1
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Sohmen B, Beck C, Frank V, Seydel T, Hoffmann I, Hermann B, Nüesch M, Grimaldo M, Schreiber F, Wolf S, Roosen‐Runge F, Hugel T. The Onset of Molecule-Spanning Dynamics in Heat Shock Protein Hsp90. Adv Sci (Weinh) 2023; 10:e2304262. [PMID: 37984887 PMCID: PMC10754087 DOI: 10.1002/advs.202304262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/06/2023] [Indexed: 11/22/2023]
Abstract
Protein dynamics have been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is largely unknown how fast (local) fluctuations can lead to slow global (allosteric) changes. Here, fast molecule-spanning dynamics on the 100 to 200 ns time scale in the heat shock protein 90 (Hsp90) are shown. Global real-space movements are assigned to dynamic modes on this time scale, which is possible by a combination of single-molecule fluorescence, quasi-elastic neutron scattering and all-atom molecular dynamics (MD) simulations. The time scale of these dynamic modes depends on the conformational state of the Hsp90 dimer. In addition, the dynamic modes are affected to various degrees by Sba1, a co-chaperone of Hsp90, depending on the location within Hsp90, which is in very good agreement with MD simulations. Altogether, this data is best described by fast molecule-spanning dynamics, which precede larger conformational changes in Hsp90 and might be the molecular basis for allostery. This integrative approach provides comprehensive insights into molecule-spanning dynamics on the nanosecond time scale for a multi-domain protein.
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Affiliation(s)
- Benedikt Sohmen
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Christian Beck
- Institute of Applied PhysicsUniversity of TübingenAuf der Morgenstelle 1072076TübingenGermany
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Veronika Frank
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Tilo Seydel
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Ingo Hoffmann
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Bianca Hermann
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Mark Nüesch
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 190CH‐8057ZurichSwitzerland
| | - Marco Grimaldo
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Frank Schreiber
- Institute of Applied PhysicsUniversity of TübingenAuf der Morgenstelle 1072076TübingenGermany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of PhysicsUniversity of FreiburgHermann‐Herder‐Strasse 379104FreiburgGermany
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms‐Research Center for Biointerfaces (BRCB)Malmö University20506MalmöSweden
- Division of Physical ChemistryLund UniversityNaturvetarvägen 1422100LundSweden
| | - Thorsten Hugel
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
- Signalling Research Centers BIOSS and CIBSSUniversity of FreiburgSchänzlestrasse 1879104FreiburgGermany
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2
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Hassani AN, Haris L, Appel M, Seydel T, Stadler AM, Kneller GR. Signature of functional enzyme dynamics in quasielastic neutron scattering spectra: The case of phosphoglycerate kinase. J Chem Phys 2023; 159:141102. [PMID: 37818999 DOI: 10.1063/5.0166124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
We present an analysis of high-resolution quasi-elastic neutron scattering spectra of phosphoglycerate kinase which elucidates the influence of the enzymatic activity on the dynamics of the protein. We show that in the active state the inter-domain motions are amplified and the intra-domain asymptotic power-law relaxation ∝t-α is accelerated, with a reduced coefficient α. Employing an energy landscape picture of protein dynamics, this observation can be translated into a widening of the distribution of energy barriers separating conformational substates of the protein.
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Affiliation(s)
- Abir N Hassani
- Centre de Biophysique Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Luman Haris
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Markus Appel
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Tilo Seydel
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Andreas M Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
- Laboratoire des biomolécules, Département de chimie, Ecole Normale Supérieure, 75005 Paris, France
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3
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Mosca I, Pounot K, Beck C, Colin L, Matsarskaia O, Grapentin C, Seydel T, Schreiber F. Biophysical Determinants for the Viscosity of Concentrated Monoclonal Antibody Solutions. Mol Pharm 2023; 20:4698-4713. [PMID: 37549226 DOI: 10.1021/acs.molpharmaceut.3c00440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Monoclonal antibodies (mAbs) are particularly relevant for therapeutics due to their high specificity and versatility, and mAb-based drugs are hence used to treat numerous diseases. The increased patient compliance of self-administration motivates the formulation of products for subcutaneous (SC) administration. The associated challenge is to formulate highly concentrated antibody solutions to achieve a significant therapeutic effect, while limiting their viscosity and preserving their physicochemical stability. Protein-protein interactions (PPIs) are in fact the root cause of several potential problems concerning the stability, manufacturability, and delivery of a drug product. The understanding of macroscopic viscosity requires an in-depth knowledge on protein diffusion, PPIs, and self-association/aggregation. Here, we study the self-diffusion of different mAbs of the IgG1 subtype in aqueous solution as a function of the concentration and temperature by quasi-elastic neutron scattering (QENS). QENS allows us to probe the short-time self-diffusion of the molecules and therefore to determine the hydrodynamic mAb cluster size and to gain information on the internal mAb dynamics. Small-angle neutron scattering (SANS) is jointly employed to probe structural details and to understand the nature and intensity of PPIs. Complementary information is provided by molecular dynamics (MD) simulations and viscometry, thus obtaining a comprehensive picture of mAb diffusion.
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Affiliation(s)
- Ilaria Mosca
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Kévin Pounot
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Louise Colin
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Olga Matsarskaia
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | | | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
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4
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Hirschmann F, Lopez H, Roosen-Runge F, Seydel T, Schreiber F, Oettel M. Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G. J Chem Phys 2023; 158:084112. [PMID: 36859072 DOI: 10.1063/5.0132493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al., J. Phys. Chem. B 116, 8045 (2012)] and is employed here to compare findings for the compact BSA molecule and the more anisotropic IgG molecule. We define several modified coarse-grained models of BSA and IgG, which differ in their internal constraints and thus account for a variation of flexibility. We study denser solutions of the coarse-grained models with purely repulsive molecules (achievable by suitable salt conditions) and address the effect of packing and flexibility on dynamic and static behavior. Translational and rotational self-diffusivity is enhanced for more elastic models. Finally, we discuss a number of effective sphere sizes for the BSA molecule, which can be defined from its static and dynamic properties. Here, it is found that the effective sphere diameters lie between 4.9 and 6.1 nm, corresponding to a relative spread of about ±10% around a mean of 5.5 nm.
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Affiliation(s)
- Frank Hirschmann
- Institute for Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Hender Lopez
- School of Physics, Clinical and Optometric Sciences, Technological University Dublin, Grangegorman D07 ADY7, Ireland
| | - Felix Roosen-Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Tilo Seydel
- Institut Max von Laue-Paul Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Frank Schreiber
- Institute for Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Martin Oettel
- Institute for Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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5
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Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Seydel T, Beck C, Petrillo C, Derreumaux P, Melchionna S, Sterpone F, Peters J, Paciaroni A. Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death. ACS Cent Sci 2023; 9:93-102. [PMID: 36712493 PMCID: PMC9881203 DOI: 10.1021/acscentsci.2c01078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 05/30/2023]
Abstract
Temperature variations have a big impact on bacterial metabolism and death, yet an exhaustive molecular picture of these processes is still missing. For instance, whether thermal death is determined by the deterioration of the whole or a specific part of the proteome is hotly debated. Here, by monitoring the proteome dynamics of E. coli, we clearly show that only a minor fraction of the proteome unfolds at the cell death. First, we prove that the dynamical state of the E. coli proteome is an excellent proxy for temperature-dependent bacterial metabolism and death. The proteome diffusive dynamics peaks at about the bacterial optimal growth temperature, then a dramatic dynamical slowdown is observed that starts just below the cell's death temperature. Next, we show that this slowdown is caused by the unfolding of just a small fraction of proteins that establish an entangling interprotein network, dominated by hydrophobic interactions, across the cytoplasm. Finally, the deduced progress of the proteome unfolding and its diffusive dynamics are both key to correctly reproduce the E. coli growth rate.
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Affiliation(s)
- Daniele Di Bari
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
| | - Stepan Timr
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- J.
Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, 182 23Prague 8, Czechia
| | - Marianne Guiral
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, BIP, CNRS, Aix-Marseille Université, 13400Marseille, France
| | | | - Tilo Seydel
- Institut
Laue-Langevin, 38000Grenoble, France
| | | | - Caterina Petrillo
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut Universitaire de France, 75005Paris, France
| | - Simone Melchionna
- ISC-CNR,
Dipartimento di Fisica, Università
Sapienza, 00185Rome, Italy
- Lexma
Technology1337 Massachusetts
Avenue, Arlington, Massachusetts02476, United States
| | - Fabio Sterpone
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
| | - Judith Peters
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
- Institut Universitaire de France, 75005Paris, France
| | - Alessandro Paciaroni
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
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6
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Bertini L, Libera V, Ripanti F, Seydel T, Paolantoni M, Orecchini A, Petrillo C, Comez L, Paciaroni A. Role of fast dynamics in the complexation of G-quadruplexes with small molecules. Phys Chem Chem Phys 2022; 24:29232-29240. [PMID: 36445842 DOI: 10.1039/d2cp03602a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-quadruplexes (G4s) formed by the human telomeric sequence AG3 (TTAG3)3 (Tel22) play a key role in cancer and aging. We combined elastic incoherent neutron scattering (EINS) and quasielastic incoherent neutron scattering (QENS) to characterize the internal dynamics of Tel22 G4s and to assess how it is affected by complexation with two standard ligands, Berberine and BRACO19. We show that the interaction with the two ligands induces an increase of the overall mobility of Tel22 as quantified by the mean squared displacements (MSD) of hydrogen atoms. At the same time, the complexes display a lower stiffness than G4 alone. Two different types of motion characterize the G4 nanosecond timescale dynamics. Upon complexation, an increasing fraction of G4 atomic groups participate in this fast dynamics, along with an increase in the relevant characteristic length scales. We suggest that the entropic contribution to the conformational free energy of these motions might be crucial for the complexation mechanisms.
