1
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Gulotta A, Bucciarelli S, Roosen-Runge F, Holderer O, Schurtenberger P, Stradner A. Testing mixing rules for structural and dynamical quantities in multi-component crowded protein solutions. APL Bioeng 2024; 8:026116. [PMID: 38827499 PMCID: PMC11143939 DOI: 10.1063/5.0204201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/14/2024] [Indexed: 06/04/2024] Open
Abstract
Crowding effects significantly influence the phase behavior and the structural and dynamic properties of the concentrated protein mixtures present in the cytoplasm of cells or in the blood serum. This poses enormous difficulties for our theoretical understanding and our ability to predict the behavior of these systems. While the use of course grained colloid-inspired models allows us to reproduce the key physical solution properties of concentrated monodisperse solutions of individual proteins, we lack corresponding theories for complex polydisperse mixtures. Here, we test the applicability of simple mixing rules in order to predict solution properties of protein mixtures. We use binary mixtures of the well-characterized bovine eye lens proteins α and γB crystallin as model systems. Combining microrheology with static and dynamic scattering techniques and observations of the phase diagram for liquid-liquid phase separation, we show that reasonably accurate descriptions are possible for macroscopic and mesoscopic signatures, while information on the length scale of the individual protein size requires more information on cross-component interaction.
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Affiliation(s)
- Alessandro Gulotta
- Division for Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | - Saskia Bucciarelli
- Division for Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | | | - Olaf Holderer
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Garching, Germany
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2
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Kumar G, Ardekani AM. Concentration-Dependent Diffusion of Monoclonal Antibodies: Underlying Mechanisms of Anomalous Diffusion. Mol Pharm 2024; 21:2212-2222. [PMID: 38572979 DOI: 10.1021/acs.molpharmaceut.3c00973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The development, storage, transport, and subcutaneous delivery of highly concentrated monoclonal antibody formulations pose significant challenges due to the high solution viscosity and low diffusion of the antibody molecules in crowded environments. These issues often stem from the self-associating behavior of the antibody molecules, potentially leading to aggregation. In this work, we used a dissipative particle dynamics-based coarse-grained model to investigate the diffusion behavior of IgG1 antibody molecules in aqueous solutions with 15 and 32 mM NaCl and antibody concentrations ranging from 10 to 400 mg/mL. We determined the coarse-grained interaction parameters by matching the calculated structure factor with the computational and experimental data from the literature. Our results indicate Fickian diffusion for antibody concentrations of 10 and 25 mg/mL and anomalous diffusion for concentrations exceeding 50 mg/mL. The anomalous diffusion was observed for ∼0.33 to 0.4 μs, followed by Fickian diffusion for all antibody concentrations. We observed a strong linear correlation between the diffusion behavior of the antibody molecules (diffusion coefficient D and anomalous diffusion exponent α) and the amount of aggregates present in the solution and between the amount of aggregates and the Coulomb interaction energy. The investigation of underlying mechanisms for anomalous diffusion revealed that in crowded environments at high antibody concentrations, the attractive interaction between electrostatically complementary regions of the antibody molecules could further bring the neighboring molecules closer to one another, ultimately resulting in aggregate formation. Further, the Coulomb attraction can continue to draw more molecules together, forming larger aggregates.
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Affiliation(s)
- Gaurav Kumar
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Arezoo M Ardekani
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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3
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Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
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Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
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4
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Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
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5
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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] [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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6
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Skóra T, Janssen M, Carlson A, Kondrat S. Crowding-Regulated Binding of Divalent Biomolecules. PHYSICAL REVIEW LETTERS 2023; 130:258401. [PMID: 37418731 DOI: 10.1103/physrevlett.130.258401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/08/2023] [Indexed: 07/09/2023]
Abstract
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity-the extent to which the binding of a second molecule is enhanced after binding a first molecule-by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an immunoglobulin G binds antigens on a surface.
