsurface environments.
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Affiliation(s)
- Robert C. Miller
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNew YorkUSA
| | - Cody Cummings
- Center for High Energy X‐ray Sciences (CHEXS)IthacaNew YorkUSA
| | - Qingqiu Huang
- Center for High Energy X‐ray Sciences (CHEXS)IthacaNew YorkUSA
| | - Nozomi Ando
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNew YorkUSA
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28
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Brosey CA, Shen R, Moiani D, Jones DE, Burnett K, Hura GL, Tainer JA. Applying HT-SAXS to chemical ligand screening. Methods Enzymol 2022; 678:331-350. [PMID: 36641213 PMCID: PMC11239221 DOI: 10.1016/bs.mie.2022.09.022] [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] [Indexed: 11/28/2022]
Abstract
Chemical probes are invaluable tools for investigating essential biological processes. Understanding how small-molecule probes engage biomolecular conformations is critical to developing their functional selectivity. High-throughput solution X-ray scattering is well-positioned to profile target-ligand complexes during probe development, bringing conformational insight and selection to traditional ligand binding assays. Access to high-quality synchrotron SAXS datasets and high-throughput data analysis now allows routine academic users to incorporate conformational information into small-molecule development pipelines. Here we describe a general approach for benchmarking and preparing HT-SAXS chemical screens from small fragment libraries. Using the allosteric oxidoreductase Apoptosis-Inducing Factor (AIF) as an exemplary system, we illustrate how HT-SAXS efficiently identifies an allosteric candidate among hits of a microscale thermophoresis ligand screen. We discuss considerations for pursuing HT-SAXS chemical screening with other systems of interest and reflect on advances to extend screening throughput and sensitivity.
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Affiliation(s)
- Chris A Brosey
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.
| | - Runze Shen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Davide Moiani
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kathryn Burnett
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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29
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Chatzimagas L, Hub JS. Structure and ensemble refinement against SAXS data: Combining MD simulations with Bayesian inference or with the maximum entropy principle. Methods Enzymol 2022; 678:23-54. [PMID: 36641209 DOI: 10.1016/bs.mie.2022.09.014] [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: 11/27/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a powerful method for tracking conformational transitions of proteins or soft-matter complexes in solution. However, the interpretation of the experimental data is challenged by the low spatial resolution and the low information content of the data, which lead to a high risk of overinterpreting the data. Here, we illustrate how SAXS data can be integrated into all-atom molecular dynamics (MD) simulation to derive atomic structures or heterogeneous ensembles that are compatible with the data. Besides providing atomistic insight, the MD simulation adds physicochemical information, as encoded in the MD force fields, which greatly reduces the risk of overinterpretation. We present an introduction into the theory of SAXS-driven MD simulations as implemented in GROMACS-SWAXS, a modified version of the GROMACS simulation software. We discuss SAXS-driven parallel-replica ensemble refinement with commitment to the maximum entropy principle as well as a Bayesian formulation of SAXS-driven structure refinement. Practical considerations for running and interpreting the simulations are presented. The methods are freely available via GitLab at https://gitlab.com/cbjh/gromacs-swaxs.
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Affiliation(s)
- Leonie Chatzimagas
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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30
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Weng Y, Su CJ, Jiang H, Chiang CW. Photoredox C-H functionalization leads the site-selective phenylalanine bioconjugation. Sci Rep 2022; 12:18994. [PMID: 36348051 PMCID: PMC9643349 DOI: 10.1038/s41598-022-23481-6] [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: 07/30/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
Abstract
Site-selectively chemical bioconjugation of peptides and proteins can improve the therapeutic exploration of modified protein drugs. Only 3.8% natural abundance of phenylalanine in protein and nearly 90% of proteins contain at least one phenylalanine residue in their sequenced, showing the potential in biopharmaceutical utility of the phenylalanine bioconjugation. However, the covalent bioconjugation of native phenylalanine is one of the most challenging problems in protein modification. Herein, an approach to protein modification is described that relies on a photoredox method for the site-selective bioconjugation of phenylalanine. This methodology has been validated on peptides as well as protein insulin using a straightforward and mild condition. In addition, based on characterization by near-UV CD spectroscopy and small angle X-ray scattering (SAXS), this pyrazole labeling approach permitted the insulin hexamer to completely dissociate into the monomeric form, thus making it a potential candidate for use as rapid-acting insulin for the treatment of diabetes.
