1
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Dutagaci B, Nawrocki G, Goodluck J, Ashkarran AA, Hoogstraten CG, Lapidus LJ, Feig M. Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments. eLife 2021; 10:64004. [PMID: 33496264 PMCID: PMC7877912 DOI: 10.7554/elife.64004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Phase separation processes are increasingly being recognized as important organizing mechanisms of biological macromolecules in cellular environments. Well-established drivers of phase separation are multi-valency and intrinsic disorder. Here, we show that globular macromolecules may condense simply based on electrostatic complementarity. More specifically, phase separation of mixtures between RNA and positively charged proteins is described from a combination of multiscale computer simulations with microscopy and spectroscopy experiments. Phase diagrams were mapped out as a function of molecular concentrations in experiment and as a function of molecular size and temperature via simulations. The resulting condensates were found to retain at least some degree of internal dynamics varying as a function of the molecular composition. The results suggest a more general principle for phase separation that is based primarily on electrostatic complementarity without invoking polymer properties as in most previous studies. Simulation results furthermore suggest that such phase separation may occur widely in heterogenous cellular environment between nucleic acid and protein components.
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Affiliation(s)
- Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Joyce Goodluck
- Department of Physics, Michigan State University, East Lansing, United States
| | - Ali Akbar Ashkarran
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, United States
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Lisa J Lapidus
- Department of Physics, Michigan State University, East Lansing, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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2
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Reciprocal effects of multi-walled carbon nanotubes and oppositely charged surfactants in bulk water and at interfaces. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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3
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Matsarskaia O, Roosen‐Runge F, Schreiber F. Multivalent ions and biomolecules: Attempting a comprehensive perspective. Chemphyschem 2020; 21:1742-1767. [PMID: 32406605 PMCID: PMC7496725 DOI: 10.1002/cphc.202000162] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.
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Affiliation(s)
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Faculty of Health and SocietyMalmö UniversitySweden
- Division of Physical ChemistryLund UniversitySweden
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4
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Watanabe C, Kobori Y, Yamamoto J, Kinjo M, Yanagisawa M. Quantitative Analysis of Membrane Surface and Small Confinement Effects on Molecular Diffusion. J Phys Chem B 2020; 124:1090-1098. [PMID: 31939302 DOI: 10.1021/acs.jpcb.9b10558] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular behaviors in small liquid droplets (picoliter scale), such as phase transitions and chemical reactions, are essential for the industrial application of small droplets and their use as artificial cells. However, the droplets often differ from those in bulk solutions (milliliter scale). Since the droplet size is much larger than the molecular size, the so-called size effect that draws these differences has attracted attention as a target to be solved. Although the small volume and the membrane surface surrounding the droplet are thought to be the origin of the size effect, there were little attempts to separate and quantify them. To solve the problem, we develop a series of systems for the evaluation. Using these systems, we have evaluated the size effect of concentrated polymer solutions on molecular diffusion by dividing it into small volume and membrane surface contributions. Our results demonstrate that the size effect on the molecular diffusion originates from the long-range interaction with the surface enhanced with decreasing volume. The quantitative size effect revealed by the systems provides novel insights in the biophysical understanding of molecular behaviors in cells and to the regulation and design of micrometer-sized materials.