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Affiliation(s)
- Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mathijs Janssen
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
- Norwegian University of Life Sciences, Faculty of Science and Technology, Pb 5003, 1433 Ås, Norway
| | - Andreas Carlson
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
| | - Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute for Computational Physics, University of Stuttgart, Stuttgart 70569, Germany
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7
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Fuentes-Lemus E, Davies MJ. Effect of crowding, compartmentalization and nanodomains on protein modification and redox signaling - current state and future challenges. Free Radic Biol Med 2023; 196:81-92. [PMID: 36657730 DOI: 10.1016/j.freeradbiomed.2023.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Biological milieus are highly crowded and heterogeneous systems where organization of macromolecules within nanodomains (e.g. membraneless compartments) is vital to the regulation of metabolic processes. There is an increasing interest in understanding the effects that such packed environments have on different biochemical and biological processes. In this context, the redox biochemistry and redox signaling fields are moving towards investigating oxidative processes under conditions that exhibit these key features of biological systems in order to solve existing paradigms including those related to the generation and transmission of specific redox signals within and between cells in both normal physiology and under conditions of oxidative stress. This review outlines the effects that crowding, nanodomain formation and altered local viscosities can have on biochemical processes involving proteins, and then discusses some of the reactions and pathways involving proteins and oxidants that may, or are known to, be modulated by these factors. We postulate that knowledge of protein modification processes (e.g. kinetics, pathways and product formation) under conditions that mimic biological milieus, will provide a better understanding of the response of cells to endogenous and exogenous stressors, and their role in ageing, signaling, health and disease.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, Panum Institute, Blegdamsvej 3, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, Blegdamsvej 3, University of Copenhagen, Copenhagen, 2200, Denmark
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8
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Lenton S, Fagerberg E, Tully M, Skepö M. From dilute to concentrated solutions of intrinsically disordered proteins: Interpretation and analysis of collected data. Methods Enzymol 2022; 678:299-330. [PMID: 36641212 DOI: 10.1016/bs.mie.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) have a broad energy landscape and consequently sample many different conformations in solution. The innate flexibility of IDPs is exploited in their biological function, and in many instances allows a single IDP to regulate a range of processes in vivo. Due to their highly flexible nature, characterizing the structural properties of IDPs is not straightforward. Often solution-based methods such as Nuclear Magnetic Resonance (NMR), Förster Resonance Energy Transfer (FRET), and Small-Angle X-ray Scattering (SAXS) are used. SAXS is indeed a powerful technique to study the structural and conformational properties of IDPs in solution, and from the obtained SAXS spectra, information about the average size, shape, and extent of oligomerization can be determined. In this chapter, we will introduce model-free methods that can be used to interpret SAXS data and introduce methods that can be used to interpret SAXS data beyond analytical models, for example, by using atomistic and different levels of coarse-grained models in combination with molecular dynamics (MD) and Monte Carlo simulations.
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Affiliation(s)
- Samuel Lenton
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | - Eric Fagerberg
- Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | - Mark Tully
- BioSAXS beamline, BM29, European Synchrotron Radiation Facility, ESRF, Grenoble, France
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, Lund, Sweden; LINXS-Institute of Advanced Neutron and X-ray Science, Lund, Sweden.
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9
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Fuentes-Lemus E, Reyes JS, López-Alarcón C, Davies MJ. Crowding modulates the glycation of plasma proteins: In vitro analysis of structural modifications to albumin and transferrin and identification of sites of modification. Free Radic Biol Med 2022; 193:551-566. [PMID: 36336230 DOI: 10.1016/j.freeradbiomed.2022.10.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
Protein modification occurs in biological milieus that are characterized by high concentrations of (macro)molecules (i.e. heterogeneous and packed environments). Recent data indicate that crowding can modulate the extent and rate of protein oxidation, however its effect on other post-translational modifications remains to be explored. In this work we hypothesized that crowding would affect the glycation of plasma proteins. Physiologically-relevant concentrations of albumin (35 mg mL-1) and transferrin (2 mg mL-1) were incubated with methylglyoxal and glyoxal (5 μM-5 mM), two α-oxoaldehyde metabolites that are elevated in the plasma of people with diabetes. Crowding was induced by adding dextran or ficoll polymers. Electrophoresis, electron microscopy, fluorescence spectroscopy and mass spectrometry were employed to investigate the structural consequences of glycation under crowded conditions. Our data demonstrate that crowding modulates the extent of formation of transferrin cross-links, and also the modification pathways in both albumin and transferrin. Arginine was the most susceptible residue to modification, with lysine and cysteine also affected. Loss of 0.48 and 7.28 arginine residues per protein molecule were determined on incubation with 500 μM methylglyoxal for albumin and transferrin, respectively. Crowding did not influence the extent of loss of arginine and lysine for either protein, but the sites of modification, detected by LC-MS, were different between dilute and crowded conditions. These data confirm the relevance of studying modification processes under conditions that closely mimic biological milieus. These data unveil additional factors that influence the pattern and extent of protein modification, and their structural consequences, in biological systems.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, Panum Institute, Blegdamsvej 3, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Juan S Reyes
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Camilo López-Alarcón
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, Blegdamsvej 3, University of Copenhagen, Copenhagen, 2200, Denmark.
