1
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Scott HL, Burns-Casamayor V, Dixson AC, Standaert RF, Stanley CB, Stingaciu LR, Carrillo JMY, Sumpter BG, Katsaras J, Qiang W, Heberle FA, Mertz B, Ashkar R, Barrera FN. Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184349. [PMID: 38815687 DOI: 10.1016/j.bbamem.2024.184349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
Cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.
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Affiliation(s)
- Haden L Scott
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America
| | - Violeta Burns-Casamayor
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America
| | - Andrew C Dixson
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America
| | - Robert F Standaert
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America; C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Christopher B Stanley
- Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge, TN 37831, United States of America; Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Laura-Roxana Stingaciu
- Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; JCNS1, FZJ outstation at SNS, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Jan-Michael Y Carrillo
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Center for Nanophase Materials Sciences, Oak Ridge, TN 37831, United States of America
| | - Bobby G Sumpter
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Center for Nanophase Materials Sciences, Oak Ridge, TN 37831, United States of America
| | - John Katsaras
- Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge, TN 37831, United States of America; Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States of America
| | - Wei Qiang
- Department of Chemistry, the State University of New York, Binghamton, NY 13902, United States of America
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, TN 37920, United States of America
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States of America; West Virginia University Cancer Institute, Morgantown, WV 26506, United States of America
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, United States of America; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, United States of America.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, United States of America.
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2
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Beck TL, Carloni P, Asthagiri DN. All-Atom Biomolecular Simulation in the Exascale Era. J Chem Theory Comput 2024; 20:1777-1782. [PMID: 38382017 DOI: 10.1021/acs.jctc.3c01276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML techniques, that model biomolecular motions over unprecedented length and time scales. This new capability holds the potential to revolutionize our understanding of fundamental biological processes. Here we report on some of the major advances that were discussed at a recent CECAM workshop in Pisa, Italy, on the topic with a primary focus on atomic-level simulations. First, we highlight examples of current large-scale biomolecular simulations and the future possibilities enabled by crossing the exascale threshold. Next, we discuss challenges to be overcome in optimizing the usage of these powerful resources. Finally, we close by listing several grand challenge problems that could be investigated with this new computer architecture.
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Affiliation(s)
- Thomas L Beck
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Paolo Carloni
- INM-9/IAS-5 Computational Biomedicine, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-54245 Jülich, Germany
- Department of Physics, RWTH Aachen University, D-52078 Aachen, Germany
| | - Dilipkumar N Asthagiri
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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3
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Laurent H, Hughes MDG, Walko M, Brockwell DJ, Mahmoudi N, Youngs TGA, Headen TF, Dougan L. Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering. Biomacromolecules 2023; 24:4869-4879. [PMID: 37874935 PMCID: PMC10646990 DOI: 10.1021/acs.biomac.3c00583] [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: 06/14/2023] [Revised: 10/03/2023] [Indexed: 10/26/2023]
Abstract
Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled β hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model β hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.
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Affiliation(s)
- Harrison Laurent
- School
of Physics and Astronomy, University of
Leeds, Leeds, United Kingdom, LS2
9JT
| | - Matt D. G. Hughes
- School
of Physics and Astronomy, University of
Leeds, Leeds, United Kingdom, LS2
9JT
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom LS2
9JT
| | - Martin Walko
- School
of Chemistry, University of Leeds, Leeds, United
Kingdom, LS2 9JT
| | - David J. Brockwell
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom LS2
9JT
| | - Najet Mahmoudi
- ISIS
Neutron and Muon Source, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, United Kingdom, OX11 0QX
| | - Tristan G. A. Youngs
- ISIS
Neutron and Muon Source, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, United Kingdom, OX11 0QX
| | - Thomas F. Headen
- ISIS
Neutron and Muon Source, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, United Kingdom, OX11 0QX
| | - Lorna Dougan
- School
of Physics and Astronomy, University of
Leeds, Leeds, United Kingdom, LS2
9JT
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom LS2
9JT
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4
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Rowbotham JS, Nicholson JH, Ramirez MA, Urata K, Todd PMT, Karunanithy G, Lauterbach L, Reeve HA, Baldwin AJ, Vincent KA. Biocatalytic reductive amination as a route to isotopically labelled amino acids suitable for analysis of large proteins by NMR. Chem Sci 2023; 14:12160-12165. [PMID: 37969586 PMCID: PMC10631221 DOI: 10.1039/d3sc01718d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/20/2023] [Indexed: 11/17/2023] Open
Abstract
We demonstrate an atom-efficient and easy to use H2-driven biocatalytic platform for the enantioselective incorporation of 2H-atoms into amino acids. By combining the biocatalytic deuteration catalyst with amino acid dehydrogenase enzymes capable of reductive amination, we synthesised a library of multiply isotopically labelled amino acids from low-cost isotopic precursors, such as 2H2O and 15NH4+. The chosen approach avoids the use of pre-labeled 2H-reducing agents, and therefore vastly simplifies product cleanup. Notably, this strategy enables 2H, 15N, and an asymmetric centre to be introduced at a molecular site in a single step, with full selectivity, under benign conditions, and with near 100% atom economy. The method facilitates the preparation of amino acid isotopologues on a half-gram scale. These amino acids have wide applicability in the analytical life sciences, and in particular for NMR spectroscopic analysis of proteins. To demonstrate the benefits of the approach for enabling the workflow of protein NMR chemists, we prepared l-[α-2H,15N, β-13C]-alanine and integrated it into a large (>400 kDa) heat-shock protein oligomer, which was subsequently analysable by methyl-TROSY techniques, revealing new structural information.