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Affiliation(s)
- Chiho Watanabe
- Komaba Institute for Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan
| | - Yuta Kobori
- Komaba Institute for Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan.,Department of Applied Physics , Tokyo University of Agriculture and Technology , Naka-cho 2-24-16 , Koganei , Tokyo 184-8588 , Japan
| | - Johtaro Yamamoto
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Central 6, Higashi 1-1-1 , Tsukuba , Ibaraki 305-8568 , Japan
| | - Masataka Kinjo
- Faculty of Advanced Life Science , Hokkaido University , Kita-21 Nishi-11 Kita-ku , Sapporo , Hokkaido 001-0021 , Japan
| | - Miho Yanagisawa
- Komaba Institute for Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan.,Department of Basic Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan
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5
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Tran NHN, Shagaghi N, Clayton AHA. Using fluorescence lifetime dequenching to estimate the average quinary stoichiometry of proteins in living cells. Methods Appl Fluoresc 2019; 8:014003. [PMID: 31622968 DOI: 10.1088/2050-6120/ab4ebb] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Biological proteins are understood in terms of five structural levels-primary, secondary, tertiary, quaternary and quinary. The quinary structure is defined as the set of macromolecular interactions that are transient in vivo. This includes non-covalent protein-protein interactions occurring within the crowded intracellular environment. For much of twentieth century science, the canonical approach to studying biological proteins involved test tube environments. These uncrowded in vitro studies inadvertently failed to replicate and observe the quinary structures present within the original cells. Consequently, contemporary literature surrounding the fifth level of protein organisation is lacking. In particular, there is a lack of literature on the size of transient clusters within living cells. In an attempt to reconcile this gap in knowledge, we propose a quantitative method for estimating the average quinary stoichiometry in living cells. The method is based on lifetime self-quenching of fluorescently-labelled proteins in living cells. Close approach of two or more proteins in a quinary complex will result in self-quenching of the fluorescence lifetime from the fluorescent labels. Our method utilises the random mixing of proteins during cell division to mix fluorescently labelled with unlabelled proteins. Such mixing reduces the probability of adjacency between labelled proteins and, hence, decreases the probability of fluorescence lifetime quenching from labels. By monitoring fluorescence lifetime dequenching during multiple cell divisions, we can determine the average quinary structure in living proliferating cells. We demonstrate this method with a case study on cultured HeLa cells. The average quinary stoichiometry was found to be between five and six. That is, at any given point in time, there are five or six weakly interacting partners in the immediate neighbourhood of any given protein.
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Affiliation(s)
- Nguyen H N Tran
- Centre for Micro-Photonics, Department of Physics and Astronomy, School of Science, Faculty of Science Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
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6
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Ota C, Takano K. Spectroscopic Analysis of Protein-Crowded Environments Using the Charge-Transfer Fluorescence Probe 8-Anilino-1-Naphthalenesulfonic Acid. Chemphyschem 2019; 20:1456-1466. [PMID: 30945450 DOI: 10.1002/cphc.201900226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/01/2019] [Indexed: 12/11/2022]
Abstract
The molecular behaviors of proteins under crowding conditions are crucial for understanding the protein actions in intracellular environments. Under a crowded environment, the distance between protein molecules is almost the same size as the molecular level, thus, both the excluded volume effect and short ranged soft chemical interaction on protein surface could induce the complicated influence on the protein behavior cooperatively. Recently, various kinds of analytical approaches from macroscopic to microscopic aspects have been made to evaluate the crowding effect. The method, however, has not been established to evaluate the surface specific interactions on protein surface. In this study, the analytical method to evaluate the crowding effect has been suggested by using a charge-transfer fluorescence probe, ANS. By employing the unique property of ANS attaching to charged residues on the surface of lysozyme, the crowding effect was focused, while the case was compared as a reference, in which ANS is confined in hydrophobic pockets of BSA. Consequently, the surface specific changes of fluorescence spectra were readily observed under the crowded environment, whereas the fluorescence spectra of ANS in protein inside did not change. This result suggests the fluorescence spectra of ANS binding to protein surface have the capability to estimate the crowding effect of proteins.
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Affiliation(s)
- Chikashi Ota
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
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7
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Bergman MJ, Garting T, Schurtenberger P, Stradner A. Experimental Evidence for a Cluster Glass Transition in Concentrated Lysozyme Solutions. J Phys Chem B 2019; 123:2432-2438. [PMID: 30785749 PMCID: PMC6550439 DOI: 10.1021/acs.jpcb.8b11781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Lysozyme
is known to form equilibrium clusters at pH ≈ 7.8
and at low ionic strength as a result of a mixed potential. While
this cluster formation and the related dynamic and static structure
factors have been extensively investigated, its consequences on the
macroscopic dynamic behavior expressed by the zero shear viscosity
η0 remain controversial. Here we present results
from a systematic investigation of η0 using two complementary
passive microrheology techniques, dynamic light scattering based tracer
microrheology, and multiple particle tracking using confocal microscopy.