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10
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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] [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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11
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Beck C, Grimaldo M, Lopez H, Da Vela S, Sohmen B, Zhang F, Oettel M, Barrat JL, Roosen-Runge F, Schreiber F, Seydel T. Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture. J Phys Chem B 2022; 126:7400-7408. [PMID: 36112146 PMCID: PMC9527755 DOI: 10.1021/acs.jpcb.2c02380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The crowded environment of biological systems such as
the interior
of living cells is occupied by macromolecules with a broad size distribution.
This situation of polydispersity might influence the dependence of
the diffusive dynamics of a given tracer macromolecule in a monodisperse
solution on its hydrodynamic size and on the volume fraction. The
resulting size dependence of diffusive transport crucially influences
the function of a living cell. Here, we investigate a simplified model
system consisting of two constituents in aqueous solution, namely,
of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin
(Ig), systematically depending on the total volume fraction and ratio
of these constituents. From high-resolution quasi-elastic neutron
spectroscopy, the separate apparent short-time diffusion coefficients
for BSA and Ig in the mixture are extracted, which show substantial
deviations from the diffusion coefficients measured in monodisperse
solutions at the same total volume fraction. These deviations can
be modeled quantitatively using results from the short-time rotational
and translational diffusion in a two-component hard sphere system
with two distinct, effective hydrodynamic radii. Thus, we find that
a simple colloid picture well describes short-time diffusion in binary
mixtures as a function of the mixing ratio and the total volume fraction.
Notably, the self-diffusion of the smaller protein BSA in the mixture
is faster than the diffusion in a pure BSA solution, whereas the self-diffusion
of Ig in the mixture is slower than in the pure Ig solution.
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Affiliation(s)
- Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Marco Grimaldo
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, D07 XT95 Grangegorman, Ireland
| | - Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Benedikt Sohmen
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Martin Oettel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | | | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
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12
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Słyk E, Skóra T, Kondrat S. How macromolecules softness affects diffusion under crowding. SOFT MATTER 2022; 18:5366-5370. [PMID: 35833511 DOI: 10.1039/d2sm00357k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Diffusion in a macromolecularly crowded environment is essential for many intracellular processes, from metabolism and catalysis to gene transcription and translation. So far, theoretical and experimental work has focused on anomalous subdiffusion, and the effects of interactions, shapes, and composition, while the compactness or softness of macromolecules has received less attention. Herein, we use Brownian dynamics simulations to study how the softness of crowders affects macromolecular diffusion. We find that in most cases, soft crowders slow down the diffusion less effectively than hard crowders like Ficoll. For instance, at a 30% occupied volume fraction, the diffusion in Ficoll70 is about 20% slower than in soft crowders of the same size. However, our simulations indicate that elongated macromolecules, such as double-stranded DNA pieces, can diffuse comparably or even faster in hard crowders. We relate these effects to the volume excluded by soft and hard crowders to different tracers. Our results show that the softness and shape of macromolecules are crucial factors determining diffusion under crowding, relevant to diverse intracellular environments.
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Affiliation(s)
- Edyta Słyk
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
| | - Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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13
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Liu D, Qiu Y, Li Q, Zhang H. Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072110. [PMID: 35408509 PMCID: PMC9000840 DOI: 10.3390/molecules27072110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein-water HBs, and less protein-PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein-solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.
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14
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Belushkin AV. Comparison of the Possibilities of Inelastic Scattering of Synchrotron Radiation and Neutrons for Studying Atomic, Molecular, and Magnetic Dynamics in Condensed Matter. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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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] [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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16
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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 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.
