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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Senft MD, Maier R, Hiremath A, Zhang F, Schreiber F. Effective interactions and phase behavior of protein solutions in the presence of hexamine cobalt(III) chloride. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:119. [PMID: 38051398 PMCID: PMC10698144 DOI: 10.1140/epje/s10189-023-00376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
Abstract
It is well established that deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) exhibit a reentrant condensation (RC) phase behavior in the presence of the trivalent hexamine cobalt(III) cations (Hac) which can be important for their packing and folding. A similar behavior can be observed for negatively charged globular proteins in the presence of trivalent metal cations, such as Y3+ or La3+. This phase behavior is mainly driven by charge inversion upon an increasing salt concentration for a fixed protein concentration (cp). However, as Hac exhibits structural differences compared to other multivalent metal cations, with six ammonia ligands (NH3) covalently bonded to the central cobalt atom, it is not clear that Hac can induce a similar phase behavior for proteins. In this work, we systematically investigate whether negatively charged globular proteins β-lactoglobulin (BLG), bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) feature Hac-induced RC. Effective protein-protein interactions were investigated by small-angle X-ray scattering. The reduced second virial coefficient (B2/B2HS) was obtained as a function of salt concentration. The virial coefficient analysis performed confirms the reentrant interaction (RI) behavior for BLG without actually inducing RC, given the insufficient strengths of the interactions for the latter to occur. In contrast, the strength of attraction for BSA, HSA and OVA are too weak to show RC. Model free analysis of the inverse intensity [Formula: see text] also supports this finding. Looking at different q-range by employing static (SLS) and dynamic light scattering experiments, the presence of RI behavior can be confirmed. The results are further discussed in view of metal cation binding sites in nucleic acids (DNA and RNA), where Hac induced RC phase behavior.
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Affiliation(s)
- Maximilian D Senft
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany.
| | - Ralph Maier
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Anusha Hiremath
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany.
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
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3
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Sohmen B, Beck C, Frank V, Seydel T, Hoffmann I, Hermann B, Nüesch M, Grimaldo M, Schreiber F, Wolf S, Roosen‐Runge F, Hugel T. The Onset of Molecule-Spanning Dynamics in Heat Shock Protein Hsp90. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304262. [PMID: 37984887 PMCID: PMC10754087 DOI: 10.1002/advs.202304262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/06/2023] [Indexed: 11/22/2023]
Abstract
Protein dynamics have been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is largely unknown how fast (local) fluctuations can lead to slow global (allosteric) changes. Here, fast molecule-spanning dynamics on the 100 to 200 ns time scale in the heat shock protein 90 (Hsp90) are shown. Global real-space movements are assigned to dynamic modes on this time scale, which is possible by a combination of single-molecule fluorescence, quasi-elastic neutron scattering and all-atom molecular dynamics (MD) simulations. The time scale of these dynamic modes depends on the conformational state of the Hsp90 dimer. In addition, the dynamic modes are affected to various degrees by Sba1, a co-chaperone of Hsp90, depending on the location within Hsp90, which is in very good agreement with MD simulations. Altogether, this data is best described by fast molecule-spanning dynamics, which precede larger conformational changes in Hsp90 and might be the molecular basis for allostery. This integrative approach provides comprehensive insights into molecule-spanning dynamics on the nanosecond time scale for a multi-domain protein.