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Affiliation(s)
- Jack S Rowbotham
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Jake H Nicholson
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Miguel A Ramirez
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Kouji Urata
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Peter M T Todd
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Gogulan Karunanithy
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory Oxford UK
| | - Lars Lauterbach
- Technische Universität Berlin, Institute for Chemistry Straße des 17. Juni 135 10437 Berlin Germany
| | - Holly A Reeve
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
| | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory Oxford UK
- Kavli Institute for Nanoscience Discovery, University of Oxford Oxford OX1 3QU UK
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory South Parks Road Oxford UK
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5
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Georgiadis M, Menzel M, Reuter JA, Born DE, Kovacevich SR, Alvarez D, Taghavi HM, Schroeter A, Rudin M, Gao Z, Guizar-Sicairos M, Weiss TM, Axer M, Rajkovic I, Zeineh MM. Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering. Acta Biomater 2023; 164:317-331. [PMID: 37098400 PMCID: PMC10811447 DOI: 10.1016/j.actbio.2023.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/27/2023]
Abstract
Myelinated axons (nerve fibers) efficiently transmit signals throughout the brain via action potentials. Multiple methods that are sensitive to axon orientations, from microscopy to magnetic resonance imaging, aim to reconstruct the brain's structural connectome. As billions of nerve fibers traverse the brain with various possible geometries at each point, resolving fiber crossings is necessary to generate accurate structural connectivity maps. However, doing so with specificity is a challenging task because signals originating from oriented fibers can be influenced by brain (micro)structures unrelated to myelinated axons. X-ray scattering can specifically probe myelinated axons due to the periodicity of the myelin sheath, which yields distinct peaks in the scattering pattern. Here, we show that small-angle X-ray scattering (SAXS) can be used to detect myelinated, axon-specific fiber crossings. We first demonstrate the capability using strips of human corpus callosum to create artificial double- and triple-crossing fiber geometries, and we then apply the method in mouse, pig, vervet monkey, and human brains. We compare results to polarized light imaging (3D-PLI), tracer experiments, and to outputs from diffusion MRI that sometimes fails to detect crossings. Given its specificity, capability of 3-dimensional sampling and high resolution, SAXS could serve as a ground truth for validating fiber orientations derived using diffusion MRI as well as microscopy-based methods. STATEMENT OF SIGNIFICANCE: To study how the nerve fibers in our brain are interconnected, scientists need to visualize their trajectories, which often cross one another. Here, we show the unique capacity of small-angle X-ray scattering (SAXS) to study these fiber crossings without use of labeling, taking advantage of SAXS's specificity to myelin - the insulating sheath that is wrapped around nerve fibers. We use SAXS to detect double and triple crossing fibers and unveil intricate crossings in mouse, pig, vervet monkey, and human brains. This non-destructive method can uncover complex fiber trajectories and validate other less specific imaging methods (e.g., MRI or microscopy), towards accurate mapping of neuronal connectivity in the animal and human brain.
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Affiliation(s)
- Marios Georgiadis
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA; Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland.
| | - Miriam Menzel
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany; Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - Jan A Reuter
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Donald E Born
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Dario Alvarez
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Aileen Schroeter
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Markus Rudin
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Zirui Gao
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - Thomas M Weiss
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, USA
| | - Markus Axer
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Ivan Rajkovic
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, USA
| | - Michael M Zeineh
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA
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6
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Yang R, Kvetny M, Brown W, Ogbonna EN, Wang G. A Single-Entity Method for Actively Controlled Nucleation and High-Quality Protein Crystal Synthesis. Anal Chem 2023. [PMID: 37243709 DOI: 10.1021/acs.analchem.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Lack of controls and understanding in nucleation, which proceeds crystal growth and other phase transitions, has been a bottleneck challenge in chemistry, materials, biology, and other fields. The exemplary needs for better methods for biomacromolecule crystallization include (1) synthesizing crystals for high-resolution structure determinations in fundamental research and (2) tuning the crystal habit and thus the corresponding properties in materials and pharmaceutical applications. Herein, a deterministic method is established capable of sustaining the nucleation and growth of a single crystal using the protein lysozyme as a prototype. The supersaturation is localized at the interface between a sample and a precipitant solution, spatially confined by the tip of a single nanopipette. The exchange of matter between the two solutions determines the supersaturation, which is controlled by electrokinetic ion transport driven by an external potential waveform. Nucleation and subsequent crystal growth disrupt the ionic current limited by the nanotip and are detected. The nucleation and growth of individual single crystals are measured in real time. Electroanalytical and optical signatures are elucidated as feedbacks with which active controls in crystal quality and method consistency are achieved: five out of five crystals diffract at a true atomic resolution of up to 1.2 Å. As controls, those synthesized under less optimized conditions diffract poorly. The crystal habits during the growth process are tuned successfully by adjusting the flux. The universal mechanism of nano-transport kinetics, together with the correlations of the diffraction quality and crystal habit with the crystallization control parameters, lay the foundation for the generalization to other materials systems.
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Affiliation(s)
- Ruoyu Yang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Maksim Kvetny
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Warren Brown
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Edwin N Ogbonna
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Gangli Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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7
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Ankner JF, Ashkar R, Browning JF, Charlton TR, Doucet M, Halbert CE, Islam F, Karim A, Kharlampieva E, Kilbey SM, Lin JYY, Phan MD, Smith GS, Sukhishvili SA, Thermer R, Veith GM, Watkins EB, Wilson D. Cinematic reflectometry using QIKR, the quite intense kinetics reflectometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:013302. [PMID: 36725568 DOI: 10.1063/5.0122279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/14/2022] [Indexed: 06/18/2023]
Abstract
The Quite Intense Kinetics Reflectometer (QIKR) will be a general-purpose, horizontal-sample-surface neutron reflectometer. Reflectometers measure the proportion of an incident probe beam reflected from a surface as a function of wavevector (momentum) transfer to infer the distribution and composition of matter near an interface. The unique scattering properties of neutrons make this technique especially useful in the study of soft matter, biomaterials, and materials used in energy storage. Exploiting the increased brilliance of the Spallation Neutron Source Second Target Station, QIKR will collect specular and off-specular reflectivity data faster than the best existing such machines. It will often be possible to collect complete specular reflectivity curves using a single instrument setting, enabling "cinematic" operation, wherein the user turns on the instrument and "films" the sample. Samples in time-dependent environments (e.g., temperature, electrochemical, or undergoing chemical alteration) will be observed in real time, in favorable cases with frame rates as fast as 1 Hz. Cinematic data acquisition promises to make time-dependent measurements routine, with time resolution specified during post-experiment data analysis. This capability will be deployed to observe such processes as in situ polymer diffusion, battery electrode charge-discharge cycles, hysteresis loops, and membrane protein insertion into lipid layers.
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Affiliation(s)
- J F Ankner
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - J F Browning
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - T R Charlton
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Doucet
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - C E Halbert
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - F Islam
- Neutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - A Karim
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
| | - E Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - S M Kilbey
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - J Y Y Lin
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M D Phan
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - G S Smith
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - S A Sukhishvili
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - R Thermer
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - G M Veith
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E B Watkins
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D Wilson
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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8
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Exploring the Limits of Biological Complexity Amenable to Studies by Incoherent Neutron Spectroscopy. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081219. [PMID: 36013398 PMCID: PMC9410259 DOI: 10.3390/life12081219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms.