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17
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Cisse A, Schachner-Nedherer AL, Appel M, Beck C, Ollivier J, Leitinger G, Prassl R, Kornmueller K, Peters J. Dynamics of Apolipoprotein B-100 in Interaction with Detergent Probed by Incoherent Neutron Scattering. J Phys Chem Lett 2021; 12:12402-12410. [PMID: 34939807 DOI: 10.1021/acs.jpclett.1c03141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Apolipoprotein B-100 (apo B-100) is the protein moiety of both low- and very-low-density lipoproteins, whose role is crucial to cholesterol and triglyceride transport. Aiming at the molecular dynamics' details of apo B-100, scarcely studied, we performed elastic and quasi-elastic incoherent neutron scattering (EINS, QENS) experiments combining different instruments and time scales. Similar to classical membrane proteins, the solubilization results in remaining detergent, here Nonidet P-40 (NP40). Therefore, we propose a framework for QENS studies of protein-detergent complexes, with the introduction of a combined model, including the experimental apo B-100/NP40 ratio. Relying on the simultaneous analysis of all QENS amplitudes, this approach is sensitive enough to separate both contributions. Its application identified two points: (i) apo B-100 slow dynamics and (ii) the acceleration of NP40 dynamics in the presence of apo B-100. Direct translation of the exposed methodology now makes the investigation of more membrane proteins by neutron spectroscopy achievable.
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Affiliation(s)
- Aline Cisse
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
| | | | | | - Christian Beck
- Institut Laue Langevin, 38042 Grenoble, France
- Institut of Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | | | | | | | | | - Judith Peters
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
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18
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Fuentes-Lemus E, Reyes JS, Gamon LF, López-Alarcón C, Davies MJ. Effect of macromolecular crowding on protein oxidation: Consequences on the rate, extent and oxidation pathways. Redox Biol 2021; 48:102202. [PMID: 34856437 PMCID: PMC8640551 DOI: 10.1016/j.redox.2021.102202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022] Open
Abstract
Biological systems are heterogeneous and crowded environments. Such packed milieus are expected to modulate reactions both inside and outside the cell, including protein oxidation. In this work, we explored the effect of macromolecular crowding on the rate and extent of oxidation of Trp and Tyr, in free amino acids, peptides and proteins. These species were chosen as they are readily oxidized and contribute to damage propagation. Dextran was employed as an inert crowding agent, as this polymer decreases the fraction of volume available to other (macro)molecules. Kinetic analysis demonstrated that dextran enhanced the rate of oxidation of free Trp, and peptide Trp, elicited by AAPH-derived peroxyl radicals. For free Trp, the rates of oxidation were 15.0 ± 2.1 and 30.5 ± 3.4 μM min-1 without and with dextran (60 mg mL-1) respectively. Significant increases were also detected for peptide-incorporated Trp. Dextran increased the extent of Trp consumption (up to 2-fold) and induced short chain reactions. In contrast, Tyr oxidation was not affected by the presence of dextran. Studies on proteins, using SDS-PAGE and LC-MS, indicated that oxidation was also affected by crowding, with enhanced amino acid loss (45% for casein), chain reactions and altered extents of oligomer formation. The overall effects of dextran-mediated crowding were however dependent on the protein structure. Overall, these data indicate that molecular crowding, as commonly encountered in biological systems affect the rates, and extents of oxidation, and particularly of Trp residues, illustrating the importance of appropriate choice of in vitro systems to study biological oxidations.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
| | - Juan Sebastián Reyes
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luke F Gamon
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark
| | - Camilo López-Alarcón
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
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19
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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] [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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20
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Eves BJ, Doutch JJ, Terry AE, Yin H, Moulin M, Haertlein M, Forsyth VT, Flagmeier P, Knowles TPJ, Dias DM, Lotze G, Seddon AM, Squires AM. Elongation rate and average length of amyloid fibrils in solution using isotope-labelled small-angle neutron scattering. RSC Chem Biol 2021; 2:1232-1238. [PMID: 34458836 PMCID: PMC8341957 DOI: 10.1039/d1cb00001b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/06/2021] [Indexed: 12/22/2022] Open
Abstract
We demonstrate a solution method that allows both elongation rate and average fibril length of assembling amyloid fibrils to be estimated. The approach involves acquisition of real-time neutron scattering data during the initial stages of seeded growth, using contrast matched buffer to make the seeds effectively invisible to neutrons. As deuterated monomers add on to the seeds, the labelled growing ends give rise to scattering patterns that we model as cylinders whose increase in length with time gives an elongation rate. In addition, the absolute intensity of the signal can be used to determine the number of growing ends per unit volume, which in turn provides an estimate of seed length. The number of ends did not change significantly during elongation, demonstrating that any spontaneous or secondary nucleation was not significant compared with growth on the ends of pre-existing fibrils, and in addition providing a method of internal validation for the technique. Our experiments on initial growth of alpha synuclein fibrils using 1.2 mg ml-1 seeds in 2.5 mg ml-1 deuterated monomer at room temperature gave an elongation rate of 6.3 ± 0.5 Å min-1, and an average seed length estimate of 4.2 ± 1.3 μm.