The combination of these techniques with a simple but effective evaporation
approach allows for reaching concentrations close to and above the
arrest transition in a controlled and gentle way. We find a strong
increase of η0 with increasing volume fraction ϕ
with an apparent divergence at ϕ ≈ 0.35, and unambiguously
demonstrate that this is due to the existence of an arrest transition
where a cluster glass forms. These findings demonstrate the power
of tracer microrheology to investigate complex fluids, where weak
temporary bonds and limited sample volumes make measurements with
classical rheology challenging.
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Affiliation(s)
- Maxime J Bergman
- Division of Physical Chemistry, Department of Chemistry , Lund University , PO Box 124, SE-22100 Lund , Sweden
| | - Tommy Garting
- Division of Physical Chemistry, Department of Chemistry , Lund University , PO Box 124, SE-22100 Lund , Sweden
| | - Peter Schurtenberger
- Division of Physical Chemistry, Department of Chemistry , Lund University , PO Box 124, SE-22100 Lund , Sweden.,LINXS - Lund Institute of advanced Neutron and X-ray Science , SE-22100 Lund , Sweden
| | - Anna Stradner
- Division of Physical Chemistry, Department of Chemistry , Lund University , PO Box 124, SE-22100 Lund , Sweden.,LINXS - Lund Institute of advanced Neutron and X-ray Science , SE-22100 Lund , Sweden
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8
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Liu Y, Xi Y. Colloidal systems with a short-range attraction and long-range repulsion: Phase diagrams, structures, and dynamics. Curr Opin Colloid Interface Sci 2019; 39. [PMID: 34140838 DOI: 10.1016/j.cocis.2019.01.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Colloidal systems with both a short-range attraction and long-range repulsion (SALR) have rich phases compared with the traditional hard sphere systems or sticky hard sphere systems. The competition between the short-range attraction and long-range repulsion results in the frustrated phase separation, which leads to the formation of intermediate range order (IRO) structures and introduces new phases to both equilibrium and nonequilibrium phase diagrams, such as clustered fluid, cluster percolated fluid, Wigner glass, and cluster glass. One hallmark feature of many SALR systems is the appearance of the IRO peak in the interparticle structure factor, which is associated with different types of IRO structures. The relationship between the IRO peak and the clustered fluid state has been careful investigated. Not surprisingly, the morphology of clusters in solutions can be affected and controlled by the SALR potential. And the effect of the SALR potential on the dynamic properties is also reviewed here. Even though much progress has been made in understanding SALR systems, many future works are still needed to have quantitative comparisons between experiments and simulations/theories and understand the differences from different experimental systems. Owing to the large parameter space available for SALR systems, many exciting features of SALR systems are not fully explored yet. Because proteins in low-salinity solutions have SALR interactions, the understanding of SALR systems can greatly help understand protein behavior in concentrated solutions or crowded conditions.