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9
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Do C, Ashkar R, Boone C, Chen WR, Ehlers G, Falus P, Faraone A, Gardner JS, Graves V, Huegle T, Katsumata R, Kent D, Lin JYY, McHargue B, Olsen B, Wang Y, Wilson D, Z Y. EXPANSE: A time-of-flight EXPanded Angle Neutron Spin Echo spectrometer at the Second Target Station of the Spallation Neutron Source. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:075107. [PMID: 35922301 DOI: 10.1063/5.0089349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
EXPANSE, an EXPanded Angle Neutron Spin Echo instrument, has been proposed and selected as one of the first suite of instruments to be built at the Second Target Station of the Spallation Neutron Source at the Oak Ridge National Laboratory. This instrument is designed to address scientific problems that involve high-energy resolution (neV-μeV) of dynamic processes in a wide range of materials. The wide-angle detector banks of EXPANSE provide coverage of nearly two orders of magnitude in scattering wavenumbers, and the wide wavelength band affords approximately four orders of magnitude in Fourier times. This instrument will offer unique capabilities that are not available in the currently existing neutron scattering instruments in the United States. Specifically, EXPANSE will enable direct measurements of slow dynamics in the time domain over wide Q-ranges simultaneously and will also enable time-resolved spectroscopic studies. The instrument is expected to contribute to a diverse range of science areas, including soft matter, polymers, biological materials, liquids and glasses, energy materials, unconventional magnets, and quantum materials.
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Affiliation(s)
- Changwoo Do
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Rana Ashkar
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Cristina Boone
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Wei-Ren Chen
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Georg Ehlers
- Neutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Peter Falus
- Institute Laue Langevin (ILL), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonio Faraone
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, USA
| | - Jason S Gardner
- Material Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Van Graves
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Thomas Huegle
- Neutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Reika Katsumata
- Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Darian Kent
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jiao Y Y Lin
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Bill McHargue
- Neutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Bradley Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yangyang Wang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Danielle Wilson
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Y Z
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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10
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Marques MPM, Santos IP, Batista de Carvalho ALM, Mamede AP, Martins CB, Figueiredo P, Sarter M, Sakai VG, Batista de Carvalho LAE. Water dynamics in human cancer and non-cancer tissues. Phys Chem Chem Phys 2022; 24:15406-15415. [PMID: 35704895 DOI: 10.1039/d2cp00621a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Normal-to-malignant transformation is a poorly understood process associated with cellular biomechanical properties. These are strongly dependent on the dynamical behaviour of water, known to play a fundamental role in normal cellular activity and in the maintenance of the three-dimensional architecture of the tissue and the functional state of biopolymers. In this study, quasi-elastic neutron scattering was used to probe the dynamical behaviour of water in human cancer specimens and their respective surrounding normal tissue from breast and tongue, as an innovative approach for identifying particular features of malignancy. This methodology has been successfully used by the authors in human cells and was the first study of human tissues by neutron scattering techniques. A larger flexibility was observed for breast versus tongue tissues. Additionally, different dynamics were found for malignant and non-malignant specimens, depending on the tissue: higher plasticity for breast invasive cancer versus the normal, and an opposite effect for tongue. The data were interpreted in the light of two different water populations within the samples: one displaying bulk-like dynamics (extracellular and intracellular/cytoplasmic) and another with constrained flexibility (extracellular/interstitial and intracellular/hydration layers).
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Affiliation(s)
- M P M Marques
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal. .,University of Coimbra, Department of Life Sciences, 3000-456 Coimbra, Portugal
| | - I P Santos
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A L M Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A P Mamede
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - C B Martins
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - P Figueiredo
- Oncology Institute of Coimbra Francisco Gentil, 3000-075 Coimbra, Portugal
| | - M Sarter
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - V García Sakai
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - L A E Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
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11
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Sala G, Mourigal M, Boone C, Butch NP, Christianson AD, Delaire O, DeSantis AJ, Hart CL, Hermann RP, Huegle T, Kent DN, Lin JYY, Lumsden MD, Manley ME, Quirinale DG, Stone MB, Z Y. CHESS: The future direct geometry spectrometer at the second target station. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:065109. [PMID: 35778024 DOI: 10.1063/5.0089740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
CHESS, chopper spectrometer examining small samples, is a planned direct geometry neutron chopper spectrometer designed to detect and analyze weak signals intrinsic to small cross sections (e.g., small mass, small magnetic moments, or neutron absorbing materials) in powders, liquids, and crystals. CHESS is optimized to enable transformative investigations of quantum materials, spin liquids, thermoelectrics, battery materials, and liquids. The broad dynamic range of the instrument is also well suited to study relaxation processes and excitations in soft and biological matter. The 15 Hz repetition rate of the Second Target Station at the Spallation Neutron Source enables the use of multiple incident energies within a single source pulse, greatly expanding the information gained in a single measurement. Furthermore, the high flux grants an enhanced capability for polarization analysis. This enables the separation of nuclear from magnetic scattering or coherent from incoherent scattering in hydrogenous materials over a large range of energy and momentum transfer. This paper presents optimizations and technical solutions to address the key requirements envisioned in the science case and the anticipated uses of this instrument.
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Affiliation(s)
- G Sala
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Mourigal
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - C Boone
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - N P Butch
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - A D Christianson
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - O Delaire
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - A J DeSantis
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - C L Hart
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R P Hermann
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - T Huegle
- Neutron Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D N Kent
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J Y Y Lin
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M D Lumsden
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M E Manley
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D G Quirinale
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M B Stone
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Y Z
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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12
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Tominaga T, Nakagawa H, Sahara M, Oda T, Inoue R, Sugiyama M. Data Collection for Dilute Protein Solutions via a Neutron Backscattering Spectrometer. Life (Basel) 2022; 12:life12050675. [PMID: 35629343 PMCID: PMC9145923 DOI: 10.3390/life12050675] [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: 03/17/2022] [Revised: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding protein functions requires not only static but also dynamic structural information. Incoherent quasi-elastic neutron scattering (QENS), which utilizes the highly incoherent scattering ability of hydrogen, is a powerful technique for revealing the dynamics of proteins in deuterium oxide (D2O) buffer solutions. The background scattering of sample cells suitable for aqueous protein solution samples, conducted with a neutron backscattering spectrometer, was evaluated. It was found that the scattering intensity of an aluminum sample cell coated with boehmite using D2O was lower than that of a sample cell coated with regular water (H2O). The D2O-Boehmite coated cell was used for the QENS measurement of a 0.8 wt.% aqueous solution of an intrinsically disordered protein in an intrinsically disordered region of a helicase-associated endonuclease for a fork-structured type of DNA. The cell was inert against aqueous samples at 283–363 K. In addition, meticulous attention to cells with small individual weight differences and the positional reproducibility of the sample cell relative to the spectrometer neutron beam position enabled the accurate subtraction of the scattering profiles of the D2O buffer and the sample container. Consequently, high-quality information on protein dynamics could be extracted from dilute protein solutions.