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Affiliation(s)
- Benedikt Sohmen
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Christian Beck
- Institute of Applied PhysicsUniversity of TübingenAuf der Morgenstelle 1072076TübingenGermany
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Veronika Frank
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Tilo Seydel
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Ingo Hoffmann
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Bianca Hermann
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Mark Nüesch
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 190CH‐8057ZurichSwitzerland
| | - Marco Grimaldo
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Frank Schreiber
- Institute of Applied PhysicsUniversity of TübingenAuf der Morgenstelle 1072076TübingenGermany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of PhysicsUniversity of FreiburgHermann‐Herder‐Strasse 379104FreiburgGermany
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms‐Research Center for Biointerfaces (BRCB)Malmö University20506MalmöSweden
- Division of Physical ChemistryLund UniversityNaturvetarvägen 1422100LundSweden
| | - Thorsten Hugel
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
- Signalling Research Centers BIOSS and CIBSSUniversity of FreiburgSchänzlestrasse 1879104FreiburgGermany
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4
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Chowdhury AA, Manohar N, Lanzaro A, Kimball WD, Witek MA, Woldeyes MA, Majumdar R, Qian KK, Xu S, Gillilan RE, Huang Q, Truskett TM, Johnston KP. Characterizing Protein-Protein Interactions and Viscosity of a Monoclonal Antibody from Low to High Concentration Using Small-Angle X-ray Scattering and Molecular Dynamics Simulations. Mol Pharm 2023; 20:5563-5578. [PMID: 37782765 DOI: 10.1021/acs.molpharmaceut.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Understanding protein-protein interactions and formation of reversible oligomers (clusters) in concentrated monoclonal antibody (mAb) solutions is necessary for designing stable, low viscosity (η) concentrated formulations for processing and subcutaneous injection. Here we characterize the strength (K) of short-range anisotropic attractions (SRA) for 75-200 mg/mL mAb2 solutions at different pH and cosolute conditions by analyzing structure factors (Seff(q)) from small-angle X-ray scattering (SAXS) using coarse-grained molecular dynamics simulations. Best fit simulations additionally provide cluster size distributions, fractal dimensions, cluster occluded volume, and mAb coordination numbers. These equilibrium properties are utilized in a model to account for increases in viscosity caused by occluded volume in the clusters (packing effects) and dissipation of stress across lubricated fractal clusters. Seff(q) is highly sensitive to K at 75 mg/mL where mAbs can mutually align to form SRA contacts but becomes less sensitive at 200 mg/mL as steric repulsion due to packing becomes dominant. In contrast, η at 200 mg/mL is highly sensitive to SRA and the average cluster size from SAXS/simulation, which is observed to track the cluster relaxation time from shear thinning. By analyzing the distribution of sub-bead hot spots on the 3D mAb surface, we identify a strongly attractive hydrophobic patch in the complementarity determining region (CDR) at pH 4.5 that contributes to the high K and consequently large cluster sizes and high η. Adding NaCl screens electrostatic interactions and increases the impact of hydrophobic attraction on cluster size and raises η, whereas nonspecific binding of Arg attenuates all SRA, reducing η. The hydrophobic patch is absent at higher pH values, leading to smaller K, smaller clusters, and lower η. This work constitutes a first attempt to use SAXS and CG modeling to link both structural and rheological properties of concentrated mAb solutions to the energetics of specific hydrophobic patches on mAb surfaces. As such, our work opens an avenue for future research, including the possibility of designing coarse-grained models with physically meaningful interacting hot spots.
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Affiliation(s)
- Amjad A Chowdhury
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Neha Manohar
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Alfredo Lanzaro
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - William D Kimball
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Marta A Witek
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | | | - Ranajoy Majumdar
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | - Ken K Qian
- Eli Lilly and Company, Indianapolis, Indiana 46225, United States
| | - Shifeng Xu
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences at CHESS, Cornell University, Ithaca, New York 14853, United States
| | - Qingqiu Huang
- Center for High Energy X-ray Sciences at CHESS, Cornell University, Ithaca, New York 14853, United States
| | - Thomas M Truskett
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Physics, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Keith P Johnston
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Heo L, Gamage K, Valdes-Garcia G, Lapidus LJ, Feig M. Characterizing Transient Protein-Protein Interactions by Trp-Cys Quenching and Computer Simulations. J Phys Chem Lett 2022; 13:10175-10182. [PMID: 36279257 PMCID: PMC9870652 DOI: 10.1021/acs.jpclett.2c02723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Transient protein-protein interactions occur frequently under the crowded conditions encountered in biological environments. Tryptophan-cysteine quenching is introduced as an experimental approach with minimal labeling for characterizing such interactions between proteins due to its sensitivity to nano- to microsecond dynamics on subnanometer length scales. The experiments are paired with computational modeling at different resolutions including fully atomistic molecular dynamics simulations for interpretation of the experimental observables and to gain molecular-level insights. This approach is applied to model systems, villin variants and the drkN SH3 domain, in the presence of protein G crowders. It is demonstrated that Trp-Cys quenching experiments can differentiate between overall attractive and repulsive interactions between different proteins, and they can discern variations in interaction preferences at different protein surface locations. The close integration between experiment and simulations also provides an opportunity to evaluate different molecular force fields for the simulation of concentrated protein solutions.
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Affiliation(s)
- Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kasun Gamage
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Gilberto Valdes-Garcia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Lisa J. Lapidus
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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6
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Yanagisawa M, Watanabe C, Yoshinaga N, Fujiwara K. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11811-11827. [PMID: 36125172 DOI: 10.1021/acs.langmuir.2c01397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polymer micromaterials in a liquid or gel phase covered with a surfactant membrane are widely used materials in pharmaceuticals, cosmetics, and foods. In particular, cell-sized micromaterials of biopolymer solutions covered with a lipid membrane have been studied as artificial cells to understand cells from a physicochemical perspective. The characteristics and phase transitions of polymers confined to a microscopic space often differ from those in bulk systems. The effect that causes this difference is referred to as the cell-size space effect (CSE), but the specific physicochemical factors remain unclear. This study introduces the analysis of CSE on molecular diffusion, nanostructure transition, and phase separation and presents their main factors, i.e., short- and long-range interactions with the membrane surface and small volume (finite element nature). This serves as a guide for determining the dominant factors of CSE. Furthermore, we also introduce other factors of CSE such as spatial closure and the relationships among space size, the characteristic length of periodicity, the structure size, and many others produced by biomolecular assemblies through the analysis of protein reaction-diffusion systems and biochemical reactions.