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Affiliation(s)
- Yun Liu
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.,Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA.,Department of Physics & Astronomy, University of Delaware, Newark, DE, 19716, USA
| | - Yuyin Xi
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.,Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
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9
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Bleibel J, Habiger M, Lütje M, Hirschmann F, Roosen-Runge F, Seydel T, Zhang F, Schreiber F, Oettel M. Two time scales for self and collective diffusion near the critical point in a simple patchy model for proteins with floating bonds. SOFT MATTER 2018; 14:8006-8016. [PMID: 30187060 DOI: 10.1039/c8sm00599k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Using dynamic Monte Carlo and Brownian dynamics, we investigate a floating bond model in which particles can bind through mobile bonds. The maximum number of bonds (here fixed to 4) can be tuned by appropriately choosing the repulsive, nonadditive interactions among bonds and particles. We compute the static and dynamic structure factor (intermediate scattering function) in the vicinity of the gas-liquid critical point. The static structure exhibits a weak tetrahedral network character. The intermediate scattering function shows a temporal decay deviating from a single exponential, which can be described by a double exponential decay where the two time scales differ approximately by one order of magnitude. This time scale separation is robust over a range of wave numbers. The analysis of clusters in real space indicates the formation of noncompact clusters and shows a considerable stretch in the instantaneous size distribution when approaching the critical point. The average time evolution of the largest subcluster of given initial clusters with 10 or more particles also shows a double exponential decay. The observation of two time scales in the intermediate scattering function at low packing fractions is consistent with similar findings in globular protein solutions with trivalent metal ions that act as bonds between proteins.
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Affiliation(s)
- J Bleibel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.
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10
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Nawrocki G, Wang PH, Yu I, Sugita Y, Feig M. Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation. J Phys Chem B 2017; 121:11072-11084. [PMID: 29151345 PMCID: PMC5951686 DOI: 10.1021/acs.jpcb.7b08785] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.
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Affiliation(s)
- Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Po-hung Wang
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Isseki Yu
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN iTHES, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN iTHES, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minaotojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minaotojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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11
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Smirmov LP, Kulagina TP. Features of the kinetics of chemical reactions in a nanostructured liquid. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2017. [DOI: 10.1134/s1990793117050207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Palit S, Yethiraj A. Dynamics and cluster formation in charged and uncharged Ficoll70 solutions. J Chem Phys 2017; 147:074901. [DOI: 10.1063/1.4986366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Swomitra Palit
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, Newfoundland and Labrador A1B3X7, Canada
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, Newfoundland and Labrador A1B3X7, Canada
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13
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Braun MK, Grimaldo M, Roosen-Runge F, Hoffmann I, Czakkel O, Sztucki M, Zhang F, Schreiber F, Seydel T. Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion. J Phys Chem Lett 2017; 8:2590-2596. [PMID: 28525282 DOI: 10.1021/acs.jpclett.7b00658] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigate the concentration-controlled formation of clusters in β-lactoglobulin (BLG) protein solutions combining structural and dynamical scattering techniques. The static structure factor from small-angle X-ray scattering as well as de-Gennes narrowing in the nanosecond diffusion function D(q) from neutron spin echo spectroscopy support a picture of cluster formation. Using neutron backscattering spectroscopy, a monotonous increase of the average hydrodynamic cluster radius is monitored over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers. The results suggest that BLG forms compact clusters that are static on the observation time scale of several nanoseconds. The presented analysis provides a general framework to access the structure and dynamics of macromolecular assemblies in solution.
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Affiliation(s)
- Michal K Braun
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Marco Grimaldo
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Felix Roosen-Runge
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
- Division of Physical Chemistry, Department of Chemistry, Lund University , Naturvetarvägen 14, 221 00 Lund, Sweden
| | - Ingo Hoffmann
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Orsolya Czakkel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Sztucki
- ESRF - The European Synchrotron , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
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14
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Ota C, Noguchi S, Tsumoto K. The molecular interaction of a protein in highly concentrated solution investigated by Raman spectroscopy. Biopolymers 2016; 103:237-46. [PMID: 25418947 DOI: 10.1002/bip.22593] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/15/2014] [Accepted: 11/18/2014] [Indexed: 11/09/2022]
Abstract
We used Raman spectroscopy to investigate the structure and interactions of lysozyme molecules in solution over a wide range of concentrations (2.5-300 mg ml(-1)). No changes in the amide-I band were observed as the concentration was increased, but the width of the Trp band at 1555 cm(-1) and the ratios of the intensities of the Tyr bands at 856 and 837 cm(-1), the Trp bands at 870 and 877 cm(-1), and the bands at 2940 (CH stretching) and 3420 cm(-1) (OH stretching) changed as the concentration was changed. These results reveal that although the distance between lysozyme molecules changed by more than an order of magnitude over the tested concentration range, the secondary structure of the protein did not change. The changes in the molecular interactions occurred in a stepwise process as the order of magnitude of the distance between molecules changed. These results suggest that Raman bands can be used as markers to investigate the behavior of high-concentration solutions of proteins and that the use of Raman spectroscopy will lead to progress in our understanding not only of the basic science of protein behavior under concentrated (i.e., crowded) conditions but also of practical processes involving proteins, such as in the field of biopharmaceuticals.