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Affiliation(s)
- Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Ibaraki 319-1106, Japan;
- Correspondence:
| | - Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan;
- J-PARC Center, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan
| | - Masae Sahara
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Ibaraki 319-1106, Japan;
| | - Takashi Oda
- Department of Life Science, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan;
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan; (R.I.); (M.S.)
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan; (R.I.); (M.S.)
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13
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Benedetto A, Kelley EG. Absorption of the [bmim][Cl] Ionic Liquid in DMPC Lipid Bilayers across Their Gel, Ripple, and Fluid Phases. J Phys Chem B 2022; 126:3309-3318. [PMID: 35472281 PMCID: PMC9082605 DOI: 10.1021/acs.jpcb.2c00710] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Lipid bilayers are
a key component of cell membranes and play a
crucial role in life and in bio-nanotechnology. As a result, controlling
their physicochemical properties holds the promise of effective therapeutic
strategies. Ionic liquids (ILs)—a vast class of complex organic
electrolytes—have shown a high degree of affinity with lipid
bilayers and can be exploited in this context. However, the chemical
physics of IL absorption and partitioning into lipid bilayers is yet
to be fully understood. This work focuses on the absorption of the
model IL [bmim][Cl] into 1,2-dimyristoyl-sn-glycero-3-phosphocholine
(DMPC) lipid bilayers across their gel, ripple, and fluid phases.
Here, by small-angle neutron scattering, we show that (i) the IL cations
are absorbed in the lipid bilayer in all its thermodynamic phases
and (ii) the amount of IL inserted into the lipid phase increased
with increasing temperature, changing from three to four IL cations
per 10 lipids with increasing temperature from 10 °C in the gel
phase to 40 °C in the liquid phase, respectively. An explicative
hypothesis, based on the entropy gain coming from the IL hydration
water, is presented to explain the observed temperature trend. The
ability to control IL absorption with temperature can be used as a
handle to tune the effect of ILs on biomembranes and can be exploited
in bio-nanotechnological applications.
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Affiliation(s)
- Antonio Benedetto
- Department of Science, University of Roma Tre, 00146 Rome, Italy.,School of Physics, and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.,Laboratory for Neutron Scattering, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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14
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Mayer S, Munz E, Hammer S, Wagner S, Guendel A, Rolletschek H, Jakob PM, Borisjuk L, Neuberger T. Quantitative monitoring of paramagnetic contrast agents and their allocation in plant tissues via DCE-MRI. PLANT METHODS 2022; 18:47. [PMID: 35410361 PMCID: PMC8996644 DOI: 10.1186/s13007-022-00877-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Studying dynamic processes in living organisms with MRI is one of the most promising research areas. The use of paramagnetic compounds as contrast agents (CA), has proven key to such studies, but so far, the lack of appropriate techniques limits the application of CA-technologies in experimental plant biology. The presented proof-of-principle aims to support method and knowledge transfer from medical research to plant science. RESULTS In this study, we designed and tested a new approach for plant Dynamic Contrast Enhanced Magnetic Resonance Imaging (pDCE-MRI). The new approach has been applied in situ to a cereal crop (Hordeum vulgare). The pDCE-MRI allows non-invasive investigation of CA allocation within plant tissues. In our experiments, gadolinium-DTPA, the most commonly used contrast agent in medical MRI, was employed. By acquiring dynamic T1-maps, a new approach visualizes an alteration of a tissue-specific MRI parameter T1 (longitudinal relaxation time) in response to the CA. Both, the measurement of local CA concentration and the monitoring of translocation in low velocity ranges (cm/h) was possible using this CA-enhanced method. CONCLUSIONS A novel pDCE-MRI method is presented for non-invasive investigation of paramagnetic CA allocation in living plants. The temporal resolution of the T1-mapping has been significantly improved to enable the dynamic in vivo analysis of transport processes at low-velocity ranges, which are common in plants. The newly developed procedure allows to identify vascular regions and to estimate their involvement in CA allocation. Therefore, the presented technique opens a perspective for further development of CA-aided MRI experiments in plant biology.
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Affiliation(s)
- Simon Mayer
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Eberhard Munz
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Sebastian Hammer
- Institute of Experimental Physics 6, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Steffen Wagner
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Andre Guendel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Peter M Jakob
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany.
| | - Thomas Neuberger
- Huck Institutes of the Life Sciences, The Pennsylvania State University, 113 Chandlee Lab, University Park, PA, 16802, USA.
- Department of Biomedical Engineering, The Pennsylvania State University, 113 Chandlee Lab, University Park, PA, 16802, USA.
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15
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Gilbert PH, Zhang Z, Qian KK, Allen DP, Ford R, Wagner NJ, Liu Y. Aggregation Kinetics of Polysorbate 80/ m-Cresol Solutions: A Small-Angle Neutron Scattering Study. Mol Pharm 2022; 19:862-875. [PMID: 35138864 DOI: 10.1021/acs.molpharmaceut.1c00803] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polysorbate 80 (PS80), a nonionic surfactant used in pharmaceutical formulation, is known to be incompatible with m-cresol, an antimicrobial agent for multi-dose injectable formulations. This incompatibility results in increased turbidity caused by micelle aggregation progressing over weeks or longer, where storage temperature, ionic strength, and component concentration influence the aggregation kinetics. Small-angle neutron scattering (SANS) analysis of PS80/m-cresol solutions over a pharmaceutically relevant concentration range of each component reveals the cause of aggregation, the coalescence mechanism, and aggregate structure. PS80 solutions containing m-cresol concentrations below ≈2.0 mg/mL and above ≈4.5 mg/mL are kinetically stable and do not aggregate over a 50 h period. At 5 mg/mL of m-cresol, the mixture forms a kinetically stable microemulsion phase, despite being well below the aqueous solubility limit of m-cresol. Solutions containing intermediate m-cresol concentrations (2.0-4.5 mg/mL) are unstable, resulting in aggregation, coalescence, and eventual phase separation. In unstable solutions, two stages of aggregate growth (nucleation and power-law growth) are observed at m-cresol concentrations at or below ≈3.6 mg/mL. At higher m-cresol concentrations, aggregates experience a third stage of exponential growth. A single kinetic model is developed to explain the stages of aggregate growth observed in both kinetic mechanisms. This work establishes the phase diagram of PS80/m-cresol solution stability and identifies component concentrations necessary for producing stable formulations.
