1
|
Beck C, Grimaldo M, Lopez H, Da Vela S, Sohmen B, Zhang F, Oettel M, Barrat JL, Roosen-Runge F, Schreiber F, Seydel T. Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture. J Phys Chem B 2022; 126:7400-7408. [PMID: 36112146 PMCID: PMC9527755 DOI: 10.1021/acs.jpcb.2c02380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The crowded environment of biological systems such as
the interior
of living cells is occupied by macromolecules with a broad size distribution.
This situation of polydispersity might influence the dependence of
the diffusive dynamics of a given tracer macromolecule in a monodisperse
solution on its hydrodynamic size and on the volume fraction. The
resulting size dependence of diffusive transport crucially influences
the function of a living cell. Here, we investigate a simplified model
system consisting of two constituents in aqueous solution, namely,
of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin
(Ig), systematically depending on the total volume fraction and ratio
of these constituents. From high-resolution quasi-elastic neutron
spectroscopy, the separate apparent short-time diffusion coefficients
for BSA and Ig in the mixture are extracted, which show substantial
deviations from the diffusion coefficients measured in monodisperse
solutions at the same total volume fraction. These deviations can
be modeled quantitatively using results from the short-time rotational
and translational diffusion in a two-component hard sphere system
with two distinct, effective hydrodynamic radii. Thus, we find that
a simple colloid picture well describes short-time diffusion in binary
mixtures as a function of the mixing ratio and the total volume fraction.
Notably, the self-diffusion of the smaller protein BSA in the mixture
is faster than the diffusion in a pure BSA solution, whereas the self-diffusion
of Ig in the mixture is slower than in the pure Ig solution.
Collapse
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
| |
Collapse
|
2
|
Exploring the Limits of Biological Complexity Amenable to Studies by Incoherent Neutron Spectroscopy. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081219. [PMID: 36013398 PMCID: PMC9410259 DOI: 10.3390/life12081219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms.
Collapse
|
3
|
Sharma VK, Mamontov E. Multiscale lipid membrane dynamics as revealed by neutron spectroscopy. Prog Lipid Res 2022; 87:101179. [PMID: 35780913 DOI: 10.1016/j.plipres.2022.101179] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 12/22/2022]
Abstract
The plasma membrane is one of the principal structural components of the cell and, therefore, one of the key components of the cellular life. Because the membrane's dynamics links the membrane's structure and function, the complexity and the broad range of the membrane's motions are essential for the enormously diverse functionality of the cell membrane. Even for the main membrane component, the lipid bilayer, considered alone, the range and complexity of the lipid motions are remarkable. Spanning the time scale from sub-picosecond to minutes and hours, the lipid motion in a bilayer is challenging to study even when a broad array of dynamic measurement techniques is employed. Neutron scattering plays a special role among such dynamic measurement techniques, particularly, because it involves the energy transfers commensurate with the typical intra- and inter- molecular dynamics and the momentum transfers commensurate with intra- and inter-molecular distances. Thus, using neutron scattering-based techniques, the spatial and temporal information on the lipid motion can be obtained and analysed simultaneously. Protium vs. deuterium sensitivity and non-destructive character of the neutron probe add to the remarkable prowess of neutron scattering for elucidating the lipid dynamics. Herein we present an overview of the neutron scattering-based studies of lipid dynamics in model membranes, with a discussion of the direct relevance and implications to the real-life cell membranes. The latter are much more complex systems than simple model membranes, consisting of heterogeneous non-stationary domains composed of lipids, proteins, and other small molecules, such as carbohydrates. Yet many fundamental aspects of the membrane behavior and membrane interactions with other molecules can be understood from neutron scattering measurements of the model membranes. For example, such studies can provide a great deal of information on the interactions of antimicrobial compounds with the lipid matrix of a pathogen membrane, or the interactions of drug molecules with the plasma membrane. Finally, we briefly discuss the recently emerging field of neutron scattering membrane studies with a reach far beyond the model membrane systems.