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Affiliation(s)
- Ben J Eves
- Department of Chemistry, University of Bath Bath UK
| | - James J Doutch
- ISIS Facility, Rutherford Appleton Laboratory, STFC, Chilton Didcot OX11 0QX UK
| | - Ann E Terry
- MAX IV Laboratory, Lund University P.O. Box 118 Lund 221 00 Sweden
| | - Han Yin
- Department of Chemistry, University of Bath Bath UK
| | - Martine Moulin
- Life Sciences Group, Institut Laue Langevin 38042 Grenoble Cedex 9 France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue Langevin 38042 Grenoble Cedex 9 France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue Langevin 38042 Grenoble Cedex 9 France
- School of Chemistry & Physics Keele University Staffordshire ST5 5BG UK
| | - Patrick Flagmeier
- Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Centre for Misfolding Diseases, University of Cambridge Cambridge CB2 1EW UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Centre for Misfolding Diseases, University of Cambridge Cambridge CB2 1EW UK
| | - David M Dias
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Gudrun Lotze
- MAX IV Laboratory, Lund University P.O. Box 118 Lund 221 00 Sweden
| | - Annela M Seddon
- School of Physics, HH Wills Physics Laboratory, Tyndall Avenue, University of Bristol Bristol BS8 1TL UK
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21
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Roosen-Runge F, Schurtenberger P, Stradner A. Self-diffusion of nonspherical particles fundamentally conflicts with effective sphere models. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:154002. [PMID: 33498038 DOI: 10.1088/1361-648x/abdff9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Modeling diffusion of nonspherical particles presents an unsolved and considerable challenge, despite its importance for the understanding of crowding effects in biology, food technology and formulation science. A common approach in experiment and simulation is to map nonspherical objects on effective spheres to subsequently use the established predictions for spheres to approximate phenomena for nonspherical particles. Using numerical evaluation of the hydrodynamic mobility tensor, we show that this so-called effective sphere model fundamentally fails to represent the self-diffusion in solutions of ellipsoids as well as rod-like assemblies of spherical beads. The effective sphere model drastically overestimates the slowing down of self-diffusion down to volume fractions below 0.01. Furthermore, even the linear term relevant at lower volume fraction is inaccurate, linked to a fundamental misconception of effective sphere models. To overcome the severe problems related with the use of effective sphere models, we suggest a protocol to predict the short-time self-diffusion of rod-like systems, based on simulations with hydrodynamic interactions that become feasible even for more complex molecules as the essential observable shows a negligible system-size effect.
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Affiliation(s)
- Felix Roosen-Runge
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Faculty of Health and Society, Malmö University, Sweden
| | - Peter Schurtenberger
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | - Anna Stradner
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
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22
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Xie Y, Miao Y. Polarisome assembly mediates actin remodeling during polarized yeast and fungal growth. J Cell Sci 2021; 134:134/1/jcs247916. [PMID: 33419950 DOI: 10.1242/jcs.247916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dynamic assembly and remodeling of actin is critical for many cellular processes during development and stress adaptation. In filamentous fungi and budding yeast, actin cables align in a polarized manner along the mother-to-daughter cell axis, and are essential for the establishment and maintenance of polarity; moreover, they rapidly remodel in response to environmental cues to achieve an optimal system response. A formin at the tip region within a macromolecular complex, called the polarisome, is responsible for driving actin cable polymerization during polarity establishment. This polarisome undergoes dynamic assembly through spatial and temporally regulated interactions between its components. Understanding this process is important to comprehend the tuneable activities of the formin-centered nucleation core, which are regulated through divergent molecular interactions and assembly modes within the polarisome. In this Review, we focus on how intrinsically disordered regions (IDRs) orchestrate the condensation of the polarisome components and the dynamic assembly of the complex. In addition, we address how these components are dynamically distributed in and out of the assembly zone, thereby regulating polarized growth. We also discuss the potential mechanical feedback mechanisms by which the force-induced actin polymerization at the tip of the budding yeast regulates the assembly and function of the polarisome.