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Affiliation(s)
- Peter H Gilbert
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Zhenhuan Zhang
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Ken K Qian
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | - David P Allen
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | - Rachel Ford
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Norman J Wagner
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, Delaware 19716, United States
| | - Yun Liu
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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16
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Duff AP, Cagnes M, Darwish TA, Krause-Heuer AM, Moir M, Recsei C, Rekas A, Russell RA, Wilde KL, Yepuri NR. Deuteration for biological SANS: Case studies, success and challenges in chemistry and biology. Methods Enzymol 2022; 677:85-126. [DOI: 10.1016/bs.mie.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Perez-Salas U, Garg S, Gerelli Y, Porcar L. Deciphering lipid transfer between and within membranes with time-resolved small-angle neutron scattering. CURRENT TOPICS IN MEMBRANES 2021; 88:359-412. [PMID: 34862031 DOI: 10.1016/bs.ctm.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This review focuses on time-resolved neutron scattering, particularly time-resolved small angle neutron scattering (TR-SANS), as a powerful in situ noninvasive technique to investigate intra- and intermembrane transport and distribution of lipids and sterols in lipid membranes. In contrast to using molecular analogues with potentially large chemical tags that can significantly alter transport properties, small angle neutron scattering relies on the relative amounts of the two most abundant isotope forms of hydrogen: protium and deuterium to detect complex membrane architectures and transport processes unambiguously. This review discusses advances in our understanding of the mechanisms that sustain lipid asymmetry in membranes-a key feature of the plasma membrane of cells-as well as the transport of lipids between membranes, which is an essential metabolic process.
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Affiliation(s)
- Ursula Perez-Salas
- Physics Department, University of Illinois at Chicago, Chicago, IL, United States.
| | - Sumit Garg
- Physics Department, University of Illinois at Chicago, Chicago, IL, United States
| | - Yuri Gerelli
- Department of Life and Environmental Sciences, Universita` Politecnica delle Marche, Ancona, Italy
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18
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Fed-batch production of deuterated protein in Escherichia coli for neutron scattering experimentation. Methods Enzymol 2021. [PMID: 34752287 DOI: 10.1016/bs.mie.2021.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Neutron scattering is a powerful technique for determining the structure and dynamics of biological materials in a variety of environmental conditions. A distinguishing property of the neutron is its sensitivity to detecting hydrogen and distinguishing it from its isotope deuterium. This enables unique types of experiments that take advantage of this differential sensitivity called isotopic contrast variation. Using this approach, the chemistry of the system is not changed, but the visibility of individual sample components can be tuned by varying the deuterium content of the system under investigation. Deuterated proteins are commonly produced in bacterial systems that are adapted to growth in D2O minimal media. To maximize the yield of deuterium-labeled protein and efficiently utilize D2O and occasionally the deuterated substrate, fed-batch processes are routinely used to maximize biomass production without compromising cell viability. A step-by-step procedure will be described along with a case study of the production of deuterated green fluorescent protein. Limitations of the process will also be discussed.
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19
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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20
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Preparation of a Deuterated Membrane Protein for Small-Angle Neutron Scattering. Methods Mol Biol 2021. [PMID: 33877630 DOI: 10.1007/978-1-0716-1394-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter outlines a protocol developed to prepare a purified deuterated membrane protein for a small-angle neutron scattering (SANS) experiment. SANS is a noninvasive technique well suited to studying membrane protein solution structures, and deuteration enhances the signal from the protein over the background (Breyton et al., Eur Phys J E Soft Matter 36 (7):71, 2013; Garg et al., Biophys J 101 (2):370-377, 2011). We present our workflow: transformation of our plasmid into E. coli, cell growth and expression of our deuterated protein, membrane isolation, detergent solubilization, protein purification, purity assessment, and final preparation for SANS.
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21
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Abstract
Cell membranes - primarily composed of lipids, sterols, and proteins - form a dynamic interface between living cells and their environment. They act as a mechanical barrier around the cell while selectively facilitating material transport, signal transduction, and various other functions necessary for the cell viability. The complex functionality of cell membranes and the hierarchical motions and responses they exhibit demand a thorough understanding of the origin of different membrane dynamics and how they are influenced by molecular additives and environmental cues. These dynamic modes include single-molecule diffusion, thermal fluctuations, and large-scale membrane deformations, to name a few. This review highlights advances in investigating structure-driven dynamics associated with model cell membranes, with a particular focus on insights gained from neutron scattering and spectroscopy experiments. We discuss the uniqueness of neutron contrast variation and its remarkable potential in probing selective membrane structure and dynamics on spatial and temporal scales over which key biological functions occur. We also present a summary of current and future opportunities in synergistic combinations of neutron scattering with molecular dynamics (MD) simulations to gain further understanding of the molecular mechanisms underlying complex membrane functions.
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Affiliation(s)
- Sudipta Gupta
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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22
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Benedetto A, Kearley GJ. Experimental demonstration of the novel "van-Hove integral method (vHI)" for measuring diffusive dynamics by elastic neutron scattering. Sci Rep 2021; 11:14093. [PMID: 34238981 PMCID: PMC8266890 DOI: 10.1038/s41598-021-93463-7] [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: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
Quasi-elastic neutron scattering (QENS)-based on the seminal work of Nobel Laureate Brockhouse-has been one of the major methods for studying pico-second to nano-second diffusive dynamics over the past 70 years. This is regarded as an "inelastic" method for dynamics. In contrast, we recently proposed a new neutron-scattering method for dynamics, which uses the elastic line of the scattering to access system dynamics directly in the time domain (Benedetto and Kearley in Sci Rep 9:11284, 2019). This new method has been denoted "vHI" that stands for "van Hove Integral". The reason is that, under certain conditions, the measured elastic intensity corresponds to the running-time integral of the intermediate scattering function, [Formula: see text], up to a time that is inversely proportional to the energy band-width incident on the sample. As a result, [Formula: see text] is accessed from the time derivative of the measured vHI profile. vHI has been supported by numerical and Monte-Carlo simulations, but has been difficult to validate experimentally due to the lack of a suitable instrument. Here we show that vHI works in practice, which we achieved by using a simple modification to the standard QENS backscattering spectrometer methodology. Basically, we varied the neutron-energy band-widths incident at the sample via a step-wise variation of the frequency of the monochromator Doppler-drive. This provides a measurement of the vHI profile at the detectors. The same instrument and sample were also used in standard QENS mode for comparison. The intermediate scattering functions, [Formula: see text], obtained by the two methods-vHI and QENS-are strikingly similar providing a direct experimental validation of the vHI method. Perhaps surprisingly, the counting statistics of the two methods are comparable even though the instrument used was expressly designed for QENS. This shows that the methodology modification adopted here can be used in practice to access vHI profiles at many of the backscattering spectrometers worldwide. We also show that partial integrations of the measured QENS spectrum cannot provide the vHI profile, which clarifies a common misconception. At the same time, we show a novel approach which does access [Formula: see text] from QENS spectra.