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Affiliation(s)
- Chikashi Ota
- Department of Scientific & Semiconductor Instruments R&D, Application Development Center, Horiba Ltd., Minami-ku, Kyoto 601-8510, Japan
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15
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Barhoum S, Palit S, Yethiraj A. Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 94-95:1-10. [PMID: 27247282 DOI: 10.1016/j.pnmrs.2016.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments - in this article, we feature aqueous systems involving polymers, surfactants and proteins - the link between dynamics and size is harder to unpack due to macromolecular crowding and confinement. In this review, we demonstrate that the pulsed-field gradient NMR technique, with its spectral separation of different chemical components, is ideal for studying the dynamics of the entire system simultaneously and without labelling, in a wide range of systems. The simultaneous measurement of the dynamics of multiple components allows for internal consistency checks and enables quantitative statements about the link between macromolecular dynamics, size, complex formation and crowding in soft materials.
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Affiliation(s)
- Suliman Barhoum
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Swomitra Palit
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John's, Newfoundland and Labrador, Canada
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16
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Grimaldo M, Roosen-Runge F, Hennig M, Zanini F, Zhang F, Zamponi M, Jalarvo N, Schreiber F, Seydel T. Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution. J Phys Chem Lett 2015; 6:2577-2582. [PMID: 26266736 DOI: 10.1021/acs.jpclett.5b01073] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs = 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchy particles. The finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.
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Affiliation(s)
- Marco Grimaldo
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Felix Roosen-Runge
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
| | - Marcus Hennig
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Fabio Zanini
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Fajun Zhang
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Michaela Zamponi
- §Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- ∥JCNS Outstation at the MLZ, Lichtenbergstraße 1, D-85747 Garching, Germany
| | - Niina Jalarvo
- §Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- ⊥Chemical and Engineering Materials Division, Neutron Sciences Directorate, and JCNS Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Frank Schreiber
- ‡Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Tilo Seydel
- †Institut Max von Laue - Paul Langevin (ILL), CS 20156, 71 avenue des Martyrs, F-38042 Grenoble, France
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17
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Soraruf D, Roosen-Runge F, Grimaldo M, Zanini F, Schweins R, Seydel T, Zhang F, Roth R, Oettel M, Schreiber F. Protein cluster formation in aqueous solution in the presence of multivalent metal ions--a light scattering study. SOFT MATTER 2014; 10:894-902. [PMID: 24835564 DOI: 10.1039/c3sm52447g] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The formation of protein clusters as precursors for crystallization and phase separation is of fundamental and practical interest in protein science. Using multivalent ions, the strengths of both long-range Coulomb repulsion and short-range attraction can be tuned in protein solutions, representing a well-controlled model system to study static and dynamic properties of clustering during the transition from a charge-stabilized to an aggregate regime. Here, we study compressibility, diffusion, and size of solutes by means of static (SLS) and dynamic light scattering (DLS) in solutions of bovine serum albumin (BSA) and YCl3. For this and comparable systems, an increasing screening and ultimately inversion of the protein surface charge induce a rich phase behavior including reentrant condensation, liquid-liquid phase separation and crystallization, which puts the cluster formation in the context of precursor formation and nucleation of liquid and crystalline phases. We find that, approaching the turbid aggregate regime with increasing salt concentration cs, the diffusion coefficients decrease and the scattered intensity increases by orders of magnitude, evidencing increasing correlation lengths likely associated with clustering. The combination of static and dynamic observations suggests the formation of BSA clusters with a size on the order of 100 nm. The global thermodynamic state seems to be stable over at least several hours. Surprisingly, results on collective diffusion and inverse compressibility from different protein concentrations can be rescaled into master curves as a function of cs/c*, where c* is the critical salt concentration of the transition to the turbid aggregate regime.
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Affiliation(s)
- Daniel Soraruf
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.
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18
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Moroney BF, Stait-Gardner T, Ghadirian B, Yadav NN, Price WS. Numerical analysis of NMR diffusion measurements in the short gradient pulse limit. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:165-175. [PMID: 23887027 DOI: 10.1016/j.jmr.2013.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/17/2013] [Accepted: 06/18/2013] [Indexed: 06/02/2023]
Abstract
Pulsed gradient spin-echo (PGSE) NMR diffusion measurements provide a powerful technique for probing porous media. The derivation of analytical mathematical models for analysing such experiments is only straightforward for ideal restricting geometries and rapidly becomes intractable as the geometrical complexity increases. Consequently, in general, numerical methods must be employed. Here, a highly flexible method for calculating the results of PGSE NMR experiments in porous systems in the short gradient pulse limit based on the finite element method is presented. The efficiency and accuracy of the method is verified by comparison with the known solutions to simple pore geometries (parallel planes, a cylindrical pore, and a spherical pore) and also to Monte Carlo simulations. The approach is then applied to modelling the more complicated cases of parallel semipermeable planes and a pore hopping model. Finally, the results of a PGSE measurement on a toroidal pore, a geometry for which there is presently no current analytical solution, are presented. This study shows that this approach has great potential for modelling the results of PGSE experiments on real (3D) porous systems. Importantly, the FEM approach provides far greater accuracy in simulating PGSE diffraction data.
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Affiliation(s)
- Benjamin F Moroney
- Nanoscale Organisation and Dynamics Group, University of Western Sydney, Penrith, NSW 2751, Australia
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19
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Cametti C, Marchetti S, Onori G. Lysozyme Hydration in Concentrated Aqueous Solutions. Effect of an Equilibrium Cluster Phase. J Phys Chem B 2012; 117:104-10. [DOI: 10.1021/jp308863h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Cametti
- Department of Physics, “La Sapienza” University of Rome and CNR-INFM-SOFT, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - S. Marchetti
- Department of Physics, University of Florence, Via G. Sansone, I-50019 Sesto
Fiorentino, Florence, Italy
| | - G. Onori
- Department of Physics, University of Perugia, Via A. Pascoli, I-06123 Perugia,
Italy
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20
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Kowalczyk P, Ciach A, Gauden P, Terzyk A. Equilibrium clusters in concentrated lysozyme protein solutions. J Colloid Interface Sci 2011; 363:579-84. [DOI: 10.1016/j.jcis.2011.07.043] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/13/2011] [Accepted: 07/14/2011] [Indexed: 02/02/2023]
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21
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Tokuyama M, Moriki T, Kimura Y. Self-diffusion of biomolecules in solution. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:051402. [PMID: 21728529 DOI: 10.1103/physreve.83.051402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Indexed: 05/31/2023]
Abstract
A simple soft-core model potential is proposed to discuss the self-diffusion of biomolecules in solution. Extensive Brownian-dynamics simulations are performed to obtain the long-time self-diffusion coefficient. Then the simulation results are compared with the experimental data from a unified point of view recently obtained for suspensions of hard spheres. Thus, it is shown that the proposed potential can qualitatively well describe the experimental data.
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Affiliation(s)
- Michio Tokuyama
- World Premier International Research Center, Advanced Institute for Materials Research and Institute of Fluid Science, Tohoku University, Sendai, Japan
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