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Affiliation(s)
- Ying Xie
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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23
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Roosen-Runge F, Gulotta A, Bucciarelli S, Casal-Dujat L, Garting T, Skar-Gislinge N, Obiols-Rabasa M, Farago B, Zaccarelli E, Schurtenberger P, Stradner A. Crowding in the Eye Lens: Modeling the Multisubunit Protein β-Crystallin with a Colloidal Approach. Biophys J 2020; 119:2483-2496. [PMID: 33189682 PMCID: PMC7822730 DOI: 10.1016/j.bpj.2020.10.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/07/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022] Open
Abstract
We present a multiscale characterization of aqueous solutions of the bovine eye lens protein βH crystallin from dilute conditions up to dynamical arrest, combining dynamic light scattering, small-angle x-ray scattering, tracer-based microrheology, and neutron spin echo spectroscopy. We obtain a comprehensive explanation of the observed experimental signatures from a model of polydisperse hard spheres with additional weak attraction. In particular, the model predictions quantitatively describe the multiscale dynamical results from microscopic nanometer cage diffusion over mesoscopic micrometer gradient diffusion up to macroscopic viscosity. Based on a comparative discussion with results from other crystallin proteins, we suggest an interesting common pathway for dynamical arrest in all crystallin proteins, with potential implications for the understanding of crowding effects in the eye lens.
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Affiliation(s)
| | | | | | | | - Tommy Garting
- Division of Physical Chemistry, Lund University, Lund, Sweden
| | | | | | | | - Emanuela Zaccarelli
- Institute for Complex Systems, National Research Council, Uos Sapienza, Rome, Italy; Department of Physics, Sapienza Università di Roma, Rome, Italy
| | | | - Anna Stradner
- Division of Physical Chemistry, Lund University, Lund, Sweden.
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24
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Zhou F, Wang H, Zhang Z. Diffusion of Anisotropic Colloids in Periodic Arrays of Obstacles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11866-11872. [PMID: 32927949 DOI: 10.1021/acs.langmuir.0c01884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Colloidal suspensions in confined geometries exhibit rich diffusion dynamics governed by particle shapes and particle-confinement interactions. Here, we propose a colloidal system, consisting of ellipsoids in periodic array of obstacles, to investigate the confined diffusion of anisotropic colloids. From the obstacle density-dependent diffusion, we discover a decoupling of translational and rotational diffusion in which only rotational motion is localized while translational motion remains diffusive. Moreover, by evaluating the probability distributions of displacements, we found Brownian but non-Gaussian diffusion behaviors with increasing the obstacle densities, which originates from the shape anisotropy of the colloid and the multiplicity of the local configurations of the ellipsoids with respect to the obstacle. Our results suggest that the shape anisotropy and spatial confinements play a vital role in the diffusion dynamics. It is important for understanding the transportations of anisotropic objects in complex environments.
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Affiliation(s)
- Fang Zhou
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Huaguang Wang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Zexin Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
- Institute for Advanced Study, Soochow University, Suzhou 215006, China
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25
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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.
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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
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26
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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] [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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27
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Skóra T, Vaghefikia F, Fitter J, Kondrat S. Macromolecular Crowding: How Shape and Interactions Affect Diffusion. J Phys Chem B 2020; 124:7537-7543. [PMID: 32790396 DOI: 10.1021/acs.jpcb.0c04846] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A significant fraction of the cell volume is occupied by various proteins, polysaccharides, nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical and experimental work so far have mainly focused on the dependence of the mobility on the occupied volume, while the effect of a macromolecular shape received less attention. Herein, using fluorescence correlation spectroscopy (FCS) and Brownian dynamics (BD) simulations, we report on a dramatic slowdown of tracer diffusion by cylindrically shaped double-stranded (ds) DNAs (16 nm in length). We find, for instance, that the translational diffusion coefficient of a streptavidin tracer is reduced by about 60% for a volume fraction of dsDNA as low as just 5%. For comparison, for a spherical crowder (Ficoll70) the slowdown is only 10% at the same volume fraction and 60% reduction occurs at a volume fraction as high as 35%. BD simulations reveal that this reduction can be attributed to a larger volume excluded to a tracer by dsDNA particles, as compared with spherical Ficoll70 at the same volume fraction, and to the differences in the tracer-crowder attractive interactions. In addition, we find using BD simulations that rotational diffusion of dsDNA is less affected by the crowder shape than its translational motion. Our results show that diffusion in crowded systems is determined not merely by the occupied volume fraction, but that the shape and interactions can determine diffusion, which is relevant to the diverse intracellular environments inside living cells.