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Affiliation(s)
- Antonio Benedetto
- School of Physics, University College Dublin, Dublin 4, Ireland. .,Conway Institute, University College Dublin, Dublin 4, Ireland. .,Department of Sciences, University of Roma Tre, Rome, Italy. .,Laboratory for Neutron Scattering, Paul Scherrer Institute, Villigen, Switzerland.
| | - Gordon J Kearley
- School of Physics, University College Dublin, Dublin 4, Ireland.,School of Chemistry, University College Dublin, Dublin 4, Ireland
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23
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Gilbert PH, Zhang Z, Qian KK, Allen DP, Wagner NJ, Liu Y. Preservative Induced Polysorbate 80 Micelle Aggregation. J Pharm Sci 2021; 110:2395-2404. [PMID: 33387597 PMCID: PMC11165925 DOI: 10.1016/j.xphs.2020.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022]
Abstract
Small angle neutron scattering (SANS) studies of a model pharmaceutical formulation reveal how formulation stability depends on the compatibility of individual components. Solutions of two common protein formulation excipients, polysorbate 80 (PS80), a nonionic surfactant that prevents aggregation, and m-cresol, an antimicrobial agent for multi-dose injectable formulations, are investigated. The addition of m-cresol to PS80 solutions leads to solution turbidity and irreversibly alters PS80 micelle morphology. This slow preservative-induced destabilization of PS80 micelles progresses over days or even weeks, which highlights the essential role that aggregation kinetics plays in preservative-surfactant interactions. The temperature-dependence of PS80 micelle growth kinetics is quantified by SANS in the presence of m-cresol. Aggregation is a two-step process, where initial formation of small aggregates is followed by a period of monotonic power-law growth, providing evidence for the mechanism. Total aggregate mass stays constant after initial aggregate formation, and addition of a pH-regulating citrate buffer dramatically accelerates aggregation kinetics.
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Affiliation(s)
- Peter H Gilbert
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, DE 19716; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Zhenhuan Zhang
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, DE 19716; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Ken K Qian
- Eli Lilly and Company, Indianapolis, IN 46225.
| | | | - Norman J Wagner
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, DE 19716.
| | - Yun Liu
- Department of Chemical and Biomolecular Engineering Department, Center for Neutron Science, University of Delaware, Newark, DE 19716; NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899.
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24
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Li D, Zhang K. Unifying the concepts of scattering and structure factor in ordered and disordered samples. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721001965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Scattering methods are widely used in many research areas to analyze and resolve material structures. Given its importance, a large number of textbooks are devoted to this topic. However, technical details in experiments and disconnection between explanations from different perspectives often confuse and frustrate beginner students and researchers. To create an effective learning path, the core concepts of scattering and structure factor are reviewed in this article in a self-contained way. Classical examples of scattering photography and intensity scanning are calculated. Sample CPU and GPU codes are provided to facilitate the understanding and application of these methods.
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Schröder GC, O’Dell WB, Swartz PD, Meilleur F. Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions. Acta Crystallogr F Struct Biol Commun 2021; 77:128-133. [PMID: 33830078 PMCID: PMC8034432 DOI: 10.1107/s2053230x21002399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/02/2021] [Indexed: 11/10/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper-oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - William B. O’Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul D. Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Smith GN. An alternative analysis of contrast-variation neutron scattering data of casein micelles in semi-deuterated milk. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:5. [PMID: 33590354 DOI: 10.1140/epje/s10189-021-00023-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Contrast-variation small-angle neutron scattering (CV-SANS) is an excellent way to determine the structure of complex, hierarchical colloids, including self-assembled biological systems. In these experiments, the scattering length density of solvents is changed (by varying the ratio of water or [Formula: see text] and heavy water or [Formula: see text]) to highlight or mask scattering from different components in the system. This approach has been used with synthetic colloids, but it is also increasingly being used in the biological and food sciences. Perhaps the most studied food colloid is the "casein micelle," a self-assembled nanometer-scale colloid of the structure-forming casein protein in milk. CV-SANS data available in the literature are typically analyzed using approximations, which may be invalid for casein micelles, as they have been shown to be sticky spheres. To assess the applicability of this approximate approach, a comprehensive set of CV-SANS data from casein micelles in diluted milk was reanalyzed using a model-based approach, where the casein micelles were formally treated as interacting spheres. In general, the conclusions of the previous study are reproduced, but this new approach makes it more straightforward to distinguish the different components in milk and can be applied to any dairy sample with known form of interparticle interactions, which offers the possibility of studying semi-deuterated milk at its native concentration.
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Affiliation(s)
- Gregory N Smith
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK.
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28
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Symmetry/Asymmetry of the NHN Hydrogen Bond in Protonated 1,8-Bis(dimethylamino)naphthalene. Symmetry (Basel) 2020. [DOI: 10.3390/sym12111924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Experimental and theoretical results are presented based on vibrational spectra and motional dynamics of 1,8-bis(dimethylamino)naphthalene (DMAN) and its protonated forms (DMANH+ and the DMANH+ HSO4− complex). The studies of these compounds have been performed in the gas phase and solid-state. Spectroscopic investigations were carried out by infrared spectroscopy (IR), Raman, and incoherent inelastic neutron scattering (IINS) experimental methods. Density functional theory (DFT) and Car–Parrinello molecular dynamics (CPMD) methods were applied to support our experimental findings. The fundamental investigations of hydrogen bridge vibrations were accomplished on the basis of isotopic substitutions (NH → ND). Special attention was paid to the bridged proton dynamics in the DMANH+ complex, which was found to be affected by interactions with the HSO4− anion.