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Affiliation(s)
- Miho Yanagisawa
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Chiho Watanabe
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima 739-8521, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, National Institute of Advanced Industrial Science and Technology, Sendai 980-8577, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, Yokohama 223-8522, Japan
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7
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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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8
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Raskar T, Niebling S, Devos JM, Yorke BA, Härtlein M, Huse N, Forsyth VT, Seydel T, Pearson AR. Structure and diffusive dynamics of aspartate α-decarboxylase (ADC) liganded with D-serine in aqueous solution. Phys Chem Chem Phys 2022; 24:20336-20347. [PMID: 35980136 PMCID: PMC9429672 DOI: 10.1039/d2cp02063g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incoherent neutron spectroscopy, in combination with dynamic light scattering, was used to investigate the effect of ligand binding on the center-of-mass self-diffusion and internal diffusive dynamics of Escherichia coli aspartate α-decarboxylase (ADC). The X-ray crystal structure of ADC in complex with the d-serine inhibitor was also determined, and molecular dynamics simulations were used to further probe the structural rearrangements that occur as a result of ligand binding. These experiments reveal that d-serine forms hydrogen bonds with some of the active site residues, that higher order oligomers of the ADC tetramer exist on ns–ms time-scales, and also show that ligand binding both affects the ADC internal diffusive dynamics and appears to further increase the size of the higher order oligomers. Neutron spectroscopy, dynamic light scattering, X-ray diffraction, and MD-simulations were used to investigate the effect of ligand binding on the structure and diffusive dynamics of Escherichia coli aspartate alpha-decarboxylase.![]()
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Affiliation(s)
- Tushar Raskar
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France.,Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
| | - Stephan Niebling
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany. .,European Molecular Biology Laboratory, Hamburg, Notkestr. 85, 22607 Hamburg, Germany
| | - Juliette M Devos
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Briony A Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford, BD7 1DP, UK
| | - Michael Härtlein
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Nils Huse
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
| | - V Trevor Forsyth
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France. .,Partnership for Structural Biology, 71 Avenue des Martyrs, Grenoble 38000, France.,Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany.
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9
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Kusova AM, Sitnitsky AE, Uversky VN, Zuev YF. Effect of Protein–Protein Interactions on Translational Diffusion of Spheroidal Proteins. Int J Mol Sci 2022; 23:ijms23169240. [PMID: 36012504 PMCID: PMC9409276 DOI: 10.3390/ijms23169240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 11/21/2022] Open
Abstract
One of the commonly accepted approaches to estimate protein–protein interactions (PPI) in aqueous solutions is the analysis of their translational diffusion. The present review article observes a phenomenological approach to analyze PPI effects via concentration dependencies of self- and collective translational diffusion coefficient for several spheroidal proteins derived from the pulsed field gradient NMR (PFG NMR) and dynamic light scattering (DLS), respectively. These proteins are rigid globular α-chymotrypsin (ChTr) and human serum albumin (HSA), and partly disordered α-casein (α-CN) and β-lactoglobulin (β-Lg). The PPI analysis enabled us to reveal the dominance of intermolecular repulsion at low ionic strength of solution (0.003–0.01 M) for all studied proteins. The increase in the ionic strength to 0.1–1.0 M leads to the screening of protein charges, resulting in the decrease of the protein electrostatic potential. The increase of the van der Waals potential for ChTr and α-CN characterizes their propensity towards unstable weak attractive interactions. The decrease of van der Waals interactions for β-Lg is probably associated with the formation of stable oligomers by this protein. The PPI, estimated with the help of interaction potential and idealized spherical molecular geometry, are in good agreement with experimental data.