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Affiliation(s)
- Tomasz Skóra
- Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Farzaneh Vaghefikia
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany
| | - Jörg Fitter
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany.,Institut für Biologische Informationsprozesse (IBI-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Svyatoslav Kondrat
- Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.,Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany.,Institut für Theoretische Physik IV, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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28
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Lipoprotein ability to exchange and remove lipids from model membranes as a function of fatty acid saturation and presence of cholesterol. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158769. [PMID: 32712249 DOI: 10.1016/j.bbalip.2020.158769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/11/2020] [Accepted: 07/19/2020] [Indexed: 11/23/2022]
Abstract
Lipoproteins play a central role in the development of atherosclerosis. High and low-density lipoproteins (HDL and LDL), known as 'good' and 'bad' cholesterol, respectively, remove and/or deposit lipids into the artery wall. Hence, insight into lipid exchange processes between lipoproteins and cell membranes is of particular importance in understanding the onset and development of cardiovascular disease. In order to elucidate the impact of phospholipid tail saturation and the presence of cholesterol in cell membranes on these processes, neutron reflection was employed in the present investigation to follow lipid exchange with both HDL and LDL against model membranes. Mirroring clinical risk factors for the development of atherosclerosis, lower exchange was observed in the presence of cholesterol, as well as for an unsaturated phospholipid, compared to faster exchange when using a fully saturated phospholipid. These results highlight the importance of membrane composition on the interaction with lipoproteins, chiefly the saturation level of the lipids and presence of cholesterol, and provide novel insight into factors of importance for build-up and reversibility of atherosclerotic plaque. In addition, the correlation between the results and well-established clinical risk factors suggests that the approach taken can be employed also for understanding a broader set of risk factors including, e.g., effects of triglycerides and oxidative stress, as well as local effects of drugs on atherosclerotic plaque formation.
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Zhu K, Su H. Generalization of Langevin Dynamics from Spatio-Temporal Dressed Dynamics Perspective. J Phys Chem A 2020; 124:3269-3275. [PMID: 32162515 DOI: 10.1021/acs.jpca.0c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding multiscale dynamics characteristics has been the holy grail in a broad range of scientific disciplines from physics, chemistry, to biology, and beyond. The seminal Langevin equation successfully unravels remarkable details of Brownian motion dynamics involving stochastic collisions from the fluidic medium. However, extraordinary phenomena beyond the scope of Langevin dynamics were observed to exhibit a series of multiscale dynamic features in recent years. Here, an explicit spatio-temporal coupled kernel is developed to provide the microscopic account for delicate dynamic coupling between particle and medium in the dressed dynamics perspective. This methodology is applied to investigate an aqueous solvation shell model with an explicit spatial boundary to illustrate the significance of spatial and temporal coupling, leading to a general temporal profile of dressed dynamics over 12 orders of magnitude in time In particular, the time-resolved viscosity is formulated to address the remarkable enhancement of viscosity measured by the liquid cell electron microscopy. The understanding of dressed dynamics processes will be greatly enriched by further studies on the detailed dynamics that manifests the microscopic inhomogeneity of medium.
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Affiliation(s)
- Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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30
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Zhu K, Su H. Unraveling Dynamic Transitions in Time-Resolved Biomolecular Motions by A Dressed Diffusion Model. J Phys Chem A 2020; 124:613-617. [PMID: 31589443 DOI: 10.1021/acs.jpca.9b08142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent experimental data reveal the complexity of diffusion dynamics beyond the scope of classical Brownian dynamics. The particles exhibit diverse diffusive motions from the anomalous toward classical diffusion over a wide range of temporal scales. Here a dressed diffusion model is developed to account for non-Brownian phenomena. By coupling the particle dynamics with a local field, the dressed diffusion model generalizes the Langevin equation through coupled damping kernels and generates the salient feature of time-dependent diffusion dynamics reported in the experimental measurements of biomolecules. The dressed diffusion model provides one quantitative aspect for future endeavors in this rapid-growing field.
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Affiliation(s)
- Kaicheng Zhu
- Department of Chemistry , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong
| | - Haibin Su
- Department of Chemistry , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong
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