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Hybrid Biopolymer and Lipid Nanoparticles with Improved Transfection Efficacy for mRNA. Cells 2020; 9:cells9092034. [PMID: 32899484 PMCID: PMC7563888 DOI: 10.3390/cells9092034] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
Hybrid nanoparticles from lipidic and polymeric components were assembled to serve as vehicles for the transfection of messenger RNA (mRNA) using different portions of the cationic lipid DOTAP (1,2-Dioleoyl-3-trimethylammonium-propane) and the cationic biopolymer protamine as model systems. Two different sequential assembly approaches in comparison with a direct single-step protocol were applied, and molecular organization in correlation with biological activity of the resulting nanoparticle systems was investigated. Differences in the structure of the nanoparticles were revealed by thorough physicochemical characterization including small angle neutron scattering (SANS), small angle X-ray scattering (SAXS), and cryogenic transmission electron microscopy (cryo-TEM). All hybrid systems, combining lipid and polymer, displayed significantly increased transfection in comparison to lipid/mRNA and polymer/mRNA particles alone. For the hybrid nanoparticles, characteristic differences regarding the internal organization, release characteristics, and activity were determined depending on the assembly route. The systems with the highest transfection efficacy were characterized by a heterogenous internal organization, accompanied by facilitated release. Such a system could be best obtained by the single step protocol, starting with a lipid and polymer mixture for nanoparticle formation.
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30
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Hiding the Elephant in the Room with Experimental Neutrons. Biophys J 2020; 119:234-235. [PMID: 32640187 DOI: 10.1016/j.bpj.2020.05.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 10/24/2022] Open
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Kumar M, Mandal K, Blakeley MP, Wymore T, Kent SBH, Louis JM, Das A, Kovalevsky A. Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design. ACS OMEGA 2020; 5:11605-11617. [PMID: 32478251 PMCID: PMC7254801 DOI: 10.1021/acsomega.0c00835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.
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Affiliation(s)
- Mukesh Kumar
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Kalyaneswar Mandal
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue−Langevin, 38000 Grenoble, France
| | - Troy Wymore
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen B. H. Kent
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National
Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Amit Das
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Andrey Kovalevsky
- Neutron Scattering
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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Hoogerheide DP, Forsyth VT, Brown KA. Neutron scattering for STRUCTURAL BIOLOGY: Modern neutron sources illuminate the complex functions of living systems. PHYSICS TODAY 2020; 73:10.1063/pt.3.4498. [PMID: 38487716 PMCID: PMC10938470 DOI: 10.1063/pt.3.4498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Modern neutron sources illuminate the complex functions of living systems.
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Affiliation(s)
- David P Hoogerheide
- National Institute of Standards and Technology Center for Neutron Research in Gaithersburg, Maryland
| | - V Trevor Forsyth
- Institut Laue-Langevin in Grenoble, France; he also holds a chair in biophysics at Keele University in the UK
| | - Katherine A Brown
- Cavendish Laboratory at Cambridge University in the UK and at the University of Texas at Austin
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33
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Tai Y, Takaba K, Hanazono Y, Dao HA, Miki K, Takeda K. X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:1096-1106. [PMID: 31793903 DOI: 10.1107/s2059798319014608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/28/2019] [Indexed: 11/10/2022]
Abstract
Hydrogen atoms are critical to the nature and properties of proteins, and thus deuteration has the potential to influence protein function. In fact, it has been reported that some deuterated proteins show different physical and chemical properties to their protiated counterparts. Consequently, it is important to investigate protonation states around the active site when using deuterated proteins. Here, hydrogen isotope effects on the S65T/F99S/M153T/V163A variant of green fluorescent protein (GFP), in which the deprotonated B form is dominant at pH 8.5, were investigated. The pH/pD dependence of the absorption and fluorescence spectra indicates that the protonation state of the chromophore is the same in protiated GFP in H2O and protiated GFP in D2O at pH/pD 8.5, while the pKa of the chromophore became higher in D2O. Indeed, X-ray crystallographic analyses at sub-ångström resolution revealed no apparent changes in the protonation state of the chromophore between the two samples. However, detailed comparisons of the hydrogen OMIT maps revealed that the protonation state of His148 in the vicinity of the chromophore differed between the two samples. This indicates that protonation states around the active site should be carefully adjusted to be the same as those of the protiated protein when neutron crystallographic analyses of proteins are performed.
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Affiliation(s)
- Yang Tai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kiyofumi Takaba
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hoang Anh Dao
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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34
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Saouessi M, Peters J, Kneller GR. Frequency domain modeling of quasielastic neutron scattering from hydrated protein powders: Application to free and inhibited human acetylcholinesterase. J Chem Phys 2019; 151:125103. [PMID: 31575200 DOI: 10.1063/1.5121703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This article reports on a frequency domain analysis of quasielastic neutron scattering spectra from free and Huperzine-A-inhibited human acetylcholinesterase, extending a recent time domain analysis of the same experimental data [M. Saouessi et al., J. Chem. Phys. 150, 161104 (2019)]. An important technical point here is the construction of a semianalytical model for the resolution-broadened dynamic structure factor that can be fitted to the experimental spectra. We find comparable parameters as in our previous study and demonstrate that our model is sensitive to subpercent changes in the experimental data, which are caused by reversible binding of the inhibitor Huperzine A.
