101
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Goychuk I, Kharchenko VO, Metzler R. Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion. Phys Chem Chem Phys 2015; 16:16524-35. [PMID: 24985765 DOI: 10.1039/c4cp01234h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The discovery of anomalous diffusion of larger biopolymers and submicron tracers such as endogenous granules, organelles, or virus capsids in living cells, attributed to the viscoelastic nature of the cytoplasm, provokes the question whether this complex environment equally impacts the active intracellular transport of submicron cargos by molecular motors such as kinesins: does the passive anomalous diffusion of free cargo always imply its anomalously slow active transport by motors, the mean transport distance along microtubule growing sublinearly rather than linearly in time? Here we analyze this question within the widely used two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubules driven by a flashing binding potential, where the cargo particle is elastically attached to the motor. Depending on the cargo size, the loading force, the amplitude of the binding potential, the turnover frequency of the molecular motor enzyme, and the linker stiffness we demonstrate that the motor transport may turn out either normal or anomalous, as indeed measured experimentally. We show how a highly efficient normal active transport mediated by motors may emerge despite the passive anomalous diffusion of the cargo, and study the intricate effects of the elastic linker. Under different, well specified conditions the microtubule-based motor transport becomes anomalously slow and thus significantly less efficient.
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Affiliation(s)
- Igor Goychuk
- Institute for Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany.
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102
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Zhang X, Poniewierski A, Hou S, Sozański K, Wisniewska A, Wieczorek SA, Kalwarczyk T, Sun L, Hołyst R. Tracking structural transitions of bovine serum albumin in surfactant solutions by fluorescence correlation spectroscopy and fluorescence lifetime analysis. SOFT MATTER 2015; 11:2512-2518. [PMID: 25682837 DOI: 10.1039/c5sm00101c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The structural dynamics of proteins is crucial to their biological functions. A precise and convenient method to determine the structural changes of a protein is still urgently needed. Herein, we employ fluorescence correlation spectroscopy (FCS) to track the structural transition of bovine serum albumin (BSA) in low concentrated cationic (cetyltrimethylammonium chloride, CTAC), anionic (sodium dodecyl sulfate, SDS), and nonionic (pentaethylene glycol monododecyl ether, C12E5 and octaethylene glycol monododecyl ether, C12E8) surfactant solutions. BSA is labelled with the fluorescence dye called ATTO-488 (ATTO-BSA) to obtain steady fluorescence signals for measurements. We find that the diffusion coefficient of BSA decreases abruptly with the surfactant concentration in ionic surfactant solutions at concentrations below the critical micelle concentration (CMC), while it is constant in nonionic surfactant solutions. According to the Stokes-Sutherland-Einstein equation, the hydrodynamic radius of BSA in ionic surfactant solutions amounts to ∼6.5 nm, which is 1.7 times larger than in pure water or in nonionic surfactant solutions (3.9 nm). The interaction between BSA and ionic surfactant monomers is believed to cause the structural transition of BSA. We confirm this proposal by observing a sudden shift of the fluorescence lifetime of ATTO-BSA, from 2.3 ns to ∼3.0 ns, in ionic surfactant solutions at the concentration below CMC. No change in the fluorescence lifetime is detected in nonionic surfactant solutions. Moreover, by using FCS we are also able to identify whether the structural change of protein results from its self-aggregation or unfolding.
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Affiliation(s)
- Xuzhu Zhang
- Institute of Physical Chemistry, PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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103
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Zhang X, Hansing J, Netz RR, DeRouchey JE. Particle transport through hydrogels is charge asymmetric. Biophys J 2015; 108:530-9. [PMID: 25650921 PMCID: PMC4317548 DOI: 10.1016/j.bpj.2014.12.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 01/19/2023] Open
Abstract
Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks.
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Affiliation(s)
- Xiaolu Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | - Johann Hansing
- Fachbereich für Physik, Freie Universität Berlin, Berlin, Germany
| | - Roland R Netz
- Fachbereich für Physik, Freie Universität Berlin, Berlin, Germany
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
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104
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Goychuk I. Anomalous transport of subdiffusing cargos by single kinesin motors: the role of mechano-chemical coupling and anharmonicity of tether. Phys Biol 2015; 12:016013. [PMID: 25635368 DOI: 10.1088/1478-3975/12/1/016013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Here we generalize our previous model of molecular motors trafficking subdiffusing cargos in viscoelastic cytosol by (i) including mechano-chemical coupling between cyclic conformational fluctuations of the motor protein driven by the reaction of ATP hydrolysis and its translational motion within the simplest two-state model of hand-over-hand motion of kinesin, and also (ii) by taking into account the anharmonicity of the tether between the motor and the cargo (its maximally possible extension length). It is shown that the major earlier results such as occurrence of normal versus anomalous transport depending on the amplitude of binding potential, cargo size and the motor turnover frequency not only survive in this more realistic model, but the results also look very similar for the correspondingly adjusted parameters. However, this more realistic model displays a substantially larger thermodynamic efficiency due to a bidirectional mechano-chemical coupling. For realistic parameters, the maximal thermodynamic efficiency can transiently be about 50% as observed for kinesins, and even larger, surprisingly also in a novel strongly anomalous (sub)transport regime, where the motor enzymatic turnovers become also anomalously slow and cannot be characterized by a turnover rate. Here anomalously slow dynamics of the cargo enforces anomalously slow cyclic kinetics of the motor protein.
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Affiliation(s)
- Igor Goychuk
- Institute for Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, D-14476 Potsdam-Golm, Germany
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105
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Lee D, Kim M, Kim SY, Shin H, Kim SW, Park I. Investigation of the nanoviscosity effect of a G-quadruplex and single-strand DNA using fluorescence correlation spectroscopy. J Chem Phys 2015; 142:025101. [PMID: 25591385 DOI: 10.1063/1.4905113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Guanine (G)-quadruplexes are of interest because of their presence in the telomere sequence and the oncogene promoter region. Their diffusion and change of structure, especially in high viscosity solutions, are important for understanding their dynamics. G-quadruplexes may have less effective viscosity (nanoviscosity) when they are smaller than the solvent molecules. In this paper, we report the difference in the diffusion dynamics of the G-rich DNA sequences of single-strand DNA (ssDNA) and the G-quadruplex in aqueous, sucrose, and polyethylene glycol (PEG) solutions. From experiments with aqueous and sucrose solutions, we confirm that a simple diffusion model according to the viscosity is appropriate. In the PEG experiments, the nanoviscosity effect is observed according to PEG's molecular weight. In the PEG 200 solution, both the ssDNA and the G-quadruplex possess macroviscosity. In the PEG 10,000 solution, the G-quadruplex possesses nanoviscosity and the ssDNA possesses macroviscosity, whereas, in the PEG 35,000 solution, both ssDNA and the G-quadruplex possess nanoviscosity. The experimental results are consistent with the theoretical predictions.
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Affiliation(s)
- Dongkeun Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Minjung Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Soo Yong Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Hyosup Shin
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Sok Won Kim
- Department of Physics, University of Ulsan, Ulsan 680-749, South Korea
| | - Inho Park
- Department of Physics, University of Incheon, Incheon 406-772, South Korea
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106
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Nicoud L, Lattuada M, Lazzari S, Morbidelli M. Viscosity scaling in concentrated dispersions and its impact on colloidal aggregation. Phys Chem Chem Phys 2015; 17:24392-402. [DOI: 10.1039/c5cp03942h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Viscosity scaling in concentrated dispersions is identified using Brownian dynamics simulations, and its impact on colloidal aggregation is quantified.
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Affiliation(s)
- Lucrèce Nicoud
- Institute for Chemical and Bioengineering
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- CH-8093 Zurich
- Switzerland
| | - Marco Lattuada
- Adolphe Merkle Institute
- University of Fribourg
- Switzerland
| | | | - Massimo Morbidelli
- Institute for Chemical and Bioengineering
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- CH-8093 Zurich
- Switzerland
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107
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Gao Y, Neubauer M, Yang A, Johnson N, Morse M, Li G, Tang JX. Altered motility of Caulobacter Crescentus in viscous and viscoelastic media. BMC Microbiol 2014; 14:322. [PMID: 25539737 PMCID: PMC4302598 DOI: 10.1186/s12866-014-0322-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/11/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Motility of flagellated bacteria depends crucially on their organelles such as flagella and pili, as well as physical properties of the external medium, such as viscosity and matrix elasticity. We studied the motility of wild-type and two mutant strains of Caulobacter crescentus swarmer cells in two different types of media: a viscous and hyperosmotic glycerol-growth medium mixture and a viscoelastic growth medium, containing polyethylene glycol or polyethylene oxide of different defined sizes. RESULTS For all three strains in the medium containing glycerol, we found linear drops in percentage of motile cells and decreases in speed of those that remained motile to be inversely proportional to viscosity. The majority of immobilized cells lost viability, evidenced by their membrane leakage. In the viscoelastic media, we found less loss of motility and attenuated decrease of swimming speed at shear viscosity values comparable to the viscous medium. In both types of media, we found more severe loss in percentage of motile cells of wild-type than the mutants without pili, indicating that the interference of pili with flagellated motility is aggravated by increased viscosity. However, we found no difference in swimming speed among all three strains under all test conditions for the cells that remained motile. Finally, the viscoelastic medium caused no significant change in intervals between flagellar motor switches unless the motor stalled. CONCLUSION Hyperosmotic effect causes loss of motility and cell death. Addition of polymers into the cell medium also causes loss of motility due to increased shear viscosity, but the majority of immobilized bacteria remain viable. Both viscous and viscoelastic media alter the motility of flagellated bacteria without affecting the internal regulation of their motor switching behavior.
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Affiliation(s)
- Yukun Gao
- Physics Department, Brown University, Providence, RI, 02192, USA.
| | | | - Alexander Yang
- Physics Department, Brown University, Providence, RI, 02192, USA.
| | - Nathan Johnson
- Physics Department, Brown University, Providence, RI, 02192, USA.
| | - Michael Morse
- Physics Department, Brown University, Providence, RI, 02192, USA.
| | - Guanglai Li
- Physics Department, Brown University, Providence, RI, 02192, USA.
| | - Jay X Tang
- Physics Department, Brown University, Providence, RI, 02192, USA.
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108
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Wang L, Shan G, Pan P. Highly enhanced toughness of interpenetrating network hydrogel by incorporating poly(ethylene glycol) in first network. RSC Adv 2014. [DOI: 10.1039/c4ra11494a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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109
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Sozanski K, Wisniewska A, Piasecki T, Waszczuk K, Ochab-Marcinek A, Gotszalk T, Holyst R. A depletion layer in polymer solutions at an interface oscillating at the subnano- to submicrometer scale. SOFT MATTER 2014; 10:7762-7768. [PMID: 25142160 DOI: 10.1039/c4sm01280a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The mobility of segments of the polymer mesh in a solution determines the dynamic response of the depletion layer (DL) to mechanical stimuli. This phenomenon can be used to vastly decrease the local viscosity experienced by any device performing periodic motion at the nano- and microscale in complex liquids. We refined the vibrating quartz tuning fork (QTF) method to probe the viscosity of model aqueous solutions of polyethylene glycol, covering a broad range of molecular weights (3 kDa to 1 MDa) and QTF oscillation amplitudes (50 pm to 100 nm). For semidilute solutions of PEGs of high molecular weight, we found a drop of local viscosity, up to two orders of magnitude below the bulk value. We propose a simple explanation based on the motion of the depletion layer, strongly supported by rheometry and dynamic light scattering results. We show that it is possible to directly probe the viscosity of the DL and increase its thickness far above the equilibrium value. The key role is played by the rate of relaxation of the entangled system. The relevance of this paradigm ranges from the basic research on dynamics of entangled systems to design of energy-efficient nanomachines operating in a crowded environment.
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Affiliation(s)
- Krzysztof Sozanski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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110
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Appel EA, Forster RA, Rowland MJ, Scherman OA. The control of cargo release from physically crosslinked hydrogels by crosslink dynamics. Biomaterials 2014; 35:9897-9903. [PMID: 25239043 DOI: 10.1016/j.biomaterials.2014.08.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/01/2014] [Indexed: 02/04/2023]
Abstract
Controlled release of drugs and other cargo from hydrogels has been an important target for the development of next generation therapies. Despite the increasingly strong focus in this area of research, very little of the published literature has sought to develop a fundamental understanding of the role of molecular parameters in determining the mechanism and rate of cargo release. Herein, a series of physically crosslinked hydrogels have been prepared utilizing host-guest binding interactions of cucurbit[8]uril that are identical in strength (plateau modulus), concentration and structure, yet exhibit varying network dynamics on account of the use of different guests for supramolecular crosslinking. The diffusion of molecular cargo through the hydrogel matrix and the release characteristics from these hydrogels were investigated. It was determined that the release processes of the hydrogels could be directly correlated with the dynamics of the physical interactions responsible for crosslinking and corresponding time-dependent mesh size. These observations highlight that network dynamics play an indispensable role in determining the release mechanism of therapeutic cargo from a hydrogel, identifying that fine-tuning of the release characteristics can be gained through rational design of the molecular processes responsible for crosslinking in the carrier hydrogels.
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Affiliation(s)
- Eric A Appel
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rebecca A Forster
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK
| | - Matthew J Rowland
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK.
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111
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Kalwarczyk T, Sozanski K, Jakiela S, Wisniewska A, Kalwarczyk E, Kryszczuk K, Hou S, Holyst R. Length-scale dependent transport properties of colloidal and protein solutions for prediction of crystal nucleation rates. NANOSCALE 2014; 6:10340-10346. [PMID: 25074030 DOI: 10.1039/c4nr00647j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We propose a scaling equation describing transport properties (diffusion and viscosity) in the solutions of colloidal particles. We apply the equation to 23 different systems including colloids and proteins differing in size (range of diameters: 4 nm to 1 μm), and volume fractions (10(-3)-0.56). In solutions under study colloids/proteins interact via steric, hydrodynamic, van der Waals and/or electrostatic interactions. We implement contribution of those interactions into the scaling law. Finally we use our scaling law together with the literature values of the barrier for nucleation to predict crystal nucleation rates of hard-sphere like colloids. The resulting crystal nucleation rates agree with existing experimental data.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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112
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113
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Wiśniewska A, Sozański K, Kalwarczyk T, Kędra-Królik K, Pieper C, Wieczorek SA, Jakieła S, Enderlein J, Hołyst R. Scaling of activation energy for macroscopic flow in poly(ethylene glycol) solutions: Entangled – Non-entangled crossover. POLYMER 2014. [DOI: 10.1016/j.polymer.2014.07.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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114
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Skou M, Skou S, Jensen TG, Vestergaard B, Gillilan RE. In situ microfluidic dialysis for biological small-angle X-ray scattering. J Appl Crystallogr 2014; 47:1355-1366. [PMID: 25242913 DOI: 10.1107/s1600576714012618] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/30/2014] [Indexed: 11/10/2022] Open
Abstract
Owing to the demand for low sample consumption and automated sample changing capabilities at synchrotron small-angle X-ray (solution) scattering (SAXS) beamlines, X-ray microfluidics is receiving continuously increasing attention. Here, a remote-controlled microfluidic device is presented for simultaneous SAXS and ultraviolet absorption measurements during protein dialysis, integrated directly on a SAXS beamline. Microfluidic dialysis can be used for monitoring structural changes in response to buffer exchange or, as demonstrated, protein concentration. By collecting X-ray data during the concentration procedure, the risk of inducing protein aggregation due to excessive concentration and storage is eliminated, resulting in reduced sample consumption and improved data quality. The proof of concept demonstrates the effect of halted or continuous flow in the microfluidic device. No sample aggregation was induced by the concentration process at the levels achieved in these experiments. Simulations of fluid dynamics and transport properties within the device strongly suggest that aggregates, and possibly even higher-order oligomers, are preferentially retained by the device, resulting in incidental sample purification. Hence, this versatile microfluidic device enables investigation of experimentally induced structural changes under dynamically controllable sample conditions.
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Affiliation(s)
- Magda Skou
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Søren Skou
- Department of Structural Biophysics, University of Copenhagen, Universitetsparken 6, DK-2100 Copenhagen, Denmark ; MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Thomas G Jensen
- Department of Micro- and Nanotechnology, The Technical University of Denmark, Ørsteds plads, 2800 Kongens Lyngby, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Richard E Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, Ithaca, NY 14853, USA
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115
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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116
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Sekhar A, Latham MP, Vallurupalli P, Kay LE. Viscosity-Dependent Kinetics of Protein Conformational Exchange: Microviscosity Effects and the Need for a Small Viscogen. J Phys Chem B 2014; 118:4546-51. [DOI: 10.1021/jp501583t] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ashok Sekhar
- Departments
of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario Canada, M5S 1A8
| | - Michael P. Latham
- Departments
of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario Canada, M5S 1A8
| | - Pramodh Vallurupalli
- Departments
of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario Canada, M5S 1A8
| | - Lewis E. Kay
- Departments
of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario Canada, M5S 1A8
- Program
in Molecular Structure and Function, Hospital for Sick Children, 555
University Avenue, Toronto, Ontario Canada M5G 1X8
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117
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Abstract
The 20S core particle proteasome is a molecular machine playing an important role in cellular function by degrading protein substrates that no longer are required or that have become damaged. Regulation of proteasome activity occurs, in part, through a gating mechanism controlling the sizes of pores at the top and bottom ends of the symmetric proteasome barrel and restricting access to catalytic sites sequestered in the lumen of the structure. Although atomic resolution models of both open and closed states of the proteasome have been elucidated, the mechanism by which gates exchange between these states remains to be understood. Here, this is investigated by using magnetization transfer NMR spectroscopy focusing on the 20S proteasome core particle from Thermoplasma acidophilum. We show from viscosity-dependent proteasome gating kinetics that frictional forces originating from random solvent motions are critical for driving the gating process. Notably, a small effective hydrodynamic radius (EHR; <4Å) is obtained, providing a picture in which gate exchange proceeds through many steps involving only very small segment sizes. A small EHR further suggests that the kinetics of gate interconversion will not be affected appreciably by large viscogens, such as macromolecules found in the cell, so long as they are inert. Indeed, measurements in cell lysate reveal that the gate interconversion rate decreases only slightly, demonstrating that controlled studies in vitro provide an excellent starting point for understanding regulation of 20S core particle function in complex, biologically relevant environments.
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118
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Goychuk I, Kharchenko VO, Metzler R. How molecular motors work in the crowded environment of living cells: coexistence and efficiency of normal and anomalous transport. PLoS One 2014; 9:e91700. [PMID: 24626511 PMCID: PMC3953534 DOI: 10.1371/journal.pone.0091700] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/13/2014] [Indexed: 11/19/2022] Open
Abstract
Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.
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Affiliation(s)
- Igor Goychuk
- Institute for Physics and Astronomy, University of Potsdam, Potsdam-Golm, Germany
| | - Vasyl O. Kharchenko
- Institute for Physics and Astronomy, University of Potsdam, Potsdam-Golm, Germany
- Institute of Applied Physics, National Academy of Sciences of Ukraine, Sumy, Ukraine
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, Potsdam-Golm, Germany
- Department of Physics, Tampere University of Technology, Tampere, Finland
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119
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Percolation Diffusion into Self-Assembled Mesoporous Silica Microfibres. NANOMATERIALS 2014; 4:157-174. [PMID: 28348290 PMCID: PMC5304607 DOI: 10.3390/nano4010157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 01/22/2023]
Abstract
Percolation diffusion into long (11.5 cm) self-assembled, ordered mesoporous microfibres is studied using optical transmission and laser ablation inductive coupled mass spectrometry (LA-ICP-MS). Optical transmission based diffusion studies reveal rapid penetration (<5 s, D > 80 μm²∙s-¹) of Rhodamine B with very little percolation of larger molecules such as zinc tetraphenylporphyrin (ZnTPP) observed under similar loading conditions. The failure of ZnTPP to enter the microfibre was confirmed, in higher resolution, using LA-ICP-MS. In the latter case, LA-ICP-MS was used to determine the diffusion of zinc acetate dihydrate, D~3 × 10-4 nm²∙s-1. The large differences between the molecules are accounted for by proposing ordered solvent and structure assisted accelerated diffusion of the Rhodamine B based on its hydrophilicity relative to the zinc compounds. The broader implications and applications for filtration, molecular sieves and a range of devices and uses are described.
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120
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Wang L, Xin X, Guo K, Yang M, Ma X, Yuan J, Shen J, Yuan S. Ordered carbon nanotubes–n-dodecyl tetraethylene monoether liquid crystal composites through phase separation induced by poly(ethylene glycol). Phys Chem Chem Phys 2014; 16:14771-80. [DOI: 10.1039/c4cp00622d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We used a phase separation method to incorporate carbon nanotubes into the lamellar phase of a surfactant.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
| | - Xia Xin
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
- National Engineering Technology Research Center for Colloidal Materials
- Shandong University
| | - Kai Guo
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
| | - Mengzhou Yang
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
| | - Xin Ma
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
| | - Jing Yuan
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
| | - Jinglin Shen
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
| | - Shiling Yuan
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan, P. R. China
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121
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Hou S, Sun L, Wieczorek SA, Kalwarczyk T, Kaminski TS, Holyst R. Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays. Biosens Bioelectron 2014; 51:8-15. [DOI: 10.1016/j.bios.2013.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 06/29/2013] [Accepted: 07/06/2013] [Indexed: 11/24/2022]
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122
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123
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Trabelsi S, Aschi A, Othman T, Gharbi A. Effect of Small Globular Protein on the Dynamical Behavior of Long-Chain Polyelectrolyte in Dilute Regime. ADVANCES IN POLYMER TECHNOLOGY 2013. [DOI: 10.1002/adv.21406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Saber Trabelsi
- Laboratoire de Physique de la Matière Molle et Modélisation Electromagnétique, Faculté des Sciences de Tunis; Campus Universitaire; 2092 Tunisia
| | - Adel Aschi
- Laboratoire de Physique de la Matière Molle et Modélisation Electromagnétique, Faculté des Sciences de Tunis; Campus Universitaire; 2092 Tunisia
| | - Tahar Othman
- Laboratoire de Physique de la Matière Molle et Modélisation Electromagnétique, Faculté des Sciences de Tunis; Campus Universitaire; 2092 Tunisia
| | - Abdelhafidh Gharbi
- Laboratoire de Physique de la Matière Molle et Modélisation Electromagnétique, Faculté des Sciences de Tunis; Campus Universitaire; 2092 Tunisia
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124
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Sozański K, Wiśniewska A, Kalwarczyk T, Hołyst R. Activation energy for mobility of dyes and proteins in polymer solutions: from diffusion of single particles to macroscale flow. PHYSICAL REVIEW LETTERS 2013; 111:228301. [PMID: 24329475 DOI: 10.1103/physrevlett.111.228301] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/07/2013] [Indexed: 05/27/2023]
Abstract
We measure the activation energy Ea for the diffusion of molecular probes (dyes and proteins of radii from 0.52 to 6.9 nm) and for macroscopic flow in a model complex liquid-aqueous solutions of polyethylene glycol. We cover a broad range of polymer molecular weights, concentrations, and temperatures. Fluorescence correlation spectroscopy and rheometry experiments reveal a relationship between the excess of the activation energy in polymer solutions over the one in pure solvent ΔEa and simple parameters describing the structure of the system: probe radius, polymer hydrodynamic radius, and correlation length. ΔEa varies by more than an order of magnitude in the investigated systems (in the range of ca. 1-15 kJ/mol) and for probes significantly larger than the polymer hydrodynamic radius approaches the value measured for macroscopic flow. We develop an explicit formula describing the smooth transition of ΔEa from the diffusion of molecular probes to macroscopic flow. This formula is a reference for the quantitative analysis of specific interactions of moving nano-objects with their environment as well as active transport. For instance, the power developed by a molecular motor moving at constant velocity u is proportional to u2exp(Ea/RT).
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Affiliation(s)
- Krzysztof Sozański
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Agnieszka Wiśniewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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125
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Tabaka M, Kalwarczyk T, Hołyst R. Quantitative influence of macromolecular crowding on gene regulation kinetics. Nucleic Acids Res 2013; 42:727-38. [PMID: 24121687 PMCID: PMC3902910 DOI: 10.1093/nar/gkt907] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance.
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Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka, 01-224 Warsaw, Poland
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126
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Sekhar A, Vallurupalli P, Kay LE. Defining a length scale for millisecond-timescale protein conformational exchange. Proc Natl Acad Sci U S A 2013; 110:11391-6. [PMID: 23801755 PMCID: PMC3710843 DOI: 10.1073/pnas.1303273110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Although atomic resolution 3D structures of protein native states and some folding intermediates are available, the mechanism of interconversion between such states remains poorly understood. Here we study the four-helix bundle FF module, which folds via a transiently formed and sparsely populated compact on-pathway intermediate, I. Relaxation dispersion NMR spectroscopy has previously been used to elucidate the 3D structure of this intermediate and to establish that the conformational exchange between the I and the native, N, states of the FF domain is driven predominantly by water dynamics. In the present study we use NMR methods to define a length scale for the FF I-N transition, namely the effective hydrodynamic radius (EHR) that provides an average measure of the size of the structural units participating in the transition at any given time. Our experiments establish that the EHR is less than 4 Å, on the order of the size of one to two amino acid side chains, much smaller than the FF domain hydrodynamic radius (13 Å). The small magnitude of the EHR provides strong evidence that the I-N interconversion does not proceed via the synchronous motion of large clusters of amino acid residues, but rather by the exposure/burial of one or two side chains from solvent at any given time. Because the hydration of small hydrophobic solutes (< 4 Å) does not involve considerable dewetting or disruption of the water-hydrogen bonding network, the FF domain I-N transition does not require appreciable changes to the structure of the surrounding water.
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Affiliation(s)
- Ashok Sekhar
- Departments of Molecular Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Pramodh Vallurupalli
- Departments of Molecular Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Lewis E. Kay
- Departments of Molecular Genetics
- Biochemistry, and
- Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
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127
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Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents. Biophys J 2013; 103:1011-9. [PMID: 23009850 DOI: 10.1016/j.bpj.2012.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/29/2012] [Accepted: 08/02/2012] [Indexed: 01/30/2023] Open
Abstract
The crowded environment of cells poses a challenge for rapid protein-protein association. Yet, it has been established that the rates of association are similar in crowded and in dilute solutions. Here we probe the pathway leading to fast association between TEM1 β-lactamase and its inhibitor protein BLIP in crowded solutions. We show that the affinity of the encounter complex, the rate of final complex formation, and the structure of the transition state are similar in crowded solutions and in buffer. The experimental results were reproduced by calculations based on the transient-complex theory for protein association. Both experiments and calculations suggest that while crowding agents decrease the diffusion constant of the associating proteins, they also induce an effective excluded-volume attraction between them. The combination of the two opposing effects thus results in nearly identical overall association rates in diluted and crowded solutions.
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128
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Clop EM, Perillo MA, Chattah AK. 1H and 2H NMR Spin–Lattice Relaxation Probing Water: PEG Molecular Dynamics in Solution. J Phys Chem B 2012; 116:11953-8. [DOI: 10.1021/jp304569a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Eduardo M. Clop
- Instituto de Investigaciones
Biológicas y Tecnológicas (IIByT), CONICET - Facultad
de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield
1611, X5016GCA Córdoba, Argentina
| | - María A. Perillo