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Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy. .,Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) 71 avenue des Martyrs, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto, 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
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7
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Reiser M, Girelli A, Ragulskaya A, Das S, Berkowicz S, Bin M, Ladd-Parada M, Filianina M, Poggemann HF, Begam N, Akhundzadeh MS, Timmermann S, Randolph L, Chushkin Y, Seydel T, Boesenberg U, Hallmann J, Möller J, Rodriguez-Fernandez A, Rosca R, Schaffer R, Scholz M, Shayduk R, Zozulya A, Madsen A, Schreiber F, Zhang F, Perakis F, Gutt C. Resolving molecular diffusion and aggregation of antibody proteins with megahertz X-ray free-electron laser pulses. Nat Commun 2022; 13:5528. [PMID: 36130930 PMCID: PMC9490738 DOI: 10.1038/s41467-022-33154-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
X-ray free-electron lasers (XFELs) with megahertz repetition rate can provide novel insights into structural dynamics of biological macromolecule solutions. However, very high dose rates can lead to beam-induced dynamics and structural changes due to radiation damage. Here, we probe the dynamics of dense antibody protein (Ig-PEG) solutions using megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European XFEL. By varying the total dose and dose rate, we identify a regime for measuring the motion of proteins in their first coordination shell, quantify XFEL-induced effects such as driven motion, and map out the extent of agglomeration dynamics. The results indicate that for average dose rates below 1.06 kGy μs-1 in a time window up to 10 μs, it is possible to capture the protein dynamics before the onset of beam induced aggregation. We refer to this approach as correlation before aggregation and demonstrate that MHz-XPCS bridges an important spatio-temporal gap in measurement techniques for biological samples.
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Affiliation(s)
- Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Sudipta Das
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sharon Berkowicz
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Marjorie Ladd-Parada
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Mariia Filianina
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Hanna-Friederike Poggemann
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.,Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | | | - Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany
| | - Lisa Randolph
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany
| | - Yuriy Chushkin
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, CS 40220, 38043, Grenoble Cedex 9, France
| | - Tilo Seydel
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Ulrike Boesenberg
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jörg Hallmann
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Robert Rosca
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robert Schaffer
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Scholz
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Roman Shayduk
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexey Zozulya
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany.
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8
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Beck C, Grimaldo M, Lopez H, Da Vela S, Sohmen B, Zhang F, Oettel M, Barrat JL, Roosen-Runge F, Schreiber F, Seydel T. Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture. J Phys Chem B 2022; 126:7400-7408. [PMID: 36112146 PMCID: PMC9527755 DOI: 10.1021/acs.jpcb.2c02380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The crowded environment of biological systems such as
the interior
of living cells is occupied by macromolecules with a broad size distribution.
This situation of polydispersity might influence the dependence of
the diffusive dynamics of a given tracer macromolecule in a monodisperse
solution on its hydrodynamic size and on the volume fraction. The
resulting size dependence of diffusive transport crucially influences
the function of a living cell. Here, we investigate a simplified model
system consisting of two constituents in aqueous solution, namely,
of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin
(Ig), systematically depending on the total volume fraction and ratio
of these constituents. From high-resolution quasi-elastic neutron
spectroscopy, the separate apparent short-time diffusion coefficients
for BSA and Ig in the mixture are extracted, which show substantial
deviations from the diffusion coefficients measured in monodisperse
solutions at the same total volume fraction. These deviations can
be modeled quantitatively using results from the short-time rotational
and translational diffusion in a two-component hard sphere system
with two distinct, effective hydrodynamic radii. Thus, we find that
a simple colloid picture well describes short-time diffusion in binary
mixtures as a function of the mixing ratio and the total volume fraction.
Notably, the self-diffusion of the smaller protein BSA in the mixture
is faster than the diffusion in a pure BSA solution, whereas the self-diffusion
of Ig in the mixture is slower than in the pure Ig solution.
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Affiliation(s)
- Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Marco Grimaldo
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, D07 XT95 Grangegorman, Ireland
| | - Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Benedikt Sohmen
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Martin Oettel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | | | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
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9
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Raskar T, Niebling S, Devos JM, Yorke BA, Härtlein M, Huse N, Forsyth VT, Seydel T, Pearson AR. Structure and diffusive dynamics of aspartate α-decarboxylase (ADC) liganded with D-serine in aqueous solution. Phys Chem Chem Phys 2022; 24:20336-20347. [PMID: 35980136 PMCID: PMC9429672 DOI: 10.1039/d2cp02063g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incoherent neutron spectroscopy, in combination with dynamic light scattering, was used to investigate the effect of ligand binding on the center-of-mass self-diffusion and internal diffusive dynamics of Escherichia coli aspartate α-decarboxylase (ADC). The X-ray crystal structure of ADC in complex with the d-serine inhibitor was also determined, and molecular dynamics simulations were used to further probe the structural rearrangements that occur as a result of ligand binding. These experiments reveal that d-serine forms hydrogen bonds with some of the active site residues, that higher order oligomers of the ADC tetramer exist on ns–ms time-scales, and also show that ligand binding both affects the ADC internal diffusive dynamics and appears to further increase the size of the higher order oligomers. Neutron spectroscopy, dynamic light scattering, X-ray diffraction, and MD-simulations were used to investigate the effect of ligand binding on the structure and diffusive dynamics of Escherichia coli aspartate alpha-decarboxylase.![]()
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Affiliation(s)
- Tushar Raskar
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France.,Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
| | - Stephan Niebling
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany. .,European Molecular Biology Laboratory, Hamburg, Notkestr. 85, 22607 Hamburg, Germany
| | - Juliette M Devos
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Briony A Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford, BD7 1DP, UK
| | - Michael Härtlein
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Nils Huse
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
| | - V Trevor Forsyth
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France.,Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
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10
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Pounot K, Appel M, Beck C, Weik M, Schirò G, Fichou Y, Seydel T, Schreiber F. High-resolution Neutron Spectroscopy to Study Picosecond-nanosecond Dynamics of Proteins and Hydration Water. J Vis Exp 2022. [DOI: 10.3791/63664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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11
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Santamaria A, Batchu KC, Matsarskaia O, Prévost SF, Russo D, Natali F, Seydel T, Hoffmann I, Laux V, Haertlein M, Darwish TA, Russell RA, Corucci G, Fragneto G, Maestro A, Zaccai NR. Strikingly Different Roles of SARS-CoV-2 Fusion Peptides Uncovered by Neutron Scattering. J Am Chem Soc 2022; 144:2968-2979. [PMID: 35157798 PMCID: PMC8862744 DOI: 10.1021/jacs.1c09856] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 02/02/2023]
Abstract
Coronavirus disease-2019 (COVID-19), a potentially lethal respiratory illness caused by the coronavirus SARS-CoV-2, emerged in the end of 2019 and has since spread aggressively across the globe. A thorough understanding of the molecular mechanisms of cellular infection by coronaviruses is therefore of utmost importance. A critical stage in infection is the fusion between viral and host membranes. Here, we present a detailed investigation of the role of selected SARS-CoV-2 Spike fusion peptides, and the influence of calcium and cholesterol, in this fusion process. Structural information from specular neutron reflectometry and small angle neutron scattering, complemented by dynamics information from quasi-elastic and spin-echo neutron spectroscopy, revealed strikingly different functions encoded in the Spike fusion domain. Calcium drives the N-terminal of the Spike fusion domain to fully cross the host plasma membrane. Removing calcium, however, reorients the peptide back to the lipid leaflet closest to the virus, leading to significant changes in lipid fluidity and rigidity. In conjunction with other regions of the fusion domain, which are also positioned to bridge and dehydrate viral and host membranes, the molecular events leading to cell entry by SARS-CoV-2 are proposed.
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Affiliation(s)
- Andreas Santamaria
- Institut
Laue-Langevin, 38042 Grenoble, France
- Departamento
de Química Física, Universidad
Complutense de Madrid, 28040 Madrid, Spain
| | | | | | | | - Daniela Russo
- Institut
Laue-Langevin, 38042 Grenoble, France
- CNR-IOM
& INSIDE@ILL, 38042 Grenoble, France
| | - Francesca Natali
- Institut
Laue-Langevin, 38042 Grenoble, France
- CNR-IOM
& INSIDE@ILL, 38042 Grenoble, France
| | - Tilo Seydel
- Institut
Laue-Langevin, 38042 Grenoble, France
| | | | | | | | - Tamim A. Darwish
- National
Deuteration Facility, ANSTO-Sidney, Lucas Heights, NSW 2234, Australia
| | - Robert A. Russell
- National
Deuteration Facility, ANSTO-Sidney, Lucas Heights, NSW 2234, Australia
| | - Giacomo Corucci
- Institut
Laue-Langevin, 38042 Grenoble, France
- École
Doctorale de Physique, Université
Grenoble Alpes, 38400 Saint-Martin-d’Héres, France
| | - Giovanna Fragneto
- Institut
Laue-Langevin, 38042 Grenoble, France
- École
Doctorale de Physique, Université
Grenoble Alpes, 38400 Saint-Martin-d’Héres, France
| | - Armando Maestro
- Institut
Laue-Langevin, 38042 Grenoble, France
- Centro
de Física de Materiales (CSIC, UPV/EHU) − Materials
Physics Center MPC, Paseo
Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- IKERBASQUE
− Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Nathan R. Zaccai
- Cambridge
Institute for Medical Research, University
of Cambridge, Cambridge CB22 7QQ, United Kingdom
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12
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Fagerberg E, Lenton S, Nylander T, Seydel T, Skepö M. Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study. J Phys Chem B 2022; 126:789-801. [PMID: 35044776 PMCID: PMC8819652 DOI: 10.1021/acs.jpcb.1c08976] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Intrinsically disordered
proteins (IDPs) are proteins that, in
comparison with globular/structured proteins, lack a distinct tertiary
structure. Here, we use the model IDP, Histatin 5, for studying its
dynamical properties under self-crowding conditions with quasi-elastic
neutron scattering in combination with full atomistic molecular dynamics
(MD) simulations. The aim is to determine the effects of crowding
on the center-of-mass diffusion as well as the internal diffusive
behavior. The diffusion was found to decrease significantly, which
we hypothesize can be attributed to some degree of aggregation at
higher protein concentrations, (≥100 mg/mL), as indicated by
recent small-angle X-ray scattering studies. Temperature effects are
also considered and found to, largely, follow Stokes–Einstein
behavior. Simple geometric considerations fail to accurately predict
the rates of diffusion, while simulations show semiquantitative agreement
with experiments, dependent on assumptions of the ratio between translational
and rotational diffusion. A scaling law that previously was found
to successfully describe the behavior of globular proteins was found
to be inadequate for the IDP, Histatin 5. Analysis of the MD simulations
show that the width of the distribution with respect to diffusion
is not a simplistic mirroring of the distribution of radius of gyration,
hence, displaying the particular features of IDPs that need to be
accounted for.