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Affiliation(s)
- Melek Saouessi
- Centre de Biophys. Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
| | - Judith Peters
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Gerald R Kneller
- Centre de Biophys. Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
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35
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Raghuwanshi VS, Garnier G. Cellulose Nano-Films as Bio-Interfaces. Front Chem 2019; 7:535. [PMID: 31417896 PMCID: PMC6682661 DOI: 10.3389/fchem.2019.00535] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/12/2019] [Indexed: 12/12/2022] Open
Abstract
Cellulose, the most abundant polymer on earth, has enormous potential in developing bio-friendly, and sustainable technological products. In particular, cellulose films of nanoscale thickness (1-100 nm) are transparent, smooth (roughness <1 nm), and provide a large surface area interface for biomolecules immobilization and interactions. These attractive film properties create many possibilities for both fundamental studies and applications, especially in the biomedical field. The three liable-OH groups on the monomeric unit of the cellulose chain provide schemes to chemically modify the cellulose interface and engineer its properties. Here, the cellulose thin film serves as a substrate for biomolecules interactions and acts as a support for bio-diagnostics. This review focuses on the challenges and opportunities provided by engineering cellulose thin films for controlling biomolecules interactions. The first part reviews the methods for preparing cellulose thin films. These are by dispersing or dissolving pure cellulose or cellulose derivatives in a solvent to coat a substrate using the spin coating, Langmuir-Blodgett, or Langmuir-Schaefer method. It is shown how different cellulose sources, preparation, and coating methods and substrate surface pre-treatment affect the film thickness, roughness, morphology, crystallinity, swelling in water, and homogeneity. The second part analyses the bio-macromolecules interactions with the cellulose thin film interfaces. Biomolecules, such as antibodies and enzymes, are adsorbed at the cellulose-liquid interface, and analyzed dry and wet. This highlights the effect of film surface morphology, thickness, crystallinity, water intake capacity, and surface pre-treatment on biomolecule adsorption, conformation, coverage, longevity, and activity. Advance characterization of cellulose thin film interface morphology and adsorbed biomolecules interactions are next reviewed. X-ray and neutron scattering/reflectivity combined with atomic force microscopy (AFM), quartz crystal microbalance (QCM), microscopy, and ellipsometer allow visualizing, and quantifying the structural morphology of cellulose-biomolecule interphase and the respective biomolecules conformations, kinetics, and sorption mechanisms. This review provides a novel insight on the advantages and challenges of engineering cellulose thin films for biomedical applications. This is to foster the exploration at the molecular level of the interaction mechanisms between a cellulose interface and adsorbed biomolecules with respect to adsorbed molecules morphology, surface coverage, and quantity. This knowledge is to engineer a novel generation of efficient and functional biomedical devices.
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Affiliation(s)
- Vikram Singh Raghuwanshi
- Bioresource Processing Research Institute of Australia (BioPRIA), Monash University, Clayton, VIC, Australia
| | - Gil Garnier
- Bioresource Processing Research Institute of Australia (BioPRIA), Monash University, Clayton, VIC, Australia
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36
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Cachau RE, Zhu J, Nicklaus MC. The upcoming subatomic resolution revolution. Curr Opin Struct Biol 2019; 58:53-58. [PMID: 31233975 DOI: 10.1016/j.sbi.2019.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/12/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
Subatomic resolution macromolecular crystallography has been revealing the most fascinating details of macromolecular structures for many years. This most extreme form of macromolecular crystallography is going through rapid changes. A new generation of superbrilliant X-ray sources and detectors is facilitating the rapid acquisition of high-quality datasets. Equally important, a new breed of methods and highly integrated advanced computational tools for structure refinement and analysis is poised to change the way we use subatomic resolution data and reposition high-resolution macromolecular crystallography in medicinal chemistry studies. Subatomic resolution macromolecular crystallography may soon be a routine source of detailed molecular information besides precise geometries, including binding energies and other chemical descriptors, opening new possibilities of application.
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Affiliation(s)
- Raul E Cachau
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA.
| | - Jianghai Zhu
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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37
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Takaba K, Tai Y, Eki H, Dao HA, Hanazono Y, Hasegawa K, Miki K, Takeda K. Subatomic resolution X-ray structures of green fluorescent protein. IUCRJ 2019; 6:387-400. [PMID: 31098020 PMCID: PMC6503917 DOI: 10.1107/s205225251900246x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/17/2019] [Indexed: 05/06/2023]
Abstract
Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.
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Affiliation(s)
- Kiyofumi Takaba
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yang Tai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruhiko Eki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hoang-Anh Dao
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Correspondence e-mail:
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38
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Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL. Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. J Am Chem Soc 2019; 141:4711-4720. [PMID: 30834751 DOI: 10.1021/jacs.8b13613] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To compare ordered water positions from experiment with those from molecular dynamics (MD) simulations, a number of MD models of water structure in crystalline endoglucanase were calculated. The starting MD model was derived from a joint X-ray and neutron diffraction crystal structure, enabling the use of experimentally assigned protonation states. Simulations were performed in the crystalline state, using a periodic 2 × 2 × 2 supercell with explicit solvent. Water X-ray and neutron scattering density maps were computed from MD trajectories using standard macromolecular crystallography methods. In one set of simulations, harmonic restraints were applied to bias the protein structure toward the crystal structure. For these simulations, the recall of crystallographic waters using strong peaks in the MD water electron density was very good, and there also was substantial visual agreement between the boomerang-like wings of the neutron scattering density and the crystalline water hydrogen positions. An unrestrained simulation also was performed. For this simulation, the recall of crystallographic waters was much lower. For both restrained and unrestrained simulations, the strongest water density peaks were associated with crystallographic waters. The results demonstrate that it is now possible to recover crystallographic water structure using restrained MD simulations but that it is not yet reasonable to expect unrestrained MD simulations to do the same. Further development and generalization of MD water models for force-field development, macromolecular crystallography, and medicinal chemistry applications is now warranted. In particular, the combination of room-temperature crystallography, neutron diffraction, and crystalline MD simulations promises to substantially advance modeling of biomolecular solvation.
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Affiliation(s)
- Michael E Wall
- Computer, Computational, and Statistical Sciences Division , Los Alamos National Laboratory , Mail Stop B256 , Los Alamos , New Mexico 87545 , United States
| | - Gaetano Calabró
- OpenEye Scientific Software , 9 Bisbee Court, Unit D , Santa Fe , New Mexico 87507 , United States.,Department of Pharmaceutical Sciences , University of California, Irvine , 3134B Natural Sciences 1 , Irvine , California 92697 , United States
| | - Christopher I Bayly
- OpenEye Scientific Software , 9 Bisbee Court, Unit D , Santa Fe , New Mexico 87507 , United States
| | - David L Mobley
- Department of Pharmaceutical Sciences , University of California, Irvine , 3134B Natural Sciences 1 , Irvine , California 92697 , United States.,Department of Chemistry , University of California, Irvine , 3134B Natural Sciences 1 , Irvine , California 92697 , United States
| | - Gregory L Warren
- OpenEye Scientific Software , 9 Bisbee Court, Unit D , Santa Fe , New Mexico 87507 , United States
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39
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Forsyth VT, Moody P. Neutron scattering for the study of biological systems - major opportunities within a rapidly changing landscape. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1126-1128. [PMID: 30605129 DOI: 10.1107/s2059798318017886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- V Trevor Forsyth
- Partnership for Structural Biology, Institut Laue-Langevin, 6 rue Jules Horowitz, 38042 Grenoble CEDEX 9 France
| | - Peter Moody
- Henry Wellcome Laboratories for Structural Biology, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
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