Collapse
Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Mumbai 400094, India.
| | - E Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
4
|
Sala G, Mourigal M, Boone C, Butch NP, Christianson AD, Delaire O, DeSantis AJ, Hart CL, Hermann RP, Huegle T, Kent DN, Lin JYY, Lumsden MD, Manley ME, Quirinale DG, Stone MB, Z Y. CHESS: The future direct geometry spectrometer at the second target station. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:065109. [PMID: 35778024 DOI: 10.1063/5.0089740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
CHESS, chopper spectrometer examining small samples, is a planned direct geometry neutron chopper spectrometer designed to detect and analyze weak signals intrinsic to small cross sections (e.g., small mass, small magnetic moments, or neutron absorbing materials) in powders, liquids, and crystals. CHESS is optimized to enable transformative investigations of quantum materials, spin liquids, thermoelectrics, battery materials, and liquids. The broad dynamic range of the instrument is also well suited to study relaxation processes and excitations in soft and biological matter. The 15 Hz repetition rate of the Second Target Station at the Spallation Neutron Source enables the use of multiple incident energies within a single source pulse, greatly expanding the information gained in a single measurement. Furthermore, the high flux grants an enhanced capability for polarization analysis. This enables the separation of nuclear from magnetic scattering or coherent from incoherent scattering in hydrogenous materials over a large range of energy and momentum transfer. This paper presents optimizations and technical solutions to address the key requirements envisioned in the science case and the anticipated uses of this instrument.
Collapse
Affiliation(s)
- G Sala
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Mourigal
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - C Boone
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - N P Butch
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - A D Christianson
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - O Delaire
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - A J DeSantis
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - C L Hart
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R P Hermann
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - T Huegle
- Neutron Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D N Kent
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J Y Y Lin
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M D Lumsden
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M E Manley
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D G Quirinale
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M B Stone
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Y Z
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
5
|
Abstract
Proteins have dynamic structures that undergo chain motions on time scales spanning from picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential for gaining accurate insight into fundamental mechanistic aspects of the protein folding reaction. The use of high-resolution structural probes, sensitive to population distributions, has begun to enable the resolution of site-specific conformational heterogeneity at different stages of the folding reaction. Different states populated during protein folding, including the unfolded state, collapsed intermediate states, and even the native state, are found to possess significant conformational heterogeneity. Heterogeneity in protein folding and unfolding reactions originates from the reduced cooperativity of various kinds of physicochemical interactions between various structural elements of a protein, and between a protein and solvent. Heterogeneity may arise because of functional or evolutionary constraints. Conformational substates within the unfolded state and the collapsed intermediates that exchange at rates slower than the subsequent folding steps give rise to heterogeneity on the protein folding pathways. Multiple folding pathways are likely to represent distinct sequences of structure formation. Insight into the nature of the energy barriers separating different conformational states populated during (un)folding can also be obtained by resolving heterogeneity.
Collapse
Affiliation(s)
- Sandhya Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
| |
Collapse
|
6
|
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] [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.
Collapse
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
| |
Collapse
|
7
|
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 OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202227201004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
Collapse
|
8
|
Benedetto A, Kearley GJ. Experimental demonstration of the novel "van-Hove integral method (vHI)" for measuring diffusive dynamics by elastic neutron scattering. Sci Rep 2021; 11:14093. [PMID: 34238981 PMCID: PMC8266890 DOI: 10.1038/s41598-021-93463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
Quasi-elastic neutron scattering (QENS)-based on the seminal work of Nobel Laureate Brockhouse-has been one of the major methods for studying pico-second to nano-second diffusive dynamics over the past 70 years. This is regarded as an "inelastic" method for dynamics. In contrast, we recently proposed a new neutron-scattering method for dynamics, which uses the elastic line of the scattering to access system dynamics directly in the time domain (Benedetto and Kearley in Sci Rep 9:11284, 2019). This new method has been denoted "vHI" that stands for "van Hove Integral". The reason is that, under certain conditions, the measured elastic intensity corresponds to the running-time integral of the intermediate scattering function, [Formula: see text], up to a time that is inversely proportional to the energy band-width incident on the sample. As a result, [Formula: see text] is accessed from the time derivative of the measured vHI profile. vHI has been supported by numerical and Monte-Carlo simulations, but has been difficult to validate experimentally due to the lack of a suitable instrument. Here we show that vHI works in practice, which we achieved by using a simple modification to the standard QENS backscattering spectrometer methodology. Basically, we varied the neutron-energy band-widths incident at the sample via a step-wise variation of the frequency of the monochromator Doppler-drive. This provides a measurement of the vHI profile at the detectors. The same instrument and sample were also used in standard QENS mode for comparison. The intermediate scattering functions, [Formula: see text], obtained by the two methods-vHI and QENS-are strikingly similar providing a direct experimental validation of the vHI method. Perhaps surprisingly, the counting statistics of the two methods are comparable even though the instrument used was expressly designed for QENS. This shows that the methodology modification adopted here can be used in practice to access vHI profiles at many of the backscattering spectrometers worldwide. We also show that partial integrations of the measured QENS spectrum cannot provide the vHI profile, which clarifies a common misconception. At the same time, we show a novel approach which does access [Formula: see text] from QENS spectra.