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Affiliation(s)
- Eric Fagerberg
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
| | - Samuel Lenton
- Physical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
| | - Tommy Nylander
- Physical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble, France
| | - Marie Skepö
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden.,LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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13
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Hassani AN, Haris L, Appel M, Seydel T, Stadler AM, Kneller GR. Multiscale relaxation dynamics and diffusion of myelin basic protein in solution studied by quasielastic neutron scattering. J Chem Phys 2022; 156:025102. [PMID: 35032992 DOI: 10.1063/5.0077100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report an analysis of high-resolution quasielastic neutron scattering spectra from Myelin Basic Protein (MBP) in solution, comparing the spectra at three different temperatures (283, 303, and 323 K) for a pure D2O buffer and a mixture of D2O buffer with 30% of deuterated trifluoroethanol (TFE). Accompanying experiments with dynamic light scattering and Circular Dichroism (CD) spectroscopy have been performed to obtain, respectively, the global diffusion constant and the secondary structure content of the molecule for both buffers as a function of temperature. Modeling the decay of the neutron intermediate scattering function by the Mittag-Leffler relaxation function, ϕ(t) = Eα(-(t/τ)α) (0 < α < 1), we find that trifluoroethanol slows down the relaxation dynamics of the protein at 283 K and leads to a broader relaxation rate spectrum. This effect vanishes with increasing temperature, and at 323 K, its relaxation dynamics is identical in both solvents. These results are coherent with the data from dynamic light scattering, which show that the hydrodynamic radius of MBP in TFE-enriched solutions does not depend on temperature and is only slightly smaller compared to the pure D2O buffer, except for 283 K, where it is much reduced. In accordance with these observations, the CD spectra reveal that TFE induces essentially a partial transition from β-strands to α-helices, but only a weak increase in the total secondary structure content, leaving about 50% of the protein unfolded. The results show that MBP is for all temperatures and in both buffers an intrinsically disordered protein and that TFE essentially induces a reduction in its hydrodynamic radius and its relaxation dynamics at low temperatures.
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Affiliation(s)
- Abir N Hassani
- Centre de Biophysique Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
| | - Luman Haris
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Markus Appel
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Tilo Seydel
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Andreas M Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
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14
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Beck C, Pounot K, Mosca I, H Jalarvo N, Roosen-Runge F, Schreiber F, Seydel T. Notes on Fitting and Analysis Frameworks for QENS Spectra of (Soft) Colloid Suspensions. EPJ Web Conf 2022. [DOI: 10.1051/epjconf/202227201004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With continuously improving signal-to-noise ratios, a statistically sound analysis of quasi-elastic neutron scattering (QENS) spectra requires to fit increasingly complex models which poses several challenges. Simultaneous fits of the spectra for all recorded values of the momentum transfer become a standard approach. Spectrometers at spallation sources can have a complicated non-Gaussian resolution function which has to be described most accurately. At the same time, to speed up the fitting, an analytical convolution with this resolution function is of interest. Here, we discuss basic concepts to efficient approaches for fits of QENS spectra based on standard MATLAB and Python fit algorithms. We illustrate the fits with example data from IN16B, BASIS, and BATS.
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15
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Jansen M, Juranyi F, Yarema O, Seydel T, Wood V. Ligand Dynamics in Nanocrystal Solids Studied with Quasi-Elastic Neutron Scattering. ACS Nano 2021; 15:20517-20526. [PMID: 34878757 DOI: 10.1021/acsnano.1c09073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanocrystal surfaces are commonly populated by organic ligands, which play a determining role in the optical, electronic, thermal, and catalytic properties of the individual nanocrystals and their assemblies. Understanding the bonding of ligands to nanocrystal surfaces and their dynamics is therefore important for the optimization of nanocrystals for different applications. In this study, we use temperature-dependent, quasi-elastic neutron scattering (QENS) to investigate the dynamics of different surface bound alkanethiols in lead sulfide nanocrystal solids. We select alkanethiols with mono- and dithiol terminations, as well as different backbone types and lengths. QENS spectra are collected both on a time-of-flight spectrometer and on a backscattering spectrometer, allowing us to investigate ligand dynamics in a time range from a few picoseconds to nanoseconds. Through model-based analysis of the QENS data, we find that ligands can either (1) precess around a central axis, while simultaneously rotating around their own molecular axis, or (2) only undergo uniaxial rotation with no precession. We establish the percentage of ligands undergoing each type of motion, the average relaxation times, and activation energies for these motions. We determine, for example, that dithiols which link facets of neighboring nanocrystals only exhibit uniaxial rotation and that longer ligands have higher activation energies and show smaller opening angles of precession due to stronger ligand-ligand interactions. Generally, this work provides insight into the arrangement and dynamics of ligands in nanocrystal solids, which is key to understanding their mechanical and thermal properties, and, more generally, highlights the potential of QENS for studying ligand behavior.
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Affiliation(s)
- Maximilian Jansen
- Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, CH-8092 Zurich, Switzerland
| | - Fanni Juranyi
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Olesya Yarema
- Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, CH-8092 Zurich, Switzerland
| | - Tilo Seydel
- Institut Laue-Langevin (ILL), 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Vanessa Wood
- Department of Information Technology and Electrical Engineering, ETH Zurich, Gloriastrasse 35, CH-8092 Zurich, Switzerland
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16
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Girelli A, Beck C, Bäuerle F, Matsarskaia O, Maier R, Zhang F, Wu B, Lang C, Czakkel O, Seydel T, Schreiber F, Roosen-Runge F. Molecular Flexibility of Antibodies Preserved Even in the Dense Phase after Macroscopic Phase Separation. Mol Pharm 2021; 18:4162-4169. [PMID: 34637319 PMCID: PMC8564753 DOI: 10.1021/acs.molpharmaceut.1c00555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antibody therapies are typically based on high-concentration formulations that need to be administered subcutaneously. These conditions induce several challenges, inter alia a viscosity suitable for injection, sufficient solution stability, and preservation of molecular function. To obtain systematic insights into the molecular factors, we study the dynamics on the molecular level under strongly varying solution conditions. In particular, we use solutions of antibodies with poly(ethylene glycol), in which simple cooling from room temperature to freezing temperatures induces a transition from a well-dispersed solution into a phase-separated and macroscopically arrested system. Using quasi-elastic neutron scattering during in situ cooling ramps and in prethermalized measurements, we observe a strong decrease in antibody diffusion, while internal flexibility persists to a significant degree, thus ensuring the movement necessary for the preservation of molecular function. These results are relevant for a more dynamic understanding of antibodies in high-concentration formulations, which affects the formation of transient clusters governing the solution viscosity.
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Affiliation(s)
- Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.,Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Famke Bäuerle
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ralph Maier
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Baohu Wu
- Jülich Centre for Neutron Science JCNS at MLZ, Forschungszentrum Jülich, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Christian Lang
- Jülich Centre for Neutron Science JCNS at MLZ, Forschungszentrum Jülich, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Orsolya Czakkel
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Tilo Seydel
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 205 06 Malmö, Sweden
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17
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Beck C, Grimaldo M, Braun MK, Bühl L, Matsarskaia O, Jalarvo NH, Zhang F, Roosen-Runge F, Schreiber F, Seydel T. Temperature and salt controlled tuning of protein clusters. Soft Matter 2021; 17:8506-8516. [PMID: 34490428 DOI: 10.1039/d1sm00418b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of molecular assemblies in protein solutions is of strong interest both from a fundamental viewpoint and for biomedical applications. While ordered and desired protein assemblies are indispensable for some biological functions, undesired protein condensation can induce serious diseases. As a common cofactor, the presence of salt ions is essential for some biological processes involving proteins, and in aqueous suspensions of proteins can also give rise to complex phase diagrams including homogeneous solutions, large aggregates, and dissolution regimes. Here, we systematically study the cluster formation approaching the phase separation in aqueous solutions of the globular protein BSA as a function of temperature (T), the protein concentration (cp) and the concentrations of the trivalent salts YCl3 and LaCl3 (cs). As an important complement to structural, i.e. time-averaged, techniques we employ a dynamical technique that can detect clusters even when they are transient on the order of a few nanoseconds. By employing incoherent neutron spectroscopy, we unambiguously determine the short-time self-diffusion of the protein clusters depending on cp, cs and T. We determine the cluster size in terms of effective hydrodynamic radii as manifested by the cluster center-of-mass diffusion coefficients D. For both salts, we find a simple functional form D(cp, cs, T) in the parameter range explored. The calculated inter-particle attraction strength, determined from the microscopic and short-time diffusive properties of the samples, increases with salt concentration and temperature in the regime investigated and can be linked to the macroscopic behavior of the samples.
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Affiliation(s)
- Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
| | - Marco Grimaldo
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
| | - Michal K Braun
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Lena Bühl
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Olga Matsarskaia
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
| | - Niina H Jalarvo
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, and JCNS Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, USA
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Felix Roosen-Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden.
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
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18
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Pounot K, Grime GW, Longo A, Zamponi M, Noferini D, Cristiglio V, Seydel T, Garman EF, Weik M, Foderà V, Schirò G. Zinc determines dynamical properties and aggregation kinetics of human insulin. Biophys J 2021; 120:886-898. [PMID: 33545104 DOI: 10.1016/j.bpj.2020.11.2280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/08/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment, and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here, we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, in which the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced x-ray emission and x-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.
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Affiliation(s)
- Kevin Pounot
- Applied Physics, University of Tübingen, Tübingen, Baden-Würtemberg, Germany.
| | | | - Alessandro Longo
- Istituto per lo Studio dei Materiali Nanostrutturati, CNR, Palermo, Italy
| | - Michaela Zamponi
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | | | - Tilo Seydel
- Science Division, Institut Max von Laue-Paul Langevin, Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Vito Foderà
- Pharmacy, University of Copenhagen, Copenhagen, Denmark.
| | - Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France.
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19
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Lushchekina SV, Inidjel G, Martinez N, Masson P, Trovaslet-Leroy M, Nachon F, Koza MM, Seydel T, Peters J. Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase. Biomolecules 2020; 10:biom10121664. [PMID: 33322722 PMCID: PMC7763276 DOI: 10.3390/biom10121664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 01/28/2023] Open
Abstract
The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.
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Affiliation(s)
- Sofya V. Lushchekina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Gaetan Inidjel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Nicolas Martinez
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kremlevskaya str 18, 480002 Kazan, Russia;
| | - Marie Trovaslet-Leroy
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Florian Nachon
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Michael Marek Koza
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Tilo Seydel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Judith Peters
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
- Correspondence: ; Tel.: +33-4-7620-7560
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20
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Ebersberger L, Schindler T, Kirsch SA, Pluhackova K, Schambony A, Seydel T, Böckmann RA, Unruh T. Lipid Dynamics in Membranes Slowed Down by Transmembrane Proteins. Front Cell Dev Biol 2020; 8:579388. [PMID: 33195218 PMCID: PMC7649217 DOI: 10.3389/fcell.2020.579388] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Lipids and proteins, as essential components of biological cell membranes, exhibit a significant degree of freedom for different kinds of motions including lateral long-range mobility. Due to their interactions, they not only preserve the cellular membrane but also contribute to many important cellular functions as e.g., signal transport or molecular exchange of the cell with its surrounding. Many of these processes take place on a short time (up to some nanoseconds) and length scale (up to some nanometers) which is perfectly accessible by quasielastic neutron scattering (QENS) experiments and molecular dynamics (MD) simulations. In order to probe the influence of a peptide, a transmembrane sequence of the transferrin receptor (TFRC) protein, on the dynamics of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) large unilamellar vesicles (LUVs) on a nanosecond time scale, high-resolution QENS experiments and complementary MD simulations have been utilized. By using different scattering contrasts in the experiment (chain-deuterated lipids and protonated lipids, respectively), a model could be developed which allows to examine the lipid and peptide dynamics separately. The experimental results revealed a restricted lipid lateral mobility in the presence of the TFRC transmembrane peptides. Also the apparent self-diffusion coefficient of the lateral movement of the peptide molecules could be determined quantitatively for the probed short-time regime. The findings could be confirmed very precisely by MD simulations. Furthermore, the article presents an estimation for the radius of influence of the peptides on the lipid long-range dynamics which could be determined by consistently combining results from experiment and simulation.
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Affiliation(s)
- Lisa Ebersberger
- Physics Department, Institute for Crystallography and Structural Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Torben Schindler
- Physics Department, Institute for Crystallography and Structural Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sonja A Kirsch
- Computational Biology, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Alexandra Schambony
- Department Biology, Chair of Developmental Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tilo Seydel
- Science Division, Institut Laue-Langevin, Grenoble, France
| | - Rainer A Böckmann
- Computational Biology, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tobias Unruh
- Physics Department, Institute for Crystallography and Structural Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Physics Department, Center for Nanoanalysis and Electron Microscopy (CENEM) and Interdisciplinary Center for Nanostructured Films (IZNF), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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21
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Matsarskaia O, Bühl L, Beck C, Grimaldo M, Schweins R, Zhang F, Seydel T, Schreiber F, Roosen-Runge F. Evolution of the structure and dynamics of bovine serum albumin induced by thermal denaturation. Phys Chem Chem Phys 2020; 22:18507-18517. [PMID: 32780038 DOI: 10.1039/d0cp01857k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein denaturation in concentrated solutions consists of the unfolding of the native protein structure, and subsequent cross-linking into clusters or gel networks. While the kinetic evolution of structure has been studied for some cases, the underlying microscopic dynamics of proteins has so far been neglected. However, protein dynamics is essential to understand the specific nature of assembly processes, such as diffusion-limited growth, or vitrification of dense liquids. Here, we present a study on thermal denaturation of concentrated solutions of bovine serum albumin (BSA) in D2O with and without NaCl. Using small-angle scattering, we provide information on structure before, during and after denaturation. Using quasi-elastic neutron scattering, we monitor in real-time the microscopic dynamics and dynamical confinement throughout the entire denaturation process covering protein unfolding and cross-linking. After denaturation, the protein dynamics is slowed down in salty solutions compared to those in pure water, while the stability and dynamics of the native solution appears unaffected by salt. The approach presented here opens opportunities to link microscopic dynamics to emerging structural properties, with implications for assembly processes in soft and biological matter.
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Affiliation(s)
- Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France.
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22
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Pounot K, Chaaban H, Foderà V, Schirò G, Weik M, Seydel T. Tracking Internal and Global Diffusive Dynamics During Protein Aggregation by High-Resolution Neutron Spectroscopy. J Phys Chem Lett 2020; 11:6299-6304. [PMID: 32663030 DOI: 10.1021/acs.jpclett.0c01530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Proteins can misfold and form either amorphous or organized aggregates with different morphologies and features. Aggregates of amyloid nature are pathological hallmarks in so-called protein conformational diseases, including Alzheimer's and Parkinson's. Evidence prevails that the transient early phases of the reaction determine the aggregate morphology and toxicity. As a consequence, real-time monitoring of protein aggregation is of utmost importance. Here, we employed time-resolved neutron backscattering spectroscopy to follow center-of-mass self-diffusion and nano- to picosecond internal dynamics of lysozyme during aggregation into a specific β-sheet rich superstructure, called particulates, formed at the isoelectric point of the protein. Particulate formation is found to be a one-step process, and protein internal dynamics, to remain unchanged during the entire aggregation process. The time-resolved neutron backscattering spectroscopy approach developed here, in combination with standard kinetics assays, provides a unifying framework in which dynamics and conformational transitions can be related to the different aggregation pathways.
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Affiliation(s)
- Kevin Pounot
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble cedex 9, France
| | - Hussein Chaaban
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble cedex 9, France
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23
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Seydel T, Koza MM, Matsarskaia O, André A, Maiti S, Weber M, Schweins R, Prévost S, Schreiber F, Scheele M. A neutron scattering perspective on the structure, softness and dynamics of the ligand shell of PbS nanocrystals in solution. Chem Sci 2020; 11:8875-8884. [PMID: 34123141 PMCID: PMC8163380 DOI: 10.1039/d0sc02636k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/01/2020] [Indexed: 12/02/2022] Open
Abstract
Small-angle neutron and X-ray scattering, neutron backscattering and neutron time-of-flight spectroscopy are applied to reveal the structure of the ligand shell, the temperature-dependent diffusion properties and the phonon spectrum of PbS nanocrystals functionalized with oleic acid in deuterated hexane. The nanocrystals decorated with oleic acid as well as the desorbed ligand molecules exhibit simple Brownian diffusion with a Stokes-Einstein temperature-dependence and inhibited freezing. Ligand molecules desorbed from the surface show strong spatial confinement. The phonon spectrum of oleic acid adsorbed to the nanocrystal surface exhibits hybrid modes with a predominant Pb-character. Low-energy surface modes of the NCs are prominent and indicate a large mechanical softness in solution. This work provides comprehensive insights into the ligand-particle interaction of colloidal nanocrystals in solution and highlights its effect on the diffusion and vibrational properties as well as their mechanical softness.
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Affiliation(s)
- Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) 71 Avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Michael Marek Koza
- Institut Max von Laue - Paul Langevin (ILL) 71 Avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Olga Matsarskaia
- Institut Max von Laue - Paul Langevin (ILL) 71 Avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Alexander André
- Institute of Physical and Theoretical Chemistry, University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Santanu Maiti
- Institute of Applied Physics, University of Tübingen Auf der Morgenstelle 10 72076 Tübingen Germany
| | - Michelle Weber
- Institute of Physical and Theoretical Chemistry, University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Ralf Schweins
- Institut Max von Laue - Paul Langevin (ILL) 71 Avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Sylvain Prévost
- ESRF - The European Synchrotron 71 Avenue des Martyrs, CS 40220 38043 Grenoble Cedex 9 France
| | - Frank Schreiber
- Institute of Applied Physics, University of Tübingen Auf der Morgenstelle 10 72076 Tübingen Germany
- Center for Light-Matter Interaction, Sensors & Analytics LISA+, University of Tübingen Auf der Morgenstelle 15 72076 Tübingen Germany
| | - Marcus Scheele
- Institute of Physical and Theoretical Chemistry, University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
- Center for Light-Matter Interaction, Sensors & Analytics LISA+, University of Tübingen Auf der Morgenstelle 15 72076 Tübingen Germany
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24
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Edkins RM, Appel M, Seydel T, Edkins K. The modifying effect of supramolecular gel fibres on the diffusion of paracetamol and ibuprofen sodium on the picosecond timescale. Phys Chem Chem Phys 2020; 22:10838-10844. [DOI: 10.1039/d0cp01240h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quasi-elastic neutron spectroscopy reveals that model drug molecules diffuse faster in a supramolecular gel than in solution.
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Affiliation(s)
- Robert M. Edkins
- WestCHEM Department of Pure and Applied Chemistry
- Thomas Graham Building
- University of Strathclyde
- Glasgow G1 1XL
- UK
| | - Markus Appel
- Institut Max von Laue – Paul Langevin (ILL)
- F-38042 Grenoble
- France
| | - Tilo Seydel
- Institut Max von Laue – Paul Langevin (ILL)
- F-38042 Grenoble
- France
| | - Katharina Edkins
- Division of Pharmacy and Optometry
- University of Manchester
- Manchester M13 9PT
- UK
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25
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Laulumaa S, Koza MM, Seydel T, Kursula P, Natali F. A Quasielastic Neutron Scattering Investigation on the Molecular Self-Dynamics of Human Myelin Protein P2. J Phys Chem B 2019; 123:8178-8185. [PMID: 31483648 DOI: 10.1021/acs.jpcb.9b05320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human myelin protein P2 is a membrane binding protein believed to maintain correct lipid composition and organization in peripheral nerve myelin. Its function is related to its ability to stack membranes, and this function can be enhanced by the P38G mutation, whereby the overall protein structure does not change but the molecular dynamics increase. Mutations in P2 are linked to human peripheral neuropathy. Here, the dynamics of wild-type P2 and the P38G variant were studied using quasielastic neutron scattering on time scales from 10 ps to 1 ns at 300 K. The results suggest that the mutant protein dynamics are increased on both the fastest and the slowest measured time scales, by increasing the dynamics amplitude and/or the portion of atoms participating in the movement.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,European Spallation Source , Lund , Sweden
| | | | | | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,Department of Biomedicine , University of Bergen , Bergen , Norway
| | - Francesca Natali
- Institut Laue-Langevin , Grenoble , France.,CNR-IOM, OGG , Grenoble , France
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26
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Al-Ayoubi SR, Schummel PH, Cisse A, Seydel T, Peters J, Winter R. Osmolytes modify protein dynamics and function of tetrameric lactate dehydrogenase upon pressurization. Phys Chem Chem Phys 2019; 21:12806-12817. [PMID: 31165827 DOI: 10.1039/c9cp02310k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present a study of the combined effects of natural cosolvents (TMAO, glycine, urea) and pressure on the activity of the tetrameric enzyme lactate dehydrogenase (LDH). To this end, high-pressure stopped-flow methodology in concert with fast UV/Vis spectroscopic detection of product formation was applied. To reveal possible pressure effects on the stability and dynamics of the enzyme, FTIR spectroscopic and neutron scattering measurements were carried out. In neat buffer solution, the catalytic turnover number of the enzyme, kcat, increases up to 1000 bar, the pressure range where dissociation of the tetrameric species to dimers sets in. Accordingly, we obtain a negative activation volume, ΔV# = -45.3 mL mol-1. Further, the enzyme substrate complex has a larger volume compared to the enzyme and substrate in the unbound state. The neutron scattering data show that changes in the fast internal dynamics of the enzyme are not responsible for the increase of kcat upon compression. Whereas the magnitude of kcat is similar in the presence of the osmolytes, the pressure of deactivation is modulated by the addition of cosolvents. TMAO and glycine increase the pressure of deactivation, and in accordance with the observed stabilizing effect both cosolvents exhibit against denaturation and/or dissociation of proteins. While urea does not markedly affect the magnitude of the Michaelis constant, KM, both 1 M TMAO and 1 M glycine exhibit smaller KM values of about 0.07 mM and 0.05 mM below about 1 kbar. Such positive effect on the substrate affinity could be rationalized by the effect the two cosolutes impose on the thermodynamic activities of the reactants, which reflect changes in water-mediated intermolecular interactions. Our data show that the intracellular milieu, i.e., the solution conditions that have evolved, may be sufficient to maintain enzymatic activity under extreme environmental conditions, including the whole pressure range encountered on Earth.
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Affiliation(s)
- Samy R Al-Ayoubi
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
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27
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Abstract
We report the self-diffusion in ethanol-water mixtures as a function of the water-ethanol ratio measured at different temperatures using quasi-elastic neutron spectroscopy (QENS). For our protiated samples, QENS is mainly sensitive to the dominant ensemble-averaged incoherent scattering from the hydrogen atoms of the liquid mixtures. The energy range and resolution render our experiment sensitive to the picosecond time scale and nanometer length scale. These observation scales complement different scales accessible by nuclear magnetic resonance techniques. Subsequent to testing different models, we find that a simple jump-diffusion model averaging over both types of molecules, water and ethanol, best fits our data.
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Affiliation(s)
- Tilo Seydel
- Institut Laue-Langevin, 71 Avenue des Martyrs, F-38042 Grenoble, France
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28
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Grimaldo M, Lopez H, Beck C, Roosen-Runge F, Moulin M, Devos JM, Laux V, Härtlein M, Da Vela S, Schweins R, Mariani A, Zhang F, Barrat JL, Oettel M, Forsyth VT, Seydel T, Schreiber F. Protein Short-Time Diffusion in a Naturally Crowded Environment. J Phys Chem Lett 2019; 10:1709-1715. [PMID: 30897330 DOI: 10.1021/acs.jpclett.9b00345] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The interior of living cells is a dense and polydisperse suspension of macromolecules. Such a complex system challenges an understanding in terms of colloidal suspensions. As a fundamental test we employ neutron spectroscopy to measure the diffusion of tracer proteins (immunoglobulins) in a cell-like environment (cell lysate) with explicit control over crowding conditions. In combination with Stokesian dynamics simulation, we address protein diffusion on nanosecond time scales where hydrodynamic interactions dominate over negligible protein collisions. We successfully link the experimental results on these complex, flexible molecules with coarse-grained simulations providing a consistent understanding by colloid theories. Both experiments and simulations show that tracers in polydisperse solutions close to the effective particle radius Reff = ⟨ Ri3⟩1/3 diffuse approximately as if the suspension was monodisperse. The simulations further show that macromolecules of sizes R > Reff ( R < Reff) are slowed more (less) effectively even at nanosecond time scales, which is highly relevant for a quantitative understanding of cellular processes.
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Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
- LiPhy , 38402 Saint Martin d'Hères , France
| | - Christian Beck
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Felix Roosen-Runge
- Division of Physical Chemistry , Lund University , Naturvetarvägen 14 , 22100 Lund , Sweden
| | - Martine Moulin
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Juliette M Devos
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Valerie Laux
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Michael Härtlein
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Stefano Da Vela
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Ralf Schweins
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Alessandro Mariani
- European Synchrotron Radiation Facility (ESRF) , CS 40220, F-38042 Grenoble Cedex 9, France
| | - Fajun Zhang
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | | | - Martin Oettel
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - V Trevor Forsyth
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Faculty of Natural Sciences & Institute for Science and Technology in Medicine , Keele University , Staffordshire ST5 5BG , United Kingdom
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Frank Schreiber
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
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29
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Golub M, Guillon V, Gotthard G, Zeller D, Martinez N, Seydel T, Koza MM, Lafaye C, Clavel D, von Stetten D, Royant A, Peters J. Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering. J R Soc Interface 2019; 16:20180848. [PMID: 30836899 DOI: 10.1098/rsif.2018.0848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyan fluorescent proteins (CFPs) are variants of green fluorescent proteins in which the central tyrosine of the chromophore has been replaced by a tryptophan. The increased bulk of the chromophore within a compact protein and the change in the positioning of atoms capable of hydrogen bonding have made it difficult to optimize their fluorescence properties, which took approximately 15 years between the availability of the first useable CFP, enhanced cyan fluorescent protein (ECFP), and that of a variant with almost perfect fluorescence efficiency, mTurquoise2. To understand the molecular bases of the progressive improvement in between these two CFPs, we have studied by incoherent neutron scattering the dynamics of five different variants exhibiting progressively increased fluorescence efficiency along the evolution pathway. Our results correlate well with the analysis of the previously determined X-ray crystallographic structures, which show an increase in flexibility between ECFP and the second variant, Cerulean, which is then hindered in the three later variants, SCFP3A (Super Cyan Fluorescent Protein 3A), mTurquoise and mTurquoise2. This confirms that increasing the rigidity of the direct environment of the fluorescent chromophore is not the sole parameter leading to brighter fluorescent proteins and that increased flexibility in some cases may be helpful.
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Affiliation(s)
- Maksym Golub
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Virginia Guillon
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Dominik Zeller
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
| | - Nicolas Martinez
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Tilo Seydel
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Michael M Koza
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Céline Lafaye
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Damien Clavel
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Antoine Royant
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France.,3 European Synchrotron Radiation Facility , 38043 Grenoble , France
| | - Judith Peters
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
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Bleibel J, Habiger M, Lütje M, Hirschmann F, Roosen-Runge F, Seydel T, Zhang F, Schreiber F, Oettel M. Two time scales for self and collective diffusion near the critical point in a simple patchy model for proteins with floating bonds. Soft Matter 2018; 14:8006-8016. [PMID: 30187060 DOI: 10.1039/c8sm00599k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Using dynamic Monte Carlo and Brownian dynamics, we investigate a floating bond model in which particles can bind through mobile bonds. The maximum number of bonds (here fixed to 4) can be tuned by appropriately choosing the repulsive, nonadditive interactions among bonds and particles. We compute the static and dynamic structure factor (intermediate scattering function) in the vicinity of the gas-liquid critical point. The static structure exhibits a weak tetrahedral network character. The intermediate scattering function shows a temporal decay deviating from a single exponential, which can be described by a double exponential decay where the two time scales differ approximately by one order of magnitude. This time scale separation is robust over a range of wave numbers. The analysis of clusters in real space indicates the formation of noncompact clusters and shows a considerable stretch in the instantaneous size distribution when approaching the critical point. The average time evolution of the largest subcluster of given initial clusters with 10 or more particles also shows a double exponential decay. The observation of two time scales in the intermediate scattering function at low packing fractions is consistent with similar findings in globular protein solutions with trivalent metal ions that act as bonds between proteins.
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Affiliation(s)
- J Bleibel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.
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31
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Beck C, Grimaldo M, Roosen-Runge F, Braun MK, Zhang F, Schreiber F, Seydel T. Nanosecond Tracer Diffusion as a Probe of the Solution Structure and Molecular Mobility of Protein Assemblies: The Case of Ovalbumin. J Phys Chem B 2018; 122:8343-8350. [PMID: 30106587 DOI: 10.1021/acs.jpcb.8b04349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein diffusion is not only an important process ensuring biological function but can also be used as a probe to obtain information on structural properties of protein assemblies in liquid solutions. Here, we explore the oligomerization state of ovalbumin at high protein concentrations by means of its short-time self-diffusion. We employ high-resolution incoherent quasielastic neutron scattering to access the self-diffusion on nanosecond timescales, on which interparticle contacts are not altered. Our results indicate that ovalbumin in aqueous (D2O) solutions occurs in increasingly large assemblies of its monomeric subunits with rising protein concentration. It changes from nearly monomeric toward dimeric and ultimately larger than tetrameric complexes. Simultaneously, we access information on the internal molecular mobility of ovalbumin on the nanometer length scale and compare it with results obtained for bovine serum albumin, immunoglobulin, and β-lactoglobulin.
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Affiliation(s)
- Christian Beck
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France.,Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Marco Grimaldo
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France
| | - Felix Roosen-Runge
- Division of Physical Chemistry, Department of Chemistry , Lund University , Naturvetarvägen 16 , SE-22100 Lund , Sweden
| | - Michal K Braun
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Fajun Zhang
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Frank Schreiber
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Tilo Seydel
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France
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32
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Berg MC, Benetti AR, Telling MTF, Seydel T, Yu D, Daemen LL, Bordallo HN. Nanoscale Mobility of Aqueous Polyacrylic Acid in Dental Restorative Cements. ACS Appl Mater Interfaces 2018; 10:9904-9915. [PMID: 29504390 DOI: 10.1021/acsami.7b15735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hydrogen dynamics in a time range from hundreds of femtoseconds to nanoseconds can be directly analyzed using neutron spectroscopy, where information on the inelastic and quasi-elastic scattering, hereafter INS and QENS, can be obtained. In this study, we applied these techniques to understand how the nanoscale mobility of the aqueous solution of polyacrylic acid (PAA) used in conventional glass ionomer cements (GICs) changes under confinement. Combining the spectroscopic analysis with calorimetric results, we were able to separate distinct motions within both the liquid and the GICs. The QENS analysis revealed that the self-diffusion translational motion identified in the liquid is also visible in the GIC. However, as a result of the formation of the cement matrix and its setting, both translational diffusion and residence time differed from the PAA solution. When comparing the local diffusion obtained for the selected GIC, the only noticeable difference was observed for the slow dynamics associated with the polymer chain. Additionally, over short-term aging, progressive water binding to the polymer chain occurred in one of the investigated GICs. Finally, a considerable change in the density of the GIC without progressive water binding indicates an increased polymer cross-linking. Taken together, our results suggest that accurate and deep understanding of polymer-water binding, polymer cross-linking, as well as material density changes occurring during the maturation process of GIC are necessary for the development of advanced dental restorative materials.
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Affiliation(s)
- Marcella C Berg
- The Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
- European Spallation Source ESS ERIC , P.O. Box 176 , SE-221 00 Lund , Sweden
| | - Ana R Benetti
- Department of Odontology, Faculty of Health and Medical Sciences , University of Copenhagen , DK-2200 Copenhagen , Denmark
| | - Mark T F Telling
- ISIS Facility , Rutherford Appleton Laboratory , Chilton, Oxford OX11 0QX , U.K
- Department of Materials , University of Oxford , Parks Road , Oxford OX1 3PH , U.K
| | - Tilo Seydel
- Institut Max von Laue-Paul Langevin , CS 20156 , F-38042 Grenoble , France
| | - Dehong Yu
- Australian Nuclear Science and Technology Organisation , New Illawarra Road , Lucas Heights , New South Wales 2234 , Australia
| | - Luke L Daemen
- Oak Ridge National Laboratory , P.O. Box 2008 , Oak Ridge , Tennessee 37831 , United States
| | - Heloisa N Bordallo
- The Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
- European Spallation Source ESS ERIC , P.O. Box 176 , SE-221 00 Lund , Sweden
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Seydel T, Edkins RM, Jones CD, Foster JA, Bewley R, Aguilar JA, Edkins K. Increased rate of solvent diffusion in a prototypical supramolecular gel measured on the picosecond timescale. Chem Commun (Camb) 2018; 54:6340-6343. [DOI: 10.1039/c8cc02962h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvent diffusion in a prototypical supramolecular gel probed by quasi-elastic neutron scattering on the picosecond timescale is faster than that in the respective bulk solvent.
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Affiliation(s)
- Tilo Seydel
- Institut Laue-Langevin
- Boulevard des Martyrs
- France
| | - Robert M. Edkins
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
- Department of Pure and Applied Chemistry
| | | | | | - Robert Bewley
- ISIS Neutron Facility
- Rutherford Appleton Laboratory
- Didcot
- UK
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34
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Braun MK, Grimaldo M, Roosen-Runge F, Hoffmann I, Czakkel O, Sztucki M, Zhang F, Schreiber F, Seydel T. Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion. J Phys Chem Lett 2017; 8:2590-2596. [PMID: 28525282 DOI: 10.1021/acs.jpclett.7b00658] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigate the concentration-controlled formation of clusters in β-lactoglobulin (BLG) protein solutions combining structural and dynamical scattering techniques. The static structure factor from small-angle X-ray scattering as well as de-Gennes narrowing in the nanosecond diffusion function D(q) from neutron spin echo spectroscopy support a picture of cluster formation. Using neutron backscattering spectroscopy, a monotonous increase of the average hydrodynamic cluster radius is monitored over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers. The results suggest that BLG forms compact clusters that are static on the observation time scale of several nanoseconds. The presented analysis provides a general framework to access the structure and dynamics of macromolecular assemblies in solution.
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Affiliation(s)
- Michal K Braun
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Marco Grimaldo
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Felix Roosen-Runge
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
- Division of Physical Chemistry, Department of Chemistry, Lund University , Naturvetarvägen 14, 221 00 Lund, Sweden
| | - Ingo Hoffmann
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Orsolya Czakkel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Sztucki
- ESRF - The European Synchrotron , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
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35
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Da Vela S, Roosen-Runge F, Skoda MWA, Jacobs RMJ, Seydel T, Frielinghaus H, Sztucki M, Schweins R, Zhang F, Schreiber F. Effective Interactions and Colloidal Stability of Bovine γ-Globulin in Solution. J Phys Chem B 2017; 121:5759-5769. [DOI: 10.1021/acs.jpcb.7b03510] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Stefano Da Vela
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
| | - Felix Roosen-Runge
- Institut Max von Laue − Paul Langevin (ILL), CS 20156, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38042, France
| | - Maximilian W. A. Skoda
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
| | - Robert M. J. Jacobs
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tilo Seydel
- Institut Max von Laue − Paul Langevin (ILL), CS 20156, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38042, France
| | - Henrich Frielinghaus
- Jülich
Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum (JCNS at
MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, Garching D-85747, Germany
| | - Michael Sztucki
- European Synchrotron Radiation Facility (ESRF), CS 40220, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38043, France
| | - Ralf Schweins
- Institut Max von Laue − Paul Langevin (ILL), CS 20156, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38042, France
| | - Fajun Zhang
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
| | - Frank Schreiber
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
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Misuraca L, Natali F, da Silva L, Peters J, Demé B, Ollivier J, Seydel T, Laux-Lesourd V, Haertlein M, Zaccai G, Deamer D, Maurel MC. Mobility of a Mononucleotide within a Lipid Matrix: A Neutron Scattering Study. Life (Basel) 2017; 7:life7010002. [PMID: 28054992 PMCID: PMC5370402 DOI: 10.3390/life7010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022] Open
Abstract
An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction allowing the formation of RNA-like polymers, followed by encapsulation in lipid membranes. Here, we used neutron scattering and deuterium labelling to investigate 5′-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix. The aim of the research was to determine and compare how mononucleotides are captured and differently organized within matrices and multilamellar phospholipid structures and to explore the role of water in organizing the system to determine at which level the system becomes sufficiently anhydrous to lock the AMP molecules into an organized structure and initiate ester bond synthesis. Elastic incoherent neutron scattering experiments were thus employed to investigate the changes of the dynamic properties of AMP induced by embedding the molecules within the lipid matrix. The influence of AMP addition to the lipid membrane organization was determined through diffraction measurement, which also helped us to define the best working Q range for dynamical data analysis with respect to specific hydration. The use of different complementary instruments allowed coverage of a wide time-scale domain, from ns to ps, of atomic mean square fluctuations, providing evidence of a well-defined dependence of the AMP dynamics on the hydration level.
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Affiliation(s)
- Loreto Misuraca
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Francesca Natali
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali (CNR-IOM), Research Unit in Grenoble, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - Laura da Silva
- Institut de Systematique, Évolution, Biodiversité, (ISYEB) UMR 7205 CNRS-MNHN-UPMC-EPHE Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - Judith Peters
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Université Grenoble Alpes (UGA), UFR PhITEM, 621 Avenue Centrale, 38000 Grenoble, France.
| | - Bruno Demé
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | - Jacques Ollivier
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | - Tilo Seydel
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | | | - Michael Haertlein
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | - Giuseppe Zaccai
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38000 Grenoble, France.
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 17 Avenue des Martyrs, 38054 Grenoble, France.
- Centre National de la Recherche Scientifique (CNRS), 25 Avenue des Martyrs, 38000 Grenoble, France.
| | - David Deamer
- University of California, Santa Cruz, CA 95060, USA.
| | - Marie Christine Maurel
- Institut de Systematique, Évolution, Biodiversité, (ISYEB) UMR 7205 CNRS-MNHN-UPMC-EPHE Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
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Krasnov I, Seydel T, Greving I, Blankenburg M, Vollrath F, Müller M. Strain-dependent fractional molecular diffusion in humid spider silk fibres. J R Soc Interface 2016; 13:20160506. [PMID: 27628174 PMCID: PMC5046950 DOI: 10.1098/rsif.2016.0506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/22/2016] [Indexed: 11/12/2022] Open
Abstract
Spider silk is a material well known for its outstanding mechanical properties, combining elasticity and tensile strength. The molecular mobility within the silk's polymer structure on the nanometre length scale importantly contributes to these macroscopic properties. We have therefore investigated the ensemble-averaged single-particle self-dynamics of the prevailing hydrogen atoms in humid spider dragline silk fibres on picosecond time scales in situ as a function of an externally applied tensile strain. We find that the molecular diffusion in the amorphous fraction of the oriented fibres can be described by a generalized fractional diffusion coefficient Kα that is independent of the observation length scale in the probed range from approximately 0.3-3.5 nm. Kα increases towards a diffusion coefficient of the classical Fickian type with increasing tensile strain consistent with an increasing loss of memory or entropy in the polymer matrix.
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Affiliation(s)
- Igor Krasnov
- Institut für Experimentelle und Angewandte Physik, Universität Kiel, 24098 Kiel, Germany Institute of Materials Research, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany
| | - Tilo Seydel
- Institut Max von Laue-Paul Langevin (ILL), CS 20156, 38042 Grenoble, France
| | - Imke Greving
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany
| | - Malte Blankenburg
- Institut für Experimentelle und Angewandte Physik, Universität Kiel, 24098 Kiel, Germany Institute of Materials Research, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany
| | - Fritz Vollrath
- Department of Zoology, University of Oxford, Oxford OX13PS, UK
| | - Martin Müller
- Institut für Experimentelle und Angewandte Physik, Universität Kiel, 24098 Kiel, Germany Institute of Materials Research, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany
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Mitra S, Sharma VK, Garcia-Sakai V, Orecchini A, Seydel T, Johnson M, Mukhopadhyay R. Enhancement of Lateral Diffusion in Catanionic Vesicles during Multilamellar-to-Unilamellar Transition. J Phys Chem B 2016; 120:3777-84. [PMID: 27029782 DOI: 10.1021/acs.jpcb.6b02997] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Catanionic vesicles are formed spontaneously by mixing cationic and anionic dispersions in aqueous solution in suitable conditions. Because of spontaneity in formation, long-term stability, and easy modulation of size and charge, they have numerous advantages over conventional lipid-based vesicles. The dynamics of such vesicles is of interest in the field of biomedicine, as they can be used to deliver drug molecules into the cell membrane. Dynamics of catanionic vesicles based on sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB) have been studied using incoherent elastic and quasielastic neutron scattering (QENS) techniques. Neutron scattering experiments have been carried out on two backscattering spectrometers, IRIS and IN16B, which have different energy resolutions and energy transfer windows. An elastic fixed-window scan carried out using IN16B shows a phase transition at ∼307 K during the heating cycle, whereas on cooling the transition occurred at ∼294 K. DSC results are found to be in close agreement with the elastic scan data. This transition is ascribed to a structural rearrangement from a multilamellar to a unilamellar phase [ Andreozzi J. Phys. Chem. B 2010 , 114 , 8056 - 8060 ]. It is found that a model in which the surfactant molecules undergo both lateral and internal motions can describe the QENS data quite well. While the data from IRIS have contributions from both dynamical processes, the data from IN16B probe only lateral motions, as the internal motions are too fast for the energy window of the spectrometer. It is found that, through the transition, the fraction of surfactant molecules undergoing lateral motion increases of a factor of 2 from the multilamellar to the unilamellar phase, indicating an enhanced fluidity of the latter. The lateral motion is found to be Fickian in nature, while the internal motion has been described by a localized translational diffusion model. The results reported here could have direct interest for a number of applications, such as molecular transport, and the effect of specific drug molecules or hormones through the membrane.
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Affiliation(s)
- S Mitra
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai, 40085, India
| | - V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai, 40085, India
| | - V Garcia-Sakai
- Rutherford Appleton Laboratory, Science and Technology Facilities Council , Didcot OX11 0QX, U.K
| | - A Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia , Via Pascoli, I-06123 Perugia, Italy
| | - T Seydel
- Institut Laue-Langevin , BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - M Johnson
- Institut Laue-Langevin , BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai, 40085, India
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Barrett MA, Trapp M, Lohstroh W, Seydel T, Ollivier J, Ballauff M, Dencher NA, Hauß T. Alzheimer's peptide amyloid-β, fragment 22-40, perturbs lipid dynamics. Soft Matter 2016; 12:1444-51. [PMID: 26646730 DOI: 10.1039/c5sm02026c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The peptide amyloid-β (Aβ) interacts with membranes of cells in the human brain and is associated with Alzheimer's disease (AD). The intercalation of Aβ in membranes alters membrane properties, including the structure and lipid dynamics. Any change in the membrane lipid dynamics will affect essential membrane processes, such as energy conversion, signal transduction and amyloid precursor protein (APP) processing, and may result in the observed neurotoxicity associated with the disease. The influence of this peptide on membrane dynamics was studied with quasi-elastic neutron scattering, a technique which allows a wide range of observation times from picoseconds to nanoseconds, over nanometer length scales. The effect of the membrane integral neurotoxic peptide amyloid-β, residues 22-40, on the in- and out-of-plane lipid dynamics was observed in an oriented DMPC/DMPS bilayer at 15 °C, in its gel phase, and at 30 °C, near the phase transition temperature of the lipids. Near the phase-transition temperature, a 1.5 mol% of peptide causes up to a twofold decrease in the lipid diffusion coefficients. In the gel-phase, this effect is reversed, with amyloid-β(22-40) increasing the lipid diffusion coefficients. The observed changes in lipid diffusion are relevant to protein-protein interactions, which are strongly influenced by the diffusion of membrane components. The effect of the amyloid-β peptide fragment on the diffusion of membrane lipids will provide insight into the membrane's role in AD.
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Affiliation(s)
- Matthew A Barrett
- Helmholtz-Zentrum Berlin für Materialien und Energie, Lise-Meitner-Campus, Berlin, Germany.
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Foglia F, Hazael R, Simeoni GG, Appavou MS, Moulin M, Haertlein M, Trevor Forsyth V, Seydel T, Daniel I, Meersman F, McMillan PF. Water Dynamics in Shewanella oneidensis at Ambient and High Pressure using Quasi-Elastic Neutron Scattering. Sci Rep 2016; 6:18862. [PMID: 26738409 PMCID: PMC4703977 DOI: 10.1038/srep18862] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/27/2015] [Indexed: 01/22/2023] Open
Abstract
Quasielastic neutron scattering (QENS) is an ideal technique for studying water transport and relaxation dynamics at pico- to nanosecond timescales and at length scales relevant to cellular dimensions. Studies of high pressure dynamic effects in live organisms are needed to understand Earth's deep biosphere and biotechnology applications. Here we applied QENS to study water transport in Shewanella oneidensis at ambient (0.1 MPa) and high (200 MPa) pressure using H/D isotopic contrast experiments for normal and perdeuterated bacteria and buffer solutions to distinguish intracellular and transmembrane processes. The results indicate that intracellular water dynamics are comparable with bulk diffusion rates in aqueous fluids at ambient conditions but a significant reduction occurs in high pressure mobility. We interpret this as due to enhanced interactions with macromolecules in the nanoconfined environment. Overall diffusion rates across the cell envelope also occur at similar rates but unexpected narrowing of the QENS signal appears between momentum transfer values Q = 0.7-1.1 Å(-1) corresponding to real space dimensions of 6-9 Å. The relaxation time increase can be explained by correlated dynamics of molecules passing through Aquaporin water transport complexes located within the inner or outer membrane structures.
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Affiliation(s)
- Fabrizia Foglia
- Chemistry Department, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London WC1H 0AJ, UK
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Rachael Hazael
- Chemistry Department, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Giovanna G. Simeoni
- Heinz Maier-Leibnitz Zentrum (MLZ) and Physics Department, Technisches Universität München, Lichtenbergstrasse 1, D-85748 Garching, Germany
| | - Marie-Sousai Appavou
- Jülich Center for Neutron Sciences at MLZ, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, D-85748 Garching, Germany
| | - Martine Moulin
- Life Sciences Group, Carl-Ivar Brändén Building, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble cedex 9, France
| | - Michael Haertlein
- Life Sciences Group, Carl-Ivar Brändén Building, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble cedex 9, France
| | - V. Trevor Forsyth
- Life Sciences Group, Carl-Ivar Brändén Building, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble cedex 9, France
- Faculty of Natural Sciences/ISTM, Keele University, Staffordshire ST5 5BG, UK
| | - Tilo Seydel
- Science Division, Institut Laue-Langevin, CS 20156, 71 avenue des Martyrs, 38042 Grenoble cedex 9, France
| | - Isabelle Daniel
- Laboratoire de Géologie de Lyon, UMR 5276, Université Lyon 1-ENS de Lyon-CNRS, 2 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Filip Meersman
- Chemistry Department, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London WC1H 0AJ, UK
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Paul F. McMillan
- Chemistry Department, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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41
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Grimaldo M, Roosen-Runge F, Hennig M, Zanini F, Zhang F, Jalarvo N, Zamponi M, Schreiber F, Seydel T. Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation. Phys Chem Chem Phys 2016; 17:4645-55. [PMID: 25587698 DOI: 10.1039/c4cp04944f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of proteins in solution is a complex and hierarchical process, affected by the aqueous environment as well as temperature. We present a comprehensive study on nanosecond time and nanometer length scales below, at, and above the denaturation temperature Td. Our experimental data evidence dynamical processes in protein solutions on three distinct time scales. We suggest a consistent physical picture of hierarchical protein dynamics: (i) self-diffusion of the entire protein molecule is confirmed to agree with colloid theory for all temperatures where the protein is in its native conformational state. At higher temperatures T > Td, the self-diffusion is strongly obstructed by cross-linking or entanglement. (ii) The amplitude of backbone fluctuations grows with increasing T, and a transition in its dynamics is observed above Td. (iii) The number of mobile side-chains increases sharply at Td while their average dynamics exhibits only little variations. The combination of quasi-elastic neutron scattering and the presented analytical framework provides a detailed microscopic picture of the protein molecular dynamics in solution, thereby reflecting the changes of macroscopic properties such as cluster formation and gelation.
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Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue - Paul Langevin (ILL), CS 20156, F-38042 Grenoble, France.
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42
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Stadler AM, Demmel F, Ollivier J, Seydel T. Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding. Phys Chem Chem Phys 2016; 18:21527-38. [DOI: 10.1039/c6cp04146a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions.
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Affiliation(s)
- Andreas M. Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS
- Forschungszentrum Jülich GmbH
- 52425 Jülich
- Germany
| | | | | | - Tilo Seydel
- Institut Laue-Langevin
- 38042 Grenoble Cedex 9
- France
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43
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Toppozini L, Roosen-Runge F, Bewley RI, Dalgliesh RM, Perring T, Seydel T, Glyde HR, García Sakai V, Rheinstädter MC. Anomalous and anisotropic nanoscale diffusion of hydration water molecules in fluid lipid membranes. Soft Matter 2015; 11:8354-8371. [PMID: 26338138 DOI: 10.1039/c5sm01713k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We have studied nanoscale diffusion of membrane hydration water in fluid-phase lipid bilayers made of 1,2-dimyristoyl-3-phosphocholine (DMPC) using incoherent quasi-elastic neutron scattering. Dynamics were fit directly in the energy domain using the Fourier transform of a stretched exponential. By using large, 2-dimensional detectors, lateral motions of water molecules and motions perpendicular to the membranes could be studied simultaneously, resulting in 2-dimensional maps of relaxation time, τ, and stretching exponent, β. We present experimental evidence for anomalous (sub-diffusive) and anisotropic diffusion of membrane hydration water molecules over nanometer distances. By combining molecular dynamics and Brownian dynamics simulations, the potential microscopic origins for the anomaly and anisotropy of hydration water were investigated. Bulk water was found to show intrinsic sub-diffusive motion at time scales of several picoseconds, likely related to caging effects. In membrane hydration water, however, the anisotropy of confinement and local dynamical environments leads to an anisotropy of relaxation times and stretched exponents, indicative of anomalous dynamics.
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Affiliation(s)
- Laura Toppozini
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
| | | | | | | | - Toby Perring
- ISIS, Rutherford Appleton Laboratory, Didcot, UK
| | | | - Henry R Glyde
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | | | - Maikel C Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
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44
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Lenton S, Seydel T, Nylander T, Holt C, Härtlein M, Teixeira S, Zaccai G. Dynamic footprint of sequestration in the molecular fluctuations of osteopontin. J R Soc Interface 2015; 12:0506. [PMID: 26354827 PMCID: PMC4614460 DOI: 10.1098/rsif.2015.0506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/19/2015] [Indexed: 11/12/2022] Open
Abstract
The sequestration of calcium phosphate by unfolded proteins is fundamental to the stabilization of biofluids supersaturated with respect to hydroxyapatite, such as milk, blood or urine. The unfolded state of osteopontin (OPN) is thought to be a prerequisite for this activity, which leads to the formation of core-shell calcium phosphate nanoclusters. We report on the structures and dynamics of a native OPN peptide from bovine milk, studied by neutron spectroscopy and small-angle X-ray and neutron scattering. The effects of sequestration are quantified on the nanosecond- ångström resolution by elastic incoherent neutron scattering. The molecular fluctuations of the free phosphopeptide are in agreement with a highly flexible protein. An increased resilience to diffusive motions of OPN is corroborated by molecular fluctuations similar to those observed for globular proteins, yet retaining conformational flexibilities. The results bring insight into the modulation of the activity of OPN and phosphopeptides with a role in the control of biomineralization. The quantification of such effects provides an important handle for the future design of new peptides based on the dynamics-activity relationship.
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Affiliation(s)
- S Lenton
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble cedex 9, France Environment, Physical Sciences and Applied Mathematics Research Institute, Keele University, Staffordshire ST5 5BG, UK
| | - T Seydel
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble cedex 9, France
| | - T Nylander
- Division of Physical Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - C Holt
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - M Härtlein
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble cedex 9, France
| | - S Teixeira
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble cedex 9, France Environment, Physical Sciences and Applied Mathematics Research Institute, Keele University, Staffordshire ST5 5BG, UK
| | - G Zaccai
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble cedex 9, France C.N.R.S., Institut de Biologie Structurale, F-38044 Grenoble, France
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45
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Burankova T, Hempelmann R, Fossog V, Ollivier J, Seydel T, Embs JP. Proton Diffusivity in the Protic Ionic Liquid Triethylammonium Triflate Probed by Quasielastic Neutron Scattering. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04000] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatsiana Burankova
- Department
of Physical Chemistry, Saarland University, Saarbrücken, 66123, Germany
- Laboratory
for Neutron Scattering and Imaging, Paul Scherrer Institute, Villigen
PSI, Villigen 5232, Switzerland
| | - Rolf Hempelmann
- Department
of Physical Chemistry, Saarland University, Saarbrücken, 66123, Germany
| | - Verlaine Fossog
- Department
of Physical Chemistry, Saarland University, Saarbrücken, 66123, Germany
| | | | - Tilo Seydel
- Institut Laue-Langevin, Grenoble, 38000, France
| | - Jan P. Embs
- Laboratory
for Neutron Scattering and Imaging, Paul Scherrer Institute, Villigen
PSI, Villigen 5232, Switzerland
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46
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Grimaldo M, Roosen-Runge F, Hennig M, Zanini F, Zhang F, Zamponi M, Jalarvo N, Schreiber F, Seydel T. Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution. J Phys Chem Lett 2015; 6:2577-2582. [PMID: 26266736 DOI: 10.1021/acs.jpclett.5b01073] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs = 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchy particles. The finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.
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Affiliation(s)
- Marco Grimaldo
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Felix Roosen-Runge
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
| | - Marcus Hennig
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Fabio Zanini
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Fajun Zhang
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Michaela Zamponi
- §Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- ∥JCNS Outstation at the MLZ, Lichtenbergstraße 1, D-85747 Garching, Germany
| | - Niina Jalarvo
- §Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- ⊥Chemical and Engineering Materials Division, Neutron Sciences Directorate, and JCNS Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Frank Schreiber
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Tilo Seydel
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
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47
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Krasnov I, Seydel T, Müller M. Fractional dynamics in silk: From molecular picosecond subdiffusion to macroscopic long-time relaxation. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:042716. [PMID: 25974536 DOI: 10.1103/physreve.91.042716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 06/04/2023]
Abstract
Structural relaxations in humid silk fibers exposed to tensile stress have been reported to take place on a very wide range of time scales from a few milliseconds to several hours. The time-dependence of the measured tensile force following a quasi-instantaneously applied external strain on the fibers can be understood in terms of a fractional viscoelastic relaxation function introducing memory effects by which the mechanical state of a fiber depends on its tensile history. An analog fractional relaxation also gives rise to the subdiffusion observed on picosecond time scales, which governs the mobility of the amorphous polymer chains and adsorbed water on the molecular level. The reduction of the subdiffusive memory effect in stretched fibers compared to native fibers is consistent with the higher order of the polymers in the stretched state.
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Affiliation(s)
- Igor Krasnov
- Institut für Experimentelle und Angewandte Physik, Universität Kiel, D-24098 Kiel, Germany
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht (HZG), D-21502 Geesthacht, Germany
| | - Tilo Seydel
- Institut Max von Laue-Paul Langevin (ILL), CS 20156, F-38042 Grenoble, France
| | - Martin Müller
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht (HZG), D-21502 Geesthacht, Germany
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48
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Grimaldo M, Roosen-Runge F, Jalarvo N, Zamponi M, Zanini F, Hennig M, Zhang F, Schreiber F, Seydel T. High-resolution neutron spectroscopy on protein solution samples. EPJ Web of Conferences 2015. [DOI: 10.1051/epjconf/20158302005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Juranyi F, Månsson M, Gavilano JL, Mena M, Pomjakushina E, Medarde M, Sugiyama J, Kamazawa K, Batlogg B, Ott HR, Seydel T. Dynamics across the structural transitions at elevated temperatures in Na0.7CoO2. EPJ Web of Conferences 2015. [DOI: 10.1051/epjconf/20158302008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Roosen-Runge F, Seydel T. A generalized mean-squared displacement from inelastic fixed window scans of incoherent neutron scattering as a model-free indicator of anomalous diffusion confinement. EPJ Web of Conferences 2015. [DOI: 10.1051/epjconf/20158302015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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