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Affiliation(s)
- Aleksandra M. Kusova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, 420111 Kazan, Russia
| | - Aleksandr E. Sitnitsky
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, 420111 Kazan, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA
| | - Yuriy F. Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, 420111 Kazan, Russia
- Correspondence: ; Tel.: +7-(843)-2319036
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10
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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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11
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Abstract
Rho is a hexameric bacterial RNA helicase, which became a paradigm of factor-dependent transcription termination. The broadly accepted ("textbook") model posits a series of steps, wherein Rho first binds C-rich Rho utilization (rut) sites on nascent RNA, uses its ATP-dependent translocase activity to catch up with RNA polymerase (RNAP), and either pulls the transcript from the elongation complex or pushes RNAP forward, thus terminating transcription. However, this appealingly simple mechano-chemical model lacks a biological realism and is increasingly at odds with genetic and biochemical data. Here, we summarize recent structural and biochemical studies that have advanced our understanding of molecular details of RNA recognition, termination signaling, and RNAP inactivation in Rho-dependent transcription termination, rebalancing the view in favor of an alternative "allosteric" mechanism. In the revised model, Rho binds RNAP early in elongation assisted by the cofactors NusA and NusG, forming a pre-termination complex (PTC). The formation of PTC allows Rho to continuously sample nascent transcripts for a termination signal, which subsequently traps the elongation complex in an inactive state prior to its dissociation.
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Affiliation(s)
- Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, Ny, USA
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12
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Beck C, Grimaldo M, Braun MK, Bühl L, Matsarskaia O, Jalarvo NH, Zhang F, Roosen-Runge F, Schreiber F, Seydel T. Temperature and salt controlled tuning of protein clusters. SOFT MATTER 2021; 17:8506-8516. [PMID: 34490428 DOI: 10.1039/d1sm00418b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of molecular assemblies in protein solutions is of strong interest both from a fundamental viewpoint and for biomedical applications. While ordered and desired protein assemblies are indispensable for some biological functions, undesired protein condensation can induce serious diseases. As a common cofactor, the presence of salt ions is essential for some biological processes involving proteins, and in aqueous suspensions of proteins can also give rise to complex phase diagrams including homogeneous solutions, large aggregates, and dissolution regimes. Here, we systematically study the cluster formation approaching the phase separation in aqueous solutions of the globular protein BSA as a function of temperature (T), the protein concentration (cp) and the concentrations of the trivalent salts YCl3 and LaCl3 (cs). As an important complement to structural, i.e. time-averaged, techniques we employ a dynamical technique that can detect clusters even when they are transient on the order of a few nanoseconds. By employing incoherent neutron spectroscopy, we unambiguously determine the short-time self-diffusion of the protein clusters depending on cp, cs and T. We determine the cluster size in terms of effective hydrodynamic radii as manifested by the cluster center-of-mass diffusion coefficients D. For both salts, we find a simple functional form D(cp, cs, T) in the parameter range explored. The calculated inter-particle attraction strength, determined from the microscopic and short-time diffusive properties of the samples, increases with salt concentration and temperature in the regime investigated and can be linked to the macroscopic behavior of the samples.
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Affiliation(s)
- Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
| | - Marco Grimaldo
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
| | - Michal K Braun
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Lena Bühl
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Olga Matsarskaia
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
| | - Niina H Jalarvo
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, and JCNS Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, USA
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Felix Roosen-Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden.
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
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13
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Fries MR, Skoda MWA, Conzelmann NF, Jacobs RMJ, Maier R, Scheffczyk N, Zhang F, Schreiber F. Bulk phase behaviour vs interface adsorption: Effects of anions and isotopes on β-lactoglobulin (BLG) interactions. J Colloid Interface Sci 2021; 598:430-443. [PMID: 33930747 DOI: 10.1016/j.jcis.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 01/17/2023]
Abstract
HYPOTHESIS Protein adsorption is highly relevant in numerous applications ranging from food processing to medical implants. In this context, it is important to gain a deeper understanding of protein-protein and protein-surface interactions. Thus, the focus of this investigation is on the interplay of bulk properties and surface properties on protein adsorption. It was hypothesised that the type of solvent and ions in solution should significantly influence the protein's bulk and interface behaviour, which has been observed in literature and previous work for other net negatively charged, globular proteins such as bovine serum albumin (BSA). EXPERIMENTS The phase behaviour of β-lactoglobulin (BLG) with lanthanum chloride (LaCl3) and iodide (LaI3) in normal water H2O(l) and heavy water (D2O(l)) was established via optical microscopy and ultraviolet-visible spectroscopy. The formation of an adsorption layer and its properties such as thickness, density, structure, and hydration was investigated via neutron reflectivity, quartz-crystal microbalance with dissipation, and infra-red measurements. FINDINGS β-lactoglobulin does not show significant anion-induced or isotope-induced effects - neither in bulk nor at the solid-liquid interface, which deviates strongly from the behaviour of bovine serum albumin. We also provide a comprehensive discussion and comparison of protein-specific bulk and interface behaviour between bovine serum albumin and β-lactoglobulin dependent on anion, cation, solvent, and substrate properties. These findings pave the way for understanding the transition from adsorption to crystallisation.
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Affiliation(s)
- Madeleine R Fries
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Maximilian W A Skoda
- ISIS Facility, STFC, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom.
| | - Nina F Conzelmann
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Robert M J Jacobs
- Department for Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom.
| | - Ralph Maier
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Niels Scheffczyk
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Fajun Zhang
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
| | - Frank Schreiber
- Institute for Applied Physics, University of Tübingen, 72076 Tübingen, Germany.
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14
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Mutual diffusion of proteins in cold concentration gradients measured by holographic interferometry. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2021.116478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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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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16
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Bai Q, Zhang Q, Jing H, Chen J, Liang D. Liquid-Liquid Phase Separation of Peptide/Oligonucleotide Complexes in Crowded Macromolecular Media. J Phys Chem B 2020; 125:49-57. [PMID: 33373232 DOI: 10.1021/acs.jpcb.0c09225] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The membraneless organelles (MLOs) and coacervates of oppositely charged polyelectrolytes are both formed by liquid-liquid phase separation. To reveal how the crowded cell interior regulates the MLOs, we chose the coacervates formed by peptide S5 and single-stranded oligonucleotide (ss-oligo) at 1:1 charge ratio and investigated the phase separation processes in polyacrylamide (PAM) and poly(ethylene oxide) (PEO) media at varying concentrations. Results show that the droplet formation unit is the neutral primary complex, instead of individual S5 or ss-oligo. Therefore, the coacervation process can be described by the classic theory of nucleation and growth. The dynamic scaling relationships show that S5/ss-oligo coacervation undergoes in sequence the heterogeneous nucleation, diffusion-limited growth, and Brownian motion coalescence with time. The inert crowders generate multiple effects, including accelerating the growth of droplets, weakening the electrostatic attraction, and slowing down or even trapping the droplets in the crowder network. The overall effect is that both the size and size distribution of the droplets decrease with increasing crowder concentration, and the effect of PEO is stronger than that of PAM. Our study provides a further step toward a deeper understanding of the kinetics of MLOs in crowded living cells.
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Affiliation(s)
- Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Qiufen Zhang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Hairong Jing
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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17
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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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18
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Pounot K, Chaaban H, Foderà V, Schirò G, Weik M, Seydel T. Tracking Internal and Global Diffusive Dynamics During Protein Aggregation by High-Resolution Neutron Spectroscopy. J Phys Chem Lett 2020; 11:6299-6304. [PMID: 32663030 DOI: 10.1021/acs.jpclett.0c01530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Proteins can misfold and form either amorphous or organized aggregates with different morphologies and features. Aggregates of amyloid nature are pathological hallmarks in so-called protein conformational diseases, including Alzheimer's and Parkinson's. Evidence prevails that the transient early phases of the reaction determine the aggregate morphology and toxicity. As a consequence, real-time monitoring of protein aggregation is of utmost importance. Here, we employed time-resolved neutron backscattering spectroscopy to follow center-of-mass self-diffusion and nano- to picosecond internal dynamics of lysozyme during aggregation into a specific β-sheet rich superstructure, called particulates, formed at the isoelectric point of the protein. Particulate formation is found to be a one-step process, and protein internal dynamics, to remain unchanged during the entire aggregation process. The time-resolved neutron backscattering spectroscopy approach developed here, in combination with standard kinetics assays, provides a unifying framework in which dynamics and conformational transitions can be related to the different aggregation pathways.
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Affiliation(s)
- Kevin Pounot
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble cedex 9, France
| | - Hussein Chaaban
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble cedex 9, France
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19
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Schirò G. Probing the dynamics of biological matter by elastic, quasi-elastic, and inelastic neutron scattering. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202023605001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The so-called function-structure-dynamics paradigm established that a close relationship links the way biological molecules work (function), their 3-dimensional organization (structure) and the changes of this organization in time (dynamics), which characterize biomolecules as highly dynamic objects. A typical example of protein dynamics is provided by protein reactions with substrates: equilibrium thermal fluctuations of protein structure are necessary to allow the access of substrates to the active site, where the functional reaction occurs. Neutron scattering is a powerful technique to study equilibrium protein structural dynamics. The incoherent structure factor, which is dominant in neutron scattering from biological matter, is related to the time-position self correlation function of protein/solvent nuclei. Here the basic theory of neutron scattering and the principles of the technologies used to measure it are described. Some selected applications of neutron scattering for investigating the structural dynamics of biological molecules are also reviewed.
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20
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Fujiwara S, Matsuo T, Sugimoto Y, Shibata K. Segmental Motions of Proteins under Non-native States Evaluated Using Quasielastic Neutron Scattering. J Phys Chem Lett 2019; 10:7505-7509. [PMID: 31743029 DOI: 10.1021/acs.jpclett.9b03196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Characterization of the dynamics of disordered polypeptide chains is required to elucidate the behavior of intrinsically disordered proteins and proteins under non-native states related to the folding process. Here we develop a method using quasielastic neutron scattering, combined with small-angle X-ray scattering and dynamic light scattering, to evaluate segmental motions of proteins as well as diffusion of the entire molecules and local side-chain motions. We apply this method to RNase A under the unfolded and molten-globule (MG) states. The diffusion coefficients arising from the segmental motions are evaluated and found to be different between the unfolded and MG states. The values obtained here are consistent with those obtained using the fluorescence-based techniques. These results demonstrate not only feasibility of this method but also usefulness to characterize the behavior of proteins under various disordered states.
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Affiliation(s)
- Satoru Fujiwara
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
| | - Tatsuhito Matsuo
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
| | - Yasunobu Sugimoto
- Nagoya University Synchrotron Radiation Research Center , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8603 , Japan
| | - Kaoru Shibata
- Neutron Science Section, Materials and Life Science Division, J-PARC Center , Japan Atomic Energy Agency , 2-4 Shirakata , Tokai , Ibaraki 319-1195 , Japan
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21
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Xu AY, Castellanos MM, Mattison K, Krueger S, Curtis JE. Studying Excipient Modulated Physical Stability and Viscosity of Monoclonal Antibody Formulations Using Small-Angle Scattering. Mol Pharm 2019; 16:4319-4338. [DOI: 10.1021/acs.molpharmaceut.9b00687] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Amy Yuanyuan Xu
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Maria Monica Castellanos
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Kevin Mattison
- Malvern Panalytical, 117 Flanders Road, Westborough, Massachusetts 01581, United States
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Joseph E. Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
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22
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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23
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Grimaldo M, Lopez H, Beck C, Roosen-Runge F, Moulin M, Devos JM, Laux V, Härtlein M, Da Vela S, Schweins R, Mariani A, Zhang F, Barrat JL, Oettel M, Forsyth VT, Seydel T, Schreiber F. Protein Short-Time Diffusion in a Naturally Crowded Environment. J Phys Chem Lett 2019; 10:1709-1715. [PMID: 30897330 DOI: 10.1021/acs.jpclett.9b00345] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The interior of living cells is a dense and polydisperse suspension of macromolecules. Such a complex system challenges an understanding in terms of colloidal suspensions. As a fundamental test we employ neutron spectroscopy to measure the diffusion of tracer proteins (immunoglobulins) in a cell-like environment (cell lysate) with explicit control over crowding conditions. In combination with Stokesian dynamics simulation, we address protein diffusion on nanosecond time scales where hydrodynamic interactions dominate over negligible protein collisions. We successfully link the experimental results on these complex, flexible molecules with coarse-grained simulations providing a consistent understanding by colloid theories. Both experiments and simulations show that tracers in polydisperse solutions close to the effective particle radius Reff = ⟨ Ri3⟩1/3 diffuse approximately as if the suspension was monodisperse. The simulations further show that macromolecules of sizes R > Reff ( R < Reff) are slowed more (less) effectively even at nanosecond time scales, which is highly relevant for a quantitative understanding of cellular processes.
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Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
- LiPhy , 38402 Saint Martin d'Hères , France
| | - Christian Beck
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Felix Roosen-Runge
- Division of Physical Chemistry , Lund University , Naturvetarvägen 14 , 22100 Lund , Sweden
| | - Martine Moulin
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Juliette M Devos
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Valerie Laux
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Michael Härtlein
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Stefano Da Vela
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Ralf Schweins
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Alessandro Mariani
- European Synchrotron Radiation Facility (ESRF) , CS 40220, F-38042 Grenoble Cedex 9, France
| | - Fajun Zhang
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | | | - Martin Oettel
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - V Trevor Forsyth
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
- Faculty of Natural Sciences & Institute for Science and Technology in Medicine , Keele University , Staffordshire ST5 5BG , United Kingdom
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) , CS 20156, F-38042 Grenoble Cedex 9, France
| | - Frank Schreiber
- Institut für Angewandte Physik , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
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24
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Nawrocki G, Karaboga A, Sugita Y, Feig M. Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments. Phys Chem Chem Phys 2019; 21:876-883. [PMID: 30560249 DOI: 10.1039/c8cp06142d] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rotational diffusion of a protein in the presence of protein crowder molecules was analyzed via computer simulations. Cluster formation as a result of transient intermolecular contacts was identified as the dominant effect for reduced rotational diffusion upon crowding. The slow-down in diffusion was primarily correlated with direct protein-protein contacts rather than indirect interactions via shared hydration layers. But increased solvent viscosity due to crowding contributed to a lesser extent. Key protein-protein contacts correlated with a slow-down in diffusion involve largely interactions between charged and polar groups suggesting that the surface composition of a given protein and the resulting propensity for forming interactions with surrounding proteins in a crowded cellular environment may be the major determinant of its diffusive properties.
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Affiliation(s)
- Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd., Room 218 BCH, East Lansing, MI 48824, USA.
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25
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Boire A, Renard D, Bouchoux A, Pezennec S, Croguennec T, Lechevalier V, Le Floch-Fouéré C, Bouhallab S, Menut P. Soft-Matter Approaches for Controlling Food Protein Interactions and Assembly. Annu Rev Food Sci Technol 2019; 10:521-539. [PMID: 30633568 DOI: 10.1146/annurev-food-032818-121907] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animal- and plant-based proteins are present in a wide variety of raw and processed foods. They play an important role in determining the final structure of food matrices. Food proteins are diverse in terms of their biological origin, molecular structure, and supramolecular assembly. This diversity has led to segmented experimental studies that typically focus on one or two proteins but hinder a more general understanding of food protein structuring as a whole. In this review, we propose a unified view of how soft-matter physics can be used to control food protein assembly. We discuss physical models from polymer and colloidal science that best describe and predict the phase behavior of proteins. We explore the occurrence of phase transitions along two axes: increasing protein concentration and increasing molecular attraction. This review provides new perspectives on the link between the interactions, phase transitions, and assembly of proteins that can help in designing new food products and innovative food processing operations.
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Affiliation(s)
- Adeline Boire
- Biopolymères Interactions Assemblages, INRA UR1268, F-44300 Nantes, France;
| | - Denis Renard
- Biopolymères Interactions Assemblages, INRA UR1268, F-44300 Nantes, France;
| | - Antoine Bouchoux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, F-31077 Toulouse, France
| | | | | | | | | | - Saïd Bouhallab
- STLO, INRA UMR1253, Agrocampus Ouest, F-35042 Rennes, France
| | - Paul Menut
- Montpellier SupAgro, 34060 Montpellier, France; .,Ingénierie Procédés Aliments, AgroParisTech, INRA, Université Paris-Saclay, 91300 Massy, France
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Kuhlmann K, Appel M, Frick B, Magerl A. Breakthrough in neutron backscattering spectroscopy: Energy resolution improved by one order of magnitude using the GaAs 200 reflection. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:015119. [PMID: 30709183 DOI: 10.1063/1.5046476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
We have developed and tested a demonstrator for a neutron backscattering spectrometer with a tenfold enhanced energy resolution. This is made possible by taking advantage of the narrow intrinsic linewidth of the GaAs 200 Bragg reflection, which is one order of magnitude smaller than the linewidth of the currently used Si 111. First measurements yielded an unprecedented energy resolution of 78 neV FWHM, a factor of 10 narrower than the standard Si 111 configuration and about a factor of 4 smaller than the highest energy resolution currently available with Si 111. These measurements provide proof of concept for the construction of a full-scale user instrument.
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Affiliation(s)
- Kristijan Kuhlmann
- Friedrich-Alexander University Erlangen-Nürnberg, Chair for Biophysics, Henkestrasse 91, 91054 Erlangen, Germany
| | - Markus Appel
- Friedrich-Alexander University Erlangen-Nürnberg, Chair for Biophysics, Henkestrasse 91, 91054 Erlangen, Germany
| | - Bernhard Frick
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Andreas Magerl
- Friedrich-Alexander University Erlangen-Nürnberg, Chair for Biophysics, Henkestrasse 91, 91054 Erlangen, Germany
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Golub M, Martinez N, Michoud G, Ollivier J, Jebbar M, Oger P, Peters J. The Effect of Crowding on Protein Stability, Rigidity, and High Pressure Sensitivity in Whole Cells. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10419-10425. [PMID: 30086639 DOI: 10.1021/acs.langmuir.8b01240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In live cells, high concentrations up to 300-400 mg/mL, as in Eschericia coli (Ellis, R. J. Curr. Opin. Struct. Biol. 2001, 11, 114) are achieved which have effects on their proper functioning. However, in many experiments only individual parts of the cells as proteins or membranes are studied in order to get insight into these specific components and to avoid the high complexity of whole cells, neglecting by the way the influence of crowding. In the present study, we investigated cells of the order of Thermococcales, which are known to live under extreme conditions, in their intact form and after cell lysis to extract the effect of crowding on the molecular dynamics of the proteome and of water molecules. We found that some parameters characterizing the dynamics within the cells seem to be intrinsic to the cell type, as flexibility typical for the proteome, others are more specific to the cellular environment, as bulk water's residence time and some fractions of particles participating to the different motions, which make the lysed cells' dynamics similar to the one of another Thermococcale adapted to live under high hydrostatic pressure. In contrast to studies on the impact of crowding on pure proteins we show here that the release of crowding constraints on proteins leads to an increase in the rigidity and a decrease in the high pressure sensitivity. In a way similar to high pressure adaptation in piezophiles, the hydration water layer is decreased for the lysed cells, demonstrating a first link between protein adaptation and the impact of crowding or osmolytes on proteins.
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Affiliation(s)
- Maksym Golub
- Université Grenoble Alpes, CNRS and CEA, IBS , Grenoble , F-38000 , France
- Institut Laue Langevin , Grenoble Cedex 9 , F-38042 , France
| | - Nicolas Martinez
- Université Grenoble Alpes, CNRS and CEA, IBS , Grenoble , F-38000 , France
- Institut Laue Langevin , Grenoble Cedex 9 , F-38042 , France
| | - Grégoire Michoud
- Université Brest, CNRS, Ifremer, LM2E, IUEM , Plouzané , 29280 , France
| | | | - Mohamed Jebbar
- Université Brest, CNRS, Ifremer, LM2E, IUEM , Plouzané , 29280 , France
| | - Philippe Oger
- Université Lyon, INSA Lyon CNRS UMR 5240 , Villeurbanne cedex , F-69621 , France
| | - Judith Peters
- Institut Laue Langevin , Grenoble Cedex 9 , F-38042 , France
- University of Grenoble Alpes, CNRS, LIPhy , Grenoble , 38000 , France
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Beck C, Grimaldo M, Roosen-Runge F, Braun MK, Zhang F, Schreiber F, Seydel T. Nanosecond Tracer Diffusion as a Probe of the Solution Structure and Molecular Mobility of Protein Assemblies: The Case of Ovalbumin. J Phys Chem B 2018; 122:8343-8350. [PMID: 30106587 DOI: 10.1021/acs.jpcb.8b04349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein diffusion is not only an important process ensuring biological function but can also be used as a probe to obtain information on structural properties of protein assemblies in liquid solutions. Here, we explore the oligomerization state of ovalbumin at high protein concentrations by means of its short-time self-diffusion. We employ high-resolution incoherent quasielastic neutron scattering to access the self-diffusion on nanosecond timescales, on which interparticle contacts are not altered. Our results indicate that ovalbumin in aqueous (D2O) solutions occurs in increasingly large assemblies of its monomeric subunits with rising protein concentration. It changes from nearly monomeric toward dimeric and ultimately larger than tetrameric complexes. Simultaneously, we access information on the internal molecular mobility of ovalbumin on the nanometer length scale and compare it with results obtained for bovine serum albumin, immunoglobulin, and β-lactoglobulin.
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Affiliation(s)
- Christian Beck
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France.,Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Marco Grimaldo
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France
| | - Felix Roosen-Runge
- Division of Physical Chemistry, Department of Chemistry , Lund University , Naturvetarvägen 16 , SE-22100 Lund , Sweden
| | - Michal K Braun
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Fajun Zhang
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Frank Schreiber
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Tilo Seydel
- Institut Max von Laue-Paul Langevin (ILL) , B.P.156, F-38042 Grenoble , France
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Gradzielski M, Hoffmann I. Polyelectrolyte-surfactant complexes (PESCs) composed of oppositely charged components. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.01.017] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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30
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Wu B, Iwashita T, Egami T. Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited. PHYSICAL REVIEW LETTERS 2018; 120:135502. [PMID: 29694207 DOI: 10.1103/physrevlett.120.135502] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 06/08/2023]
Abstract
The de Gennes narrowing phenomenon is frequently observed by neutron or x-ray scattering measurements of the dynamics of complex systems, such as liquids, proteins, colloids, and polymers. The characteristic slowing down of dynamics in the vicinity of the maximum of the total scattering intensity is commonly attributed to enhanced cooperativity. In this Letter, we present an alternative view on its origin through the examination of the time-dependent pair correlation function, the van Hove correlation function, for a model liquid in two, three, and four dimensions. We find that the relaxation time increases monotonically with distance and the dependence on distance varies with dimension. We propose a heuristic explanation of this dependence based on a simple geometrical model. This finding sheds new light on the interpretation of the de Gennes narrowing phenomenon and the α-relaxation time.
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Affiliation(s)
- Bin Wu
- Department of Physics and Astronomy, Shull Wollan Center-Joint Institute of Neutron Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Takuya Iwashita
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Takeshi Egami
- Department of Physics and Astronomy, Shull Wollan Center-Joint Institute of Neutron Science, University of Tennessee, Knoxville, Tennessee 37996, USA
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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31
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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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32
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Zhang F. Nonclassical nucleation pathways in protein crystallization. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:443002. [PMID: 28984274 DOI: 10.1088/1361-648x/aa8253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.
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Affiliation(s)
- Fajun Zhang
- Universität Tübingen, Institut für Angewandte Physik, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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