Collapse
Affiliation(s)
- Antonio Benedetto
- School of Physics, University College Dublin, Dublin 4, Ireland.
- Conway Institute, University College Dublin, Dublin 4, Ireland.
- Department of Sciences, University of Roma Tre, Rome, Italy.
- Laboratory for Neutron Scattering, Paul Scherrer Institute, Villigen, Switzerland.
| | - Gordon J Kearley
- School of Physics, University College Dublin, Dublin 4, Ireland
- School of Chemistry, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
9
|
Bhatia S, Krishnamoorthy G, Udgaonkar JB. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein. J Am Chem Soc 2021; 143:1447-1457. [PMID: 33430589 DOI: 10.1021/jacs.0c11097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To determine experimentally how the multiple folding pathways of a protein differ, in the order in which the structural parts are assembled, has been a long-standing challenge. To resolve whether structure formation during folding can progress in multiple ways, the complex folding landscape of monellin has been characterized, structurally and temporally, using the multisite time-resolved FRET methodology. After an initial heterogeneous polypeptide chain collapse, structure formation proceeds on parallel pathways. Kinetic analysis of the population evolution data across various protein segments provides a clear structural distinction between the parallel pathways. The analysis leads to a phenomenological model that describes how and when discrete segments acquire structure independently of each other in different subensembles of protein molecules. When averaged over all molecules, structure formation is seen to progress as α-helix formation, followed by core consolidation, then β-sheet formation, and last end-to-end distance compaction. Parts of the protein that are closer in the primary sequence acquire structure before parts separated by longer sequence.
Collapse
Affiliation(s)
- Sandhya Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560 065, India.,Indian Institute of Science Education and Research, Pune 411 008, India
| | | | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560 065, India.,Indian Institute of Science Education and Research, Pune 411 008, India
| |
Collapse
|
10
|
Shou K, Sarter M, de Souza NR, de Campo L, Whitten AE, Kuchel PW, Garvey CJ, Stadler AM. Effect of red blood cell shape changes on haemoglobin interactions and dynamics: a neutron scattering study. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201507. [PMID: 33204483 PMCID: PMC7657910 DOI: 10.1098/rsos.201507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
By using a combination of experimental neutron scattering techniques, it is possible to obtain a statistical perspective on red blood cell (RBC) shape in suspensions, and the inter-relationship with protein interactions and dynamics inside the confinement of the cell membrane. In this study, we examined the ultrastructure of RBC and protein-protein interactions of haemoglobin (Hb) in them using ultra-small-angle neutron scattering and small-angle neutron scattering (SANS). In addition, we used the neutron backscattering method to access Hb motion on the ns time scale and Å length scale. Quasi-elastic neutron scattering (QENS) experiments were performed to measure diffusive motion of Hb in RBCs and in an RBC lysate. By using QENS, we probed both internal Hb dynamics and global protein diffusion, on the accessible time scale and length scale by QENS. Shape changes of RBCs and variation of intracellular Hb concentration were induced by addition of the Na+-selective ionophore monensin and the K+-selective one, valinomycin. The experimental SANS and QENS results are discussed within the framework of crowded protein solutions, where free motion of Hb is obstructed by mutual interactions.