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Affiliation(s)
- Yue Weng
- grid.34418.3a0000 0001 0727 9022Ministry-of-Education Key Laboratory for the Synthesis and Application of Organic Functional Molecule &, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, People’s Republic of China
| | - Chun-Jen Su
- grid.410766.20000 0001 0749 1496TLS BL23A, National Synchrotron Radiation Research Center (NSRRC), Hsinchu, Taiwan
| | - Haoyang Jiang
- grid.34418.3a0000 0001 0727 9022Ministry-of-Education Key Laboratory for the Synthesis and Application of Organic Functional Molecule &, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, People’s Republic of China
| | - Chien-Wei Chiang
- grid.445078.a0000 0001 2290 4690Department of Chemistry, Soochow University, Taipei, Taiwan
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31
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Whitten AE, Jeffries CM. Data analysis and modeling of small-angle neutron scattering data with contrast variation from bio-macromolecular complexes. Methods Enzymol 2022; 678:55-96. [PMID: 36641217 DOI: 10.1016/bs.mie.2022.09.015] [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: 11/11/2022]
Abstract
Small-angle neutron scattering (SANS) with contrast variation (CV) is a valuable technique in the structural biology toolchest. Accurate structural parameters-e.g., radii of gyration, volumes, dimensions, and distance distribution(s)-can be derived from the SANS-CV data to yield the shape and disposition of the individual components within stable complexes. Contrast variation is achieved through the substitution of hydrogen isotopes (1H for 2H) in molecules and solvents to alter the neutron scattering properties of each component of a complex. While SANS-CV can be used a stand-alone technique for interrogating the overall structure of biomacromolecules in solution, it also complements other methods such as small-angle X-ray scattering, crystallography, nuclear magnetic resonance, and cryo-electron microscopy. Undertaking a SANS-CV experiment is challenging, due in part to the preparation of significant quantities of monodisperse samples that may require deuterium (2H) labeling. Nevertheless, SANS-CV can be used to study a diverse range biomacromolecular complexes including protein-protein and protein-nucleic acid systems, membrane proteins, and flexible systems resistant to crystallization. This chapter describes how to approach the data analysis and modeling of SANS data, including: (1) Analysis of the forward scattering (I(0)) and calculation of theoretical estimates of contrast; (2) Analysis of the contrast dependence of the radius of gyration using the Stuhrmann plot and parallel axis theorem; (3) Calculation of composite scattering functions to evaluate the size, shape, and dispositions of individual components within a complex, and; (4) Development of real-space models to fit the SANS-CV data using volume-element bead modeling or atomistic rigid body modeling.
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Affiliation(s)
- Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia.
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o Deutsches Elektronen-Synchrotron, Hamburg, Germany.
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32
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Beck C, Grimaldo M, Lopez H, Da Vela S, Sohmen B, Zhang F, Oettel M, Barrat JL, Roosen-Runge F, Schreiber F, Seydel T. Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture. J Phys Chem B 2022; 126:7400-7408. [PMID: 36112146 PMCID: PMC9527755 DOI: 10.1021/acs.jpcb.2c02380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The crowded environment of biological systems such as
the interior
of living cells is occupied by macromolecules with a broad size distribution.
This situation of polydispersity might influence the dependence of
the diffusive dynamics of a given tracer macromolecule in a monodisperse
solution on its hydrodynamic size and on the volume fraction. The
resulting size dependence of diffusive transport crucially influences
the function of a living cell. Here, we investigate a simplified model
system consisting of two constituents in aqueous solution, namely,
of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin
(Ig), systematically depending on the total volume fraction and ratio
of these constituents. From high-resolution quasi-elastic neutron
spectroscopy, the separate apparent short-time diffusion coefficients
for BSA and Ig in the mixture are extracted, which show substantial
deviations from the diffusion coefficients measured in monodisperse
solutions at the same total volume fraction. These deviations can
be modeled quantitatively using results from the short-time rotational
and translational diffusion in a two-component hard sphere system
with two distinct, effective hydrodynamic radii. Thus, we find that
a simple colloid picture well describes short-time diffusion in binary
mixtures as a function of the mixing ratio and the total volume fraction.
Notably, the self-diffusion of the smaller protein BSA in the mixture
is faster than the diffusion in a pure BSA solution, whereas the self-diffusion
of Ig in the mixture is slower than in the pure Ig solution.
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Affiliation(s)
- Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Marco Grimaldo
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, D07 XT95 Grangegorman, Ireland
| | - Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Benedikt Sohmen
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Martin Oettel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | | | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
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Xu AY, Rinee KC, Stemple C, Castellanos MM, Bakshi K, Krueger S, Curtis JE. Counting the water: Characterize the hydration level of aluminum adjuvants using contrast matching small-angle neutron scattering. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Pérez J, Girard E. Medical contrast agents as promising tools for biomacromolecular SAXS experiments. Acta Crystallogr D Struct Biol 2022; 78:1120-1130. [PMID: 36048152 PMCID: PMC9435597 DOI: 10.1107/s2059798322007392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Lanthanide-based complexes are presented as a promising class of molecules for efficient SAXS contrast-variation experiments. Their interactions and contrast properties are analyzed for an oligomeric protein and a protein–RNA complex. Small-angle X-ray scattering (SAXS) has become an indispensable tool in structural biology, complementing atomic-resolution techniques. It is sensitive to the electron-density difference between solubilized biomacromolecules and the buffer, and provides information on molecular masses, particle dimensions and interactions, low-resolution conformations and pair distance-distribution functions. When SAXS data are recorded at multiple contrasts, i.e. at different solvent electron densities, it is possible to probe, in addition to their overall shape, the internal electron-density profile of biomacromolecular assemblies. Unfortunately, contrast-variation SAXS has been limited by the range of solvent electron densities attainable using conventional co-solutes (for example sugars, glycerol and salt) and by the fact that some biological systems are destabilized in their presence. Here, SAXS contrast data from an oligomeric protein and a protein–RNA complex are presented in the presence of iohexol and Gd-HPDO3A, two electron-rich molecules that are used in biomedical imaging and that belong to the families of iodinated and lanthanide-based complexes, respectively. Moderate concentrations of both molecules allowed solvent electron densities matching those of proteins to be attained. While iohexol yielded higher solvent electron densities (per mole), it interacted specifically with the oligomeric protein and precipitated the protein–RNA complex. Gd-HPDO3A, while less efficient (per mole), did not disrupt the structural integrity of either system, and atomic models could be compared with the SAXS data. Due to their elevated solubility and electron density, their chemical inertness, as well as the possibility of altering their physico-chemical properties, lanthanide-based complexes represent a class of molecules with promising potential for contrast-variation SAXS experiments on diverse biomacromolecular systems.
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Anitas EM. α-SAS: an integrative approach for structural modeling of biological macromolecules in solution. Acta Crystallogr D Struct Biol 2022; 78:1046-1063. [DOI: 10.1107/s2059798322006349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
Modern small-angle scattering (SAS) experiments with neutrons (SANS) or X-rays (SAXS) combined with contrast variation provide comprehensive information about the structure of large multicomponent macromolecules in solution and allow the size, shape and relative arrangement of each component to be mapped out. To obtain such information, it is essential to perform well designed experiments, in which all necessary steps, from assessing sample suitability to structure modeling, are properly executed. This paper describes α-SAS, an integrative approach that is useful for effectively planning a biological contrast-variation SAS experiment. The accurate generation of expected experimental intensities using α-SAS allows the substantial acceleratation of research into the structure and function of biomacromolecules by minimizing the time and costs associated with performing a SAS experiment. The method is validated using a few basic structures with known analytical expressions for scattering intensity and using experimental SAXS data from Arabidopsis β-amylase 1 protein and SANS data from the histidine kinase–Sda complex and from human dystrophin without and with a membrane-mimicking nanodisk. Simulation of a SANS contrast-variation experiment is performed for synthetic nanobodies that effectively neutralize SARS-CoV-2.
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36
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Bertorelle F, Wegner KD, Perić Bakulić M, Fakhouri H, Comby-Zerbino C, Sagar A, Bernadó P, Resch-Genger U, Bonačić-Koutecký V, Le Guével X, Antoine R. Tailoring the NIR-II Photoluminescence of Single Thiolated Au 25 Nanoclusters by Selective Binding to Proteins. Chemistry 2022; 28:e202200570. [PMID: 35703399 DOI: 10.1002/chem.202200570] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Indexed: 12/28/2022]
Abstract
Atomically precise gold nanoclusters are a fascinating class of nanomaterials that exhibit molecule-like properties and have outstanding photoluminescence (PL). Their ultrasmall size, molecular chemistry, and biocompatibility make them extremely appealing for selective biomolecule labeling in investigations of biological mechanisms at the cellular and anatomical levels. In this work, we report a simple route to incorporate a preformed Au25 nanocluster into a model bovine serum albumin (BSA) protein. A new approach combining small-angle X-ray scattering and molecular modeling provides a clear localization of a single Au25 within the protein to a cysteine residue on the gold nanocluster surface. Attaching Au25 to BSA strikingly modifies the PL properties with enhancement and a redshift in the second near-infrared (NIR-II) window. This study paves the way to conrol the design of selective sensitive probes in biomolecules through a ligand-based strategy to enable the optical detection of biomolecules in a cellular environment by live imaging.
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Affiliation(s)
- Franck Bertorelle
- Institut Lumière Matière, UMR5306, Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.,Nantes Université, CNRS, US2B, UMR 6286, 44000, Nantes, France
| | - K David Wegner
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstaetter-Str. 11, 12489, Berlin, Germany
| | - Martina Perić Bakulić
- Center of Excellence for Science and Technology, Integration of Mediterranean Region (STIM) at, Interdisciplinary Center for Advanced Sciences and Technology (ICAST), University of Split, Poljička cesta 35, 21000, Split, Croatia
| | - Hussein Fakhouri
- Institut Lumière Matière, UMR5306, Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.,Center of Excellence for Science and Technology, Integration of Mediterranean Region (STIM) at, Interdisciplinary Center for Advanced Sciences and Technology (ICAST), University of Split, Poljička cesta 35, 21000, Split, Croatia
| | - Clothilde Comby-Zerbino
- Institut Lumière Matière, UMR5306, Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Amin Sagar
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090, Montpellier, France
| | - Pau Bernadó
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090, Montpellier, France
| | - Ute Resch-Genger
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstaetter-Str. 11, 12489, Berlin, Germany
| | - Vlasta Bonačić-Koutecký
- Center of Excellence for Science and Technology, Integration of Mediterranean Region (STIM) at, Interdisciplinary Center for Advanced Sciences and Technology (ICAST), University of Split, Poljička cesta 35, 21000, Split, Croatia.,Chemistry Department, Humboldt University of Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Xavier Le Guével
- Institute for Advanced Biosciences, Université Grenoble Alpes/ INSERM1209/CNRS-UMR5309, 38700, La Tronche, France
| | - Rodolphe Antoine
- Institut Lumière Matière, UMR5306, Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
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A comparative study of unpasteurized and pasteurized frozen whole hen eggs using size-exclusion chromatography and small-angle X-ray scattering. Sci Rep 2022; 12:9218. [PMID: 35654960 PMCID: PMC9163139 DOI: 10.1038/s41598-022-12885-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Hen eggs are rich in proteins and are an important source of protein for humans. Pasteurized frozen whole hen eggs are widely used in cooking and confectionery and can be stored for long periods. However, processed eggs differ from raw eggs in properties such as viscosity, foaming ability, and thermal aggregation. To develop pasteurized frozen whole egg products with properties similar to those of unpasteurized whole eggs, it is necessary to establish a method that can differentiate between the two egg types with respect to the structures of their proteins. In this study, size-exclusion chromatography (SEC) and SEC coupled with small-angle X-ray scattering (SEC-SAXS) were successfully used to differentiate between the proteins in unpasteurized and pasteurized frozen whole eggs. We found that proteins in the plasma fraction of egg yolk, especially apovitellenins I and II, formed large aggregates in the pasteurized eggs, indicating that their structures are sensitive to temperature changes during pasteurization, freezing, and thawing. The results suggest that SEC and SEC-SAXS can be used to differentiate between unpasteurized and pasteurized frozen whole eggs. Additionally, they may be useful in determining molecular sizes and shapes of multiple components in various complex biological systems such as whole eggs.
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38
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Krueger S. Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs. Curr Opin Struct Biol 2022; 74:102375. [PMID: 35490650 PMCID: PMC10988784 DOI: 10.1016/j.sbi.2022.102375] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/09/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued improvements in sample preparation techniques, including deuterium labeling, neutron instrumentation and complementary techniques such as small-angle x-ray scattering (SAXS), cryo-EM, NMR and x-ray crystallography, along with the availability of more powerful structure prediction algorithms and computational resources has made SANS more important than ever as a means to obtain unique information on the structure of biological complexes in solution. In particular, the contrast variation (CV) technique, which requires a large commitment in both sample preparation and measurement time, has become more practical with the advent of these improved resources. Here, challenges and recent triumphs as well as future prospects are discussed.
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Affiliation(s)
- Susan Krueger
- NIST Center for Neutron Research, NIST, Gaithersburg, MD, 20899, USA.
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39
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Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging. Structure 2022; 30:763-776.e4. [PMID: 35338852 PMCID: PMC9081212 DOI: 10.1016/j.str.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022]
Abstract
Cataract, a clouding of the eye lens from protein precipitation, affects millions of people every year. The lens proteins, the crystallins, show extensive post-translational modifications (PTMs) in cataractous lenses. The most common PTMs, deamidation and oxidation, promote crystallin aggregation; however, it is not clear precisely how these PTMs contribute to crystallin insolubilization. Here, we report six crystal structures of the lens protein γS-crystallin (γS): one of the wild-type and five of deamidated γS variants, from three to nine deamidation sites, after sample aging. The deamidation mutations do not change the overall fold of γS; however, increasing deamidation leads to accelerated disulfide-bond formation. Addition of deamidated sites progressively destabilized protein structure, and the deamidated variants display an increased propensity for aggregation. These results suggest that the deamidated variants are useful as models for accelerated aging; the structural changes observed provide support for redox activity of γS-crystallin in the lens.
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Barclay A, Tidemand Johansen N, Tidemand FG, Arleth L, Pedersen MC. Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:483-493. [PMID: 35362471 PMCID: PMC8972807 DOI: 10.1107/s2059798322001838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022]
Abstract
The combination of online size-exclusion chromatography and small-angle X-ray scattering (SEC–SAXS) is rapidly becoming a key technique for structural investigations of elaborate biophysical samples in solution. Here, a novel model-refinement strategy centred around the technique is outlined and its utility is demonstrated by analysing data series from several SEC–SAXS experiments on phospholipid bilayer nanodiscs. Using this method, a single model was globally refined against many frames from the same data series, thereby capturing the frame-to-frame tendencies of the irradiated sample. These are compared with models refined in the traditional manner, in which refinement is based on the average profile of a set of consecutive frames from the same data series without an in-depth comparison of individual frames. This is considered to be an attractive model-refinement scheme as it considerably lowers the total number of parameters refined from the data series, produces tendencies that are automatically consistent between frames, and utilizes a considerably larger portion of the recorded data than is often performed in such experiments. Additionally, a method is outlined for correcting a measured UV absorption signal by accounting for potential peak broadening by the experimental setup.
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Protic Ionic Liquid Cation Alkyl Chain Length Effect on Lysozyme Structure. Molecules 2022; 27:molecules27030984. [PMID: 35164252 PMCID: PMC8839406 DOI: 10.3390/molecules27030984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/16/2022] Open
Abstract
Solvents that stabilize protein structures can improve and expand their biochemical applications, particularly with the growing interest in biocatalytic-based processes. Aiming to select novel solvents for protein stabilization, we explored the effect of alkylammonium nitrate protic ionic liquids (PILs)-water mixtures with increasing cation alkyl chain length on lysozyme conformational stability. Four PILs were studied, that is, ethylammonium nitrate (EAN), butylammonium nitrate (BAN), hexylammonium nitrate (HAN), and octylammonium nitrate (OAN). The surface tension, viscosity, and density of PIL-water mixtures at low to high concentrations were firstly determined, which showed that an increasing cation alkyl chain length caused a decrease in the surface tension and density as well as an increase in viscosity for all PIL solutions. Small-angle X-ray scattering (SAXS) was used to investigate the liquid nanostructure of the PIL solutions, as well as the overall size, conformational flexibility and changes to lysozyme structure. The concentrated PILs with longer alkyl chain lengths, i.e., over 10 mol% butyl-, 5 mol% hexyl- and 1 mol% octylammonium cations, possessed liquid nanostructures. This detrimentally interfered with solvent subtraction, and the more structured PIL solutions prevented quantitative SAXS analysis of lysozyme structure. The radius of gyration (Rg) of lysozyme in the less structured aqueous PIL solutions showed little change with up to 10 mol% of PIL. Kratky plots, SREFLEX models, and FTIR data showed that the protein conformation was maintained at a low PIL concentration of 1 mol% and lower when compared with the buffer solution. However, 50 mol% EAN and 5 mol% HAN significantly increased the Rg of lysozyme, indicating unfolding and aggregation of lysozyme. The hydrophobic interaction and liquid nanostructure resulting from the increased cation alkyl chain length in HAN likely becomes critical. The impact of HAN and OAN, particularly at high concentrations, on lysozyme structure was further revealed by FTIR. This work highlights the negative effect of a long alkyl chain length and high concentration of PILs on lysozyme structural stability.
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42
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Fehér B, Mihály J, Demeter A, Almásy L, Wacha A, Varga Z, Varga I, Pedersen JS, Bóta A. Advancement of Fluorescent and Structural Properties of Bovine Serum Albumin-Gold Bioconjugates in Normal and Heavy Water with pH Conditioning and Ageing. NANOMATERIALS 2022; 12:nano12030390. [PMID: 35159734 PMCID: PMC8840595 DOI: 10.3390/nano12030390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023]
Abstract
The red-emitting fluorescent properties of bovine serum albumin (BSA)–gold conjugates are commonly attributed to gold nanoclusters formed by metallic and ionized gold atoms, stabilized by the protein. Others argue that red fluorescence originates from gold cation–protein complexes instead, not gold nanoclusters. Our fluorescence and infrared spectroscopy, neutron, and X-ray small-angle scattering measurements show that the fluorescence and structural behavior of BSA–Au conjugates are different in normal and heavy water, strengthening the argument for the existence of loose ionic gold–protein complexes. The quantum yield for red-emitting luminescence is higher in heavy water (3.5%) than normal water (2.4%), emphasizing the impact of hydration effects. Changes in red luminescence are associated with the perturbations of BSA conformations and alterations to interatomic gold–sulfur and gold–oxygen interactions. The relative alignment of domains I and II, II and III, III and IV of BSA, determined from small-angle scattering measurements, indicate a loose (“expanded-like”) structure at pH 12 (pD ~12); by contrast, at pH 7 (pD ~7), a more regular formation appears with an increased distance between the I and II domains, suggesting the localization of gold atoms in these regions.
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Affiliation(s)
- Bence Fehér
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (B.F.); (J.M.); (A.W.); (Z.V.)
- Neutron Spectroscopy Department, Centre for Energy Research, Konkoly-Thege M. út 29-33, 1121 Budapest, Hungary;
| | - Judith Mihály
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (B.F.); (J.M.); (A.W.); (Z.V.)
| | - Attila Demeter
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (B.F.); (J.M.); (A.W.); (Z.V.)
- Correspondence: (A.D.); (A.B.)
| | - László Almásy
- Neutron Spectroscopy Department, Centre for Energy Research, Konkoly-Thege M. út 29-33, 1121 Budapest, Hungary;
| | - András Wacha
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (B.F.); (J.M.); (A.W.); (Z.V.)
| | - Zoltán Varga
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (B.F.); (J.M.); (A.W.); (Z.V.)
| | - Imre Varga
- Institute of Chemistry, Eötvös Loránd University (ELTE), Pázmány Péter sétány 1/A, 1117 Budapest, Hungary;
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark;
| | - Attila Bóta
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (B.F.); (J.M.); (A.W.); (Z.V.)
- Correspondence: (A.D.); (A.B.)
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Martel A, Gabel F. Time-resolved small-angle neutron scattering (TR-SANS) for structural biology of dynamic systems: Principles, recent developments, and practical guidelines. Methods Enzymol 2022; 677:263-290. [DOI: 10.1016/bs.mie.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Morrison KA, Doekhie A, Neville GM, Price GJ, Whitley P, Doutch J, Edler KJ. Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs. BBA ADVANCES 2022; 2:100033. [PMID: 37082608 PMCID: PMC10074903 DOI: 10.1016/j.bbadva.2021.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Small angle scattering techniques are beginning to be more widely utilised for structural analysis of biological systems. However, applying these techniques to study membrane proteins still remains problematic, due to sample preparation requirements and analysis of the resulting data. The development of styrene-maleic acid co-polymers (SMA) to extract membrane proteins into nanodiscs for further study provides a suitable environment for structural analysis. Methods We use small angle neutron scattering (SANS) with three different contrasts to determine structural information for two different polymer nanodisc-incorporated proteins, Outer membrane protein F (OmpF) and gramicidin. Ab initio modelling was applied to generate protein/lipid structures from the SANS data. Other complementary structural methodologies, such as DLS, CD and TEM were compared alongside this data with known protein crystal structures. Results A single-phase model was constructed for gramicidin-containing nanodiscs, which showed dimer formation in the centre of the nanodisc. For OmpF-nanodiscs we were able to construct a multi-phase model, providing structural information on the protein/lipid and polymer components of the sample. Conclusions Polymer-nanodiscs can provide a suitable platform to investigate certain membrane proteins using SANS, alongside other structural methodologies. However, differences between the published crystal structure and OmpF-nanodiscs were observed, suggesting the nanodisc structure could be altering the folding of the protein. General significance Small angle scattering techniques can provide structural information on the protein and polymer nanodisc without requiring crystallisation of the protein. Additional complementary techniques, such as ab initio modelling, can generate alternative models both the protein and nanodisc system.
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Affiliation(s)
- Kerrie A. Morrison
- Department of Chemistry, University of Bath, Bath, UK
- Department of Biology and Biochemistry, University of Bath, Bath, UK
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, UK
| | - Aswin Doekhie
- Department of Chemistry, University of Bath, Bath, UK
| | - George M. Neville
- Department of Chemistry, University of Bath, Bath, UK
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, UK
| | - Gareth J. Price
- Department of Chemistry, University of Bath, Bath, UK
- Department of Chemistry, Khalifa University, Abu Dhabi, UAE
| | - Paul Whitley
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - James Doutch
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX. UK
- Corresponding authors.
| | - Karen J. Edler
- Department of Chemistry, University of Bath, Bath, UK
- Corresponding authors.
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45
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Krueger S. Planning, executing and assessing the validity of SANS contrast variation experiments. Methods Enzymol 2022; 677:127-155. [DOI: 10.1016/bs.mie.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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46
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de Oliveira Neto M, de Freitas Fernandes A, Piiadov V, Craievich AF, de Araújo EA, Polikarpov I. SAXSMoW 3.0: New advances in the determination of the molecular weight of proteins in dilute solutions from SAXS intensity data on a relative scale. Protein Sci 2022; 31:251-258. [PMID: 34761467 PMCID: PMC8740845 DOI: 10.1002/pro.4227] [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] [Received: 10/05/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023]
Abstract
SAXSMoW (SAXS Molecular Weight) is an online platform widely used over the past few years for determination of molecular weights of proteins in dilute solutions. The scattering intensity retrieved from small-angle X-ray scattering (SAXS) raw data is the sole input to SAXSMoW for determination of molecular weights of proteins in liquid. The current updated SAXSMoW version 3.0 determines the linear dependence of the true protein volume on their apparent protein volume, based on SAXS curves calculated for 67,000 protein structures selected from the Protein Data Bank. SAXSMoW 3.0 was tested against 43 experimental SAXS scattering curves from proteins with known molecular weights. Our results demonstrate that most of the molecular weights determined for the nonglycosylated and also for the glycosylated proteins are in good agreement with their expected molecular weights. Additionally, the average discrepancies between the calculated molecular weights and their nominal values for glycosylated proteins are similar to those for nonglycosylated ones.
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Affiliation(s)
- Mario de Oliveira Neto
- Biophysics and Pharmacology DepartmentBioscience Institute, Universidade Estadual PaulistaBotucatuSão PauloBrazil
| | | | - Vassili Piiadov
- Sao Carlos Institute of PhysicsUniversity of Sao PauloSão PauloBrazil
| | | | - Evandro Ares de Araújo
- Brazilian Synchrotron Light LaboratoryBrazilian Center for Research in Energy and MaterialsCampinasSão PauloBrazil
| | - Igor Polikarpov
- Sao Carlos Institute of PhysicsUniversity of Sao PauloSão PauloBrazil
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Graewert MA, Svergun DI. Advanced sample environments and sample requirements for biological SAXS. Methods Enzymol 2022; 677:1-39. [DOI: 10.1016/bs.mie.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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48
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Gillilan RE. High-pressure SAXS, deep life, and extreme biophysics. Methods Enzymol 2022; 677:323-355. [DOI: 10.1016/bs.mie.2022.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Schroer MA, Schewa S, Gruzinov AY, Rönnau C, Lahey-Rudolph JM, Blanchet CE, Zickmantel T, Song YH, Svergun DI, Roessle M. Probing the existence of non-thermal Terahertz radiation induced changes of the protein solution structure. Sci Rep 2021; 11:22311. [PMID: 34785744 PMCID: PMC8595702 DOI: 10.1038/s41598-021-01774-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/26/2021] [Indexed: 01/14/2023] Open
Abstract
During the last decades discussions were taking place on the existence of global, non-thermal structural changes in biological macromolecules induced by Terahertz (THz) radiation. Despite numerous studies, a clear experimental proof of this effect for biological particles in solution is still missing. We developed a setup combining THz-irradiation with small angle X-ray scattering (SAXS), which is a sensitive method for detecting the expected structural changes. We investigated in detail protein systems with different shape morphologies (bovine serum albumin, microtubules), which have been proposed to be susceptible to THz-radiation, under variable parameters (THz wavelength, THz power densities up to 6.8 mW/cm2, protein concentrations). None of the studied systems and conditions revealed structural changes detectable by SAXS suggesting that the expected non-thermal THz-induced effects do not lead to alterations of the overall structures, which are revealed by scattering from dissolved macromolecules. This leaves us with the conclusion that, if such effects are present, these are either local or outside of the spectrum and power range covered by the present study.
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Affiliation(s)
- Martin A. Schroer
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany ,grid.5718.b0000 0001 2187 5445Present Address: Nanoparticle Process Technology, University of Duisburg-Essen, Lotharstr. 1, 47057 Duisburg, Germany
| | - Siawosch Schewa
- University of Applied Sciences Luebeck, Moenkhofer Weg 239, 23562 Luebeck, Germany
| | - Andrey Yu. Gruzinov
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Rönnau
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | | | - Clement E. Blanchet
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Till Zickmantel
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Young-Hwa Song
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Dmitri I. Svergun
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Manfred Roessle
- University of Applied Sciences Luebeck, Moenkhofer Weg 239, 23562 Luebeck, Germany
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