1
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Spatially confined protein assembly in hierarchical mesoporous metal-organic framework. Nat Commun 2023; 14:973. [PMID: 36810582 PMCID: PMC9944321 DOI: 10.1038/s41467-023-36533-w] [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: 07/26/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
Immobilization of biomolecules into porous materials could lead to significantly enhanced performance in terms of stability towards harsh reaction conditions and easier separation for their reuse. Metal-Organic Frameworks (MOFs), offering unique structural features, have emerged as a promising platform for immobilizing large biomolecules. Although many indirect methods have been used to investigate the immobilized biomolecules for diverse applications, understanding their spatial arrangement in the pores of MOFs is still preliminary due to the difficulties in directly monitoring their conformations. To gain insights into the spatial arrangement of biomolecules within the nanopores. We used in situ small-angle neutron scattering (SANS) to probe deuterated green fluorescent protein (d-GFP) entrapped in a mesoporous MOF. Our work revealed that GFP molecules are spatially arranged in adjacent nanosized cavities of MOF-919 to form "assembly" through adsorbate-adsorbate interactions across pore apertures. Our findings, therefore, lay a crucial foundation for the identification of proteins structural basics under confinement environment of MOFs.
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2
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Heller WT. Small-Angle Neutron Scattering for Studying Lipid Bilayer Membranes. Biomolecules 2022; 12:1591. [PMID: 36358941 PMCID: PMC9687511 DOI: 10.3390/biom12111591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 09/23/2023] Open
Abstract
Small-angle neutron scattering (SANS) is a powerful tool for studying biological membranes and model lipid bilayer membranes. The length scales probed by SANS, being from 1 nm to over 100 nm, are well-matched to the relevant length scales of the bilayer, particularly when it is in the form of a vesicle. However, it is the ability of SANS to differentiate between isotopes of hydrogen as well as the availability of deuterium labeled lipids that truly enable SANS to reveal details of membranes that are not accessible with the use of other techniques, such as small-angle X-ray scattering. In this work, an overview of the use of SANS for studying unilamellar lipid bilayer vesicles is presented. The technique is briefly presented, and the power of selective deuteration and contrast variation methods is discussed. Approaches to modeling SANS data from unilamellar lipid bilayer vesicles are presented. Finally, recent examples are discussed. While the emphasis is on studies of unilamellar vesicles, examples of the use of SANS to study intact cells are also presented.
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Affiliation(s)
- William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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3
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Qian S, Heller W, Chen WR, Christianson A, Do C, Wang Y, Lin JYY, Huegle T, Jiang C, Boone C, Hart C, Graves V. CENTAUR-The small- and wide-angle neutron scattering diffractometer/spectrometer for the Second Target Station of the Spallation Neutron Source. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:075104. [PMID: 35922314 DOI: 10.1063/5.0090527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
CENTAUR has been selected as one of the eight initial instruments to be built at the Second Target Station (STS) of the Spallation Neutron Source at Oak Ridge National Laboratory. It is a small-angle neutron scattering (SANS) and wide-angle neutron scattering (WANS) instrument with diffraction and spectroscopic capabilities. This instrument will maximally leverage the high brightness of the STS source, the state-of-the-art neutron optics, and a suite of detectors to deliver unprecedented capabilities that enable measurements over a wide range of length scales with excellent resolution, measurements on smaller samples, and time-resolved investigations of evolving structures. Notably, the simultaneous WANS and diffraction capability will be unique among neutron scattering instruments in the United States. This instrument will provide much needed capabilities for soft matter and polymer sciences, geology, biology, quantum condensed matter, and other materials sciences that need in situ and operando experiments for kinetic and/or out-of-equilibrium studies. Beam polarization and a high-resolution chopper will enable detailed structural and dynamical investigations of magnetic and quantum materials. CENTAUR's excellent resolution makes it ideal for low-angle diffraction studies of highly ordered large-scale structures, such as skyrmions, shear-induced ordering in colloids, and biomembranes. Additionally, the spectroscopic mode of this instrument extends to lower momentum transfers than are currently possible with existing spectrometers, thereby providing a unique capability for inelastic SANS studies.
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Affiliation(s)
- Shuo Qian
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - William Heller
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Wei-Ren Chen
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | | | - Changwoo Do
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Yangyang Wang
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Jiao Y Y Lin
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Thomas Huegle
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Chenyang Jiang
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Cristina Boone
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Cameron Hart
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Van Graves
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
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4
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Incorporation of Membrane Proteins Into Bicontinuous Microemulsions Through
Winsor‐III System‐Based
Extraction. J SURFACTANTS DETERG 2021. [DOI: 10.1002/jsde.12500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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5
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Qian S, Sharma VK, Clifton LA. Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15189-15211. [PMID: 33300335 DOI: 10.1021/acs.langmuir.0c02516] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H2O/D2O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.
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Affiliation(s)
- Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Veerendra Kumar Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, U.K. OX11 0QX
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6
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Pounot K, Chaaban H, Foderà V, Schirò G, Weik M, Seydel T. Tracking Internal and Global Diffusive Dynamics During Protein Aggregation by High-Resolution Neutron Spectroscopy. J Phys Chem Lett 2020; 11:6299-6304. [PMID: 32663030 DOI: 10.1021/acs.jpclett.0c01530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Proteins can misfold and form either amorphous or organized aggregates with different morphologies and features. Aggregates of amyloid nature are pathological hallmarks in so-called protein conformational diseases, including Alzheimer's and Parkinson's. Evidence prevails that the transient early phases of the reaction determine the aggregate morphology and toxicity. As a consequence, real-time monitoring of protein aggregation is of utmost importance. Here, we employed time-resolved neutron backscattering spectroscopy to follow center-of-mass self-diffusion and nano- to picosecond internal dynamics of lysozyme during aggregation into a specific β-sheet rich superstructure, called particulates, formed at the isoelectric point of the protein. Particulate formation is found to be a one-step process, and protein internal dynamics, to remain unchanged during the entire aggregation process. The time-resolved neutron backscattering spectroscopy approach developed here, in combination with standard kinetics assays, provides a unifying framework in which dynamics and conformational transitions can be related to the different aggregation pathways.
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Affiliation(s)
- Kevin Pounot
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble cedex 9, France
| | - Hussein Chaaban
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble cedex 9, France
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7
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Rai DK, Gurusaran M, Urban V, Aran K, Ma L, Li P, Qian S, Narayanan TN, Ajayan PM, Liepmann D, Sekar K, Álvarez-Cao ME, Escuder-Rodríguez JJ, Cerdán ME, González-Siso MI, Viswanathan S, Paulmurugan R, Renugopalakrishnan V. Structural determination of Enzyme-Graphene Nanocomposite Sensor Material. Sci Rep 2019; 9:15519. [PMID: 31664095 PMCID: PMC6820869 DOI: 10.1038/s41598-019-51882-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022] Open
Abstract
State-of-the-art ultra-sensitive blood glucose-monitoring biosensors, based on glucose oxidase (GOx) covalently linked to a single layer graphene (SLG), will be a valuable next generation diagnostic tool for personal glycemic level management. We report here our observations of sensor matrix structure obtained using a multi-physics approach towards analysis of small-angle neutron scattering (SANS) on graphene-based biosensor functionalized with GOx under different pH conditions for various hierarchical GOx assemblies within SLG. We developed a methodology to separately extract the average shape of GOx molecules within the hierarchical assemblies. The modeling is able to resolve differences in the average GOx dimer structure and shows that treatment under different pH conditions lead to differences within the GOx at the dimer contact region with SLG. The coupling of different analysis methods and modeling approaches we developed in this study provides a universal approach to obtain detailed structural quantifications, for establishing robust structure-property relationships. This is an essential step to obtain an insight into the structure and function of the GOx-SLG interface for optimizing sensor performance.
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Affiliation(s)
- Durgesh K Rai
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York, 14853, USA.
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne-NE1 7RU, UK
| | - Volker Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA.
| | - Kiana Aran
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94709, USA
| | - Lulu Ma
- Department of Mechanical Engineering and Materials Science, Rice University, Houston, Texas, 77005, USA
| | - Pingzuo Li
- Center for Life Sciences, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Tharangattu N Narayanan
- Tata Institute of Fundamental Research - Center for Interdisciplinary Sciences, Hyderabad, 500107, India
| | - Pulickel M Ajayan
- Department of Mechanical Engineering and Materials Science, Rice University, Houston, Texas, 77005, USA
| | - Dorian Liepmann
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94709, USA
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, India
| | - María-Efigenia Álvarez-Cao
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - Juan-José Escuder-Rodríguez
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - María-Esperanza Cerdán
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - María-Isabel González-Siso
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - Sowmya Viswanathan
- Newton Wellesley Hospital/Partners Healthcare System, Newton, Massachusetts, 02462, USA
| | - Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Dept. of Radiology, Stanford University School of Medicine, 3155 Porter Drive, Suite 2236, Palo Alto, California, 94304, USA
| | - Venkatesan Renugopalakrishnan
- Center for Life Sciences, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA.
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115, USA.
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8
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Papagiannopoulos A, Vlassi E, Radulescu A. Reorganizations inside thermally stabilized protein/polysaccharide nanocarriers investigated by small angle neutron scattering. Carbohydr Polym 2019; 218:218-225. [DOI: 10.1016/j.carbpol.2019.04.077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/10/2019] [Accepted: 04/25/2019] [Indexed: 10/26/2022]
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9
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Intrinsically Disordered Protein Exhibits Both Compaction and Expansion under Macromolecular Crowding. Biophys J 2019. [PMID: 29539394 DOI: 10.1016/j.bpj.2018.01.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Conformational malleability allows intrinsically disordered proteins (IDPs) to respond agilely to their environments, such as nonspecifically interacting with in vivo bystander macromolecules (or crowders). Previous studies have emphasized conformational compaction of IDPs due to steric repulsion by macromolecular crowders, but effects of soft attraction are largely unexplored. Here we studied the conformational ensembles of the IDP FlgM in both polymer and protein crowders by small-angle neutron scattering. As crowder concentrations increased, the mean radius of gyration of FlgM first decreased but then exhibited an uptick. Ensemble optimization modeling indicated that FlgM conformations under protein crowding segregated into two distinct populations, one compacted and one extended. Coarse-grained simulations showed that compacted conformers fit into an interstitial void and occasionally bind to a surrounding crowder, whereas extended conformers snake through interstitial crevices and bind multiple crowders simultaneously. Crowder-induced conformational segregation may facilitate various cellular functions of IDPs.
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10
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Suga K, Lai YC, Faried M, Umakoshi H. Direct Observation of Amyloid β Behavior at Phospholipid Membrane Constructed on Gold Nanoparticles. Int J Anal Chem 2018; 2018:2571808. [PMID: 30627164 PMCID: PMC6304496 DOI: 10.1155/2018/2571808] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/11/2018] [Indexed: 11/17/2022] Open
Abstract
Amyloid β (Aβ) is a potential biomarker of Alzheimer's disease (AD), and its fibrillation behavior is of interest and value. In this study, the Aβ behaviors on phospholipid membranes were observed by Membrane Surface-Enhanced Raman Spectroscopy (MSERS) method. Phospholipid (PL) membranes, consisting of DMPC and DMPS with a molar ratio of 9:1, were fabricated on gold nanoparticles with diameter of 100 nm (Au@PL). Enhancement of the Raman intensity of Au@PL was increased by Aβ, with enhancement factor about 40. The H-bonding network was disturbed in presence of NaCl which covered Au@PL and made Au@PL away from one another. When Aβ was applied with Au@PL, the H-bonding network was disturbed just after mixing. As the reaction reaches to equilibrium, Aβ attracted neighbouring Au@PL and induced aggregation of Au@PL which blocked the aggregation prone site of Aβ to inhibit further fibrillation. Based on our method, the Aβ behaviors at lipid membrane surface can be directly observed via enhanced Raman signals.
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Affiliation(s)
- Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
| | - Ying-Chen Lai
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
| | - Miftah Faried
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
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11
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Florenzano F, Veronica C, Ciasca G, Ciotti MT, Pittaluga A, Olivero G, Feligioni M, Iannuzzi F, Latina V, Maria Sciacca MF, Sinopoli A, Milardi D, Pappalardo G, Marco DS, Papi M, Atlante A, Bobba A, Borreca A, Calissano P, Amadoro G. Extracellular truncated tau causes early presynaptic dysfunction associated with Alzheimer's disease and other tauopathies. Oncotarget 2017; 8:64745-64778. [PMID: 29029390 PMCID: PMC5630290 DOI: 10.18632/oncotarget.17371] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/11/2017] [Indexed: 12/14/2022] Open
Abstract
The largest part of tau secreted from AD nerve terminals and released in cerebral spinal fluid (CSF) is C-terminally truncated, soluble and unaggregated supporting potential extracellular role(s) of NH2 -derived fragments of protein on synaptic dysfunction underlying neurodegenerative tauopathies, including Alzheimer's disease (AD). Here we show that sub-toxic doses of extracellular-applied human NH2 tau 26-44 (aka NH 2 htau) -which is the minimal active moiety of neurotoxic 20-22kDa peptide accumulating in vivo at AD synapses and secreted into parenchyma- acutely provokes presynaptic deficit in K+ -evoked glutamate release on hippocampal synaptosomes along with alteration in local Ca2+ dynamics. Neuritic dystrophy, microtubules breakdown, deregulation in presynaptic proteins and loss of mitochondria located at nerve endings are detected in hippocampal cultures only after prolonged exposure to NH 2 htau. The specificity of these biological effects is supported by the lack of any significant change, either on neuronal activity or on cellular integrity, shown by administration of its reverse sequence counterpart which behaves as an inactive control, likely due to a poor conformational flexibility which makes it unable to dynamically perturb biomembrane-like environments. Our results demonstrate that one of the AD-relevant, soluble and secreted N-terminally truncated tau forms can early contribute to pathology outside of neurons causing alterations in synaptic activity at presynaptic level, independently of overt neurodegeneration.
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Affiliation(s)
| | | | - Gabriele Ciasca
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Maria Teresa Ciotti
- Institute of Cellular Biology and Neuroscience, CNR, IRCSS Santa Lucia Foundation, Rome, Italy
| | - Anna Pittaluga
- Department of Pharmacy, Pharmacology and Toxicology Section, University of Genoa, Genoa, Viale Cembrano, Italy
| | - Gunedalina Olivero
- Department of Pharmacy, Pharmacology and Toxicology Section, University of Genoa, Genoa, Viale Cembrano, Italy
| | - Marco Feligioni
- European Brain Research Institute, Rome, Italy
- Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Milan, Italy
| | | | | | | | | | - Danilo Milardi
- Institute of Biostructures and Bioimaging, CNR, Catania, Italy
| | | | - De Spirito Marco
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Massimiliano Papi
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Anna Atlante
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa, Viale Benedetto XV, Italy
| | - Antonella Bobba
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa, Viale Benedetto XV, Italy
| | - Antonella Borreca
- Institute of Cellular Biology and Neuroscience, CNR, IRCSS Santa Lucia Foundation, Rome, Italy
| | | | - Giuseppina Amadoro
- European Brain Research Institute, Rome, Italy
- Institute of Translational Pharmacology, CNR, Rome, Italy
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12
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Shrivastava AN, Aperia A, Melki R, Triller A. Physico-Pathologic Mechanisms Involved in Neurodegeneration: Misfolded Protein-Plasma Membrane Interactions. Neuron 2017; 95:33-50. [DOI: 10.1016/j.neuron.2017.05.026] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 05/12/2017] [Accepted: 05/19/2017] [Indexed: 12/12/2022]
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13
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Natalello A, Santambrogio C, Grandori R. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:21-28. [PMID: 27730522 DOI: 10.1007/s13361-016-1490-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles. Graphical Abstract ᅟ.
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Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
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14
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Rai DK, Sharma VK, Anunciado D, O'Neill H, Mamontov E, Urban V, Heller WT, Qian S. Neutron Scattering Studies of the Interplay of Amyloid β Peptide(1-40) and An Anionic Lipid 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol. Sci Rep 2016; 6:30983. [PMID: 27503057 PMCID: PMC4995599 DOI: 10.1038/srep30983] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/05/2016] [Indexed: 12/19/2022] Open
Abstract
The interaction between lipid bilayers and Amyloid β peptide (Aβ) plays a critical role in proliferation of Alzheimer’s disease (AD). AD is expected to affect one in every 85 humans by 2050, and therefore, deciphering the interplay of Aβ and lipid bilayers at the molecular level is of profound importance. In this work, we applied an array of neutron scattering methods to study the structure and dynamics of Aβ(1–40) interacting 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) bilayers. In the structural investigations of lipid bilayer’s response to Aβ binding, Small Angle Neutron Scattering and Neutron Membrane Diffraction revealed that the Aβ anchors firmly to the highly charged DMPG bilayers in the interfacial region between water and hydrocarbon chain, and it doesn’t penetrate deeply into the bilayer. This association mode is substantiated by the dynamics studies with high resolution Quasi-Elastic Neutron Scattering experiments, showing that the addition of Aβ mainly affects the slower lateral motion of lipid molecules, especially in the fluid phase, but not the faster internal motion. The results revealed that Aβ associates with the highly charged membrane in surface with limited impact on the structure, but the altered membrane dynamics could have more influence on other membrane processes.
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Affiliation(s)
- Durgesh K Rai
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Veerendra K Sharma
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Divina Anunciado
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eugene Mamontov
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Volker Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - William T Heller
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shuo Qian
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Rai DK, Beaucage G, Ratkanthwar K, Beaucage P, Ramachandran R, Hadjichristidis N. Quantification of interaction and topological parameters of polyisoprene star polymers under good solvent conditions. Phys Rev E 2016; 93:052501. [PMID: 27300939 DOI: 10.1103/physreve.93.052501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 06/06/2023]
Abstract
Mass fractal scaling, reflected in the mass fractal dimension d_{f}, is independently impacted by topology, reflected in the connectivity dimension c, and by tortuosity, reflected in the minimum dimension d_{min}. The mass fractal dimension is related to these other dimensions by d_{f}=cd_{min}. Branched fractal structures have a higher mass fractal dimension compared to linear structures due to a higher c, and extended structures have a lower dimension compared to convoluted self-avoiding and Gaussian walks due to a lower d_{min}. It is found, in this work, that macromolecules in thermodynamic equilibrium display a fixed mass fractal dimension d_{f} under good solvent conditions, regardless of chain topology. These equilibrium structures accommodate changes in chain topology such as branching c by a decrease in chain tortuosity d_{min}. Symmetric star polymers are used to understand the structure of complex macromolecular topologies. A recently published hybrid Unified scattering function accounts for interarm correlations in symmetric star polymers along with polymer-solvent interaction for chains of arbitrary scaling dimension. Dilute solutions of linear, three-arm and six-arm polyisoprene stars are studied under good solvent conditions in deuterated p-xylene. Reduced chain tortuosity can be viewed as steric straightening of the arms. Steric effects for star topologies are quantified, and it is found that steric straightening of arms is more significant for lower-molecular-weight arms. The observation of constant d_{f} is explained through a modification of Flory-Krigbaum theory for branched polymers.
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Affiliation(s)
- Durgesh K Rai
- Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, MS-6454 Oak Ridge, Tennessee 37831, USA
| | - Gregory Beaucage
- Materials Science and Engineering, University of Cincinnati, 492 Rhodes Hall, Cincinnati, Ohio 45221, USA
| | - Kedar Ratkanthwar
- Department of Chemistry, University of Athens, Panepistimiopolis, Zografou 15771, Athens, Greece
- KAUST Catalysis Center, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peter Beaucage
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, USA
| | | | - Nikos Hadjichristidis
- KAUST Catalysis Center, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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