Collapse
Affiliation(s)
- Keyun Shou
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8: Neutron Scattering and Biological Matter), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Mona Sarter
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8: Neutron Scattering and Biological Matter), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
| | - Nicolas R. de Souza
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Liliana de Campo
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Philip W. Kuchel
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Christopher J. Garvey
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
- Biofilm—Research Center for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö, Sweden
- Lund Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8: Neutron Scattering and Biological Matter), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| |
Collapse
|
11
|
Dajnowicz S, Cheng Y, Daemen LL, Weiss KL, Gerlits O, Mueser TC, Kovalevsky A. Substrate Binding Stiffens Aspartate Aminotransferase by Altering the Enzyme Picosecond Vibrational Dynamics. ACS OMEGA 2020; 5:18787-18797. [PMID: 32775880 PMCID: PMC7408236 DOI: 10.1021/acsomega.0c01900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Protein dynamics on various time scales from femtoseconds to milliseconds impacts biological function by driving proteins to conformations conducive to ligand binding and creating functional states in enzyme catalysis. Neutron vibrational spectroscopy carried out by measuring inelastic neutron scattering from protein molecules in combination with molecular simulations has the unique ability of detecting and visualizing changes in the picosecond protein vibrational dynamics due to ligand binding. Here we present neutron vibrational spectra of a homodimeric pyridoxal 5'-phosphate-dependent enzyme, aspartate aminotransferase, obtained from the open internal aldimine and closed external aldimine conformational states. We observe that in the external aldimine state the protein structure stiffens relative to the internal aldimine state, indicating rigidified vibrational dynamics on the picosecond time scale in the low-frequency regime of 5-50 cm-1. Our molecular dynamics simulations indicate substantial changes in the picosecond dynamics of the enzyme secondary structure elements upon substrate binding, with the largest contributions from just two helices and the β-sheet.
Collapse
Affiliation(s)
- Steven Dajnowicz
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
- Department
of Chemistry and Biochemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Yongqiang Cheng
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Luke L. Daemen
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Kevin L. Weiss
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Oksana Gerlits
- Department
of Natural Sciences, Tennessee Wesleyan
University, Athens, Tennessee 37303, United States
| | - Timothy C. Mueser
- Department
of Chemistry and Biochemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Andrey Kovalevsky
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| |
Collapse
|
12
|
Bashardanesh Z, Elf J, Zhang H, van der Spoel D. Rotational and Translational Diffusion of Proteins as a Function of Concentration. ACS OMEGA 2019; 4:20654-20664. [PMID: 31858051 PMCID: PMC6906769 DOI: 10.1021/acsomega.9b02835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 05/21/2023]
Abstract
Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an α-helix in one of the proteins, an effect that was not observed in the unmodified force field.
Collapse
Affiliation(s)
- Zahedeh Bashardanesh
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Johan Elf
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology
Beijing, 100083 Beijing, China
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
- E-mail: . Phone: +46 18 4714205
| |
Collapse
|
13
|
Mamontov E, Osti NC, Tyagi M. Temperature dependence of nanoscale dynamic processes measured in living millipedes by high resolution inelastic and elastic neutron scattering. Sci Rep 2019; 9:11646. [PMID: 31406234 PMCID: PMC6691110 DOI: 10.1038/s41598-019-48270-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/01/2019] [Indexed: 12/12/2022] Open
Abstract
We have used high energy-resolution neutron scattering to probe nanoscale dynamic processes in living millipedes (Narceus americanus). We have measured the temperature dependence of the intensity of scattered neutrons that do not exchange energy with the living samples on the 1.5 ns time scale, thereby excluding the signal from the highly mobile intra- and extra-cellular bulk-like aqueous constituents in the sample. This measured “elastic” scattering intensity exhibits a non-monotonic temperature dependence, with a noticeable systematic decrease detected between 295 and 303 K on warming up from 283 to 310 K. This decrease demonstrates an excellent inverse correlation with the non-monotonic, as a function of temperature, increase in the slow diffusivity previously observed in planarian flatworms and housefly larvae. This correlation suggests the existence of a biological mechanism, possibly common between different classes (Insects and Myriapods) and even phyla (Arthropods and Platyhelminthes), that dampens the slow nanoscopic dynamics in ectothermic organisms in response to the temperature of the environment exceeding the physiologically optimal range.
Collapse
Affiliation(s)
- Eugene Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA.
| | - Naresh C Osti
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Madhusudan Tyagi
- NIST Center for Neutron Research and University of Maryland, Gaithersburg, Maryland, 20899, USA
| |
Collapse
|
14
|
Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
Collapse
|
15
|
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] [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.
Collapse
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
| |
Collapse
|
16
|
Dynamics Properties of Photosynthetic Microorganisms Probed by Incoherent Neutron Scattering. Biophys J 2019; 116:1759-1768. [PMID: 31003761 DOI: 10.1016/j.bpj.2019.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 01/06/2023] Open
Abstract
Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Hence, a more flexible environment in the PQ-binding niche has been associated to a less efficient ET. A similar function/dynamics relationship was also demonstrated in Rhodobacter sphaeroides reaction centers having inhibited ET, indicating that flexibility at the quinones region plays a crucial role in evolutionarily distant organisms. Instead, a different functional/dynamical correlation was observed in algal mutants hosting a single amino acid replacement residing in a D1 domain far from the PQ-binding niche. Noteworthy, this mutant displayed the highest degree of flexibility, and besides having a nativelike ET efficiency in physiological conditions, it acquired novel, to our knowledge, phenotypic traits enabling it to preserve a high maximal quantum yield of photosystem II photochemistry in extreme habitats. Overall, in the nanosecond timescale, the degree of the observed flexibility is related to the mutation site; in the picosecond timescale, we highlighted the presence of a more pronounced dynamic heterogeneity in all mutants compared to the native cells, which could be related to a marked chemically heterogeneous environment.
Collapse
|
17
|
Hirai M, Ajito S, Arai S, Adachi M, Shimizu R, Wakamatsu K, Takata SI, Iwase H. Observation of Protein and Lipid Membrane Structures in a Model Mimicking the Molecular-Crowding Environment of Cells Using Neutron Scattering and Cell Debris. J Phys Chem B 2019; 123:3189-3198. [DOI: 10.1021/acs.jpcb.8b12546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Mitsuhiro Hirai
- Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
| | - Satoshi Ajito
- Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
| | - Shigeki Arai
- National Institute for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Motoyasu Adachi
- National Institute for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Rumi Shimizu
- National Institute for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Kaori Wakamatsu
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin, Kiryu, Gunma 376-8515, Japan
| | - Shin-ichi Takata
- J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1106, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society, Tokai, Ibaraki 319-1106, Japan
| |
Collapse
|
18
|
Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
Collapse
Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| |
Collapse
|
19
|
Myung JS, Roosen-Runge F, Winkler RG, Gompper G, Schurtenberger P, Stradner A. Weak Shape Anisotropy Leads to a Nonmonotonic Contribution to Crowding, Impacting Protein Dynamics under Physiologically Relevant Conditions. J Phys Chem B 2018; 122:12396-12402. [PMID: 30499666 PMCID: PMC6349356 DOI: 10.1021/acs.jpcb.8b07901] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The effect of a nonspherical
particle shape on the dynamics in
crowded solutions presents a significant challenge for a comprehensive
understanding of interaction and structural relaxation in biological
and soft matter. We report that small deviations from a spherical
shape induce a nonmonotonic contribution to the crowding effect on
the short-time cage diffusion compared with spherical systems, using
molecular dynamics simulations with mesoscale hydrodynamics of a multiparticle
collision dynamics fluid in semidilute systems with volume fractions
smaller than 0.35. We show that the nonmonotonic effect due to anisotropy
is caused by the combination of a reduced relative mobility over the
entire concentration range and a looser and less homogeneous cage
packing of nonspherical particles. Our finding stresses that nonsphericity
induces new complexity, which cannot be accounted for in effective
sphere models, and is of great interest in applications such as formulations
as well as for the fundamental understanding of soft matter in general
and crowding effects in living cells in particular.
Collapse
Affiliation(s)
- Jin Suk Myung
- Division of Physical Chemistry, Department of Chemistry , Lund University , SE-221 00 Lund , Sweden
| | - Felix Roosen-Runge
- Division of Physical Chemistry, Department of Chemistry , Lund University , SE-221 00 Lund , Sweden
| | - Roland G Winkler
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation , Forschungszentrum Jülich , D-52425 Jülich , Germany
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation , Forschungszentrum Jülich , D-52425 Jülich , Germany
| | - Peter Schurtenberger
- Division of Physical Chemistry, Department of Chemistry , Lund University , SE-221 00 Lund , Sweden
| | - Anna Stradner
- Division of Physical Chemistry, Department of Chemistry , Lund University , SE-221 00 Lund , Sweden
| |
Collapse
|
20
|
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] [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.
Collapse
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
| |
Collapse
|
21
|
Stavretis SE, Mamontov E, Moseley DH, Cheng Y, Daemen LL, Ramirez-Cuesta AJ, Xue ZL. Effect of magnetic fields on the methyl rotation in a paramagnetic cobalt(ii) complex. Quasielastic neutron scattering studies. Phys Chem Chem Phys 2018; 20:21119-21126. [PMID: 30079409 DOI: 10.1039/c8cp01660g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular dynamics is a fundamental property of metal complexes. These dynamic processes, especially for paramagnetic complexes under external magnetic fields, are in general not well understood. Quasielastic neutron scattering (QENS) in 0-4 T magnetic fields has been used to study the dynamics of Co(acac)2(D2O)2 (1-d4, acac = acetylacetonate). At 80-100 K, rotation of the methyl groups on the acac ligands is the dominant dynamical process. This rotation is slowed down by the magnetic field increase. Rotation times at 80 K are 5.6(3) × 10-10 s at 0 T and 2.04(10) × 10-9 s at 4 T. The QENS studies suggest that methyl groups in these paramagnetic Co(ii) molecules do not behave as isolated units, which is consistent with results from earlier magnetic susceptibility studies indicating the presence of intermolecular interactions. DFT calculations show that unpaired electron spin density in 1 is dispersed to the atoms of both acac and H2O ligands. Methyl torsions in 1-d4 have also been observed at 5-100 K in inelastic neutron spectroscopy (INS). The QENS and INS results here help understand the dynamics of the compound in the solid state.
Collapse
Affiliation(s)
- Shelby E Stavretis
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA.
| | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
Living planarian flatworms were probed using quasielastic neutron scattering to measure, on the pico-to-nanosecond time scale and nanometer length scale, microscopic diffusion of water and cell constituents in the planarians. Measurable microscopic diffusivities were surprisingly well defined in such a complex system as living animals. The overall variation in the microscopic diffusivity of cell constituents was found to be far lower than the variation in the microscopic diffusivity of water in planarians in a temperature range of 284.5 to 304.1 K.
Collapse
|
23
|
Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017; 121:8009-8025. [PMID: 28666087 PMCID: PMC5582368 DOI: 10.1021/acs.jpcb.7b03570] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The
effects of crowding in biological environments on biomolecular
structure, dynamics, and function remain not well understood. Computer
simulations of atomistic models of concentrated peptide and protein
systems at different levels of complexity are beginning to provide
new insights. Crowding, weak interactions with other macromolecules
and metabolites, and altered solvent properties within cellular environments
appear to remodel the energy landscape of peptides and proteins in
significant ways including the possibility of native state destabilization.
Crowding is also seen to affect dynamic properties, both conformational
dynamics and diffusional properties of macromolecules. Recent simulations
that address these questions are reviewed here and discussed in the
context of relevant experiments.
Collapse
Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States.,Quantitative Biology Center, RIKEN , Kobe, Japan
| | - Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan
| | - Po-Hung Wang
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States
| | - Yuji Sugita
- Quantitative Biology Center, RIKEN , Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan.,Advanced Institute for Computational Science, RIKEN , Kobe, Japan
| |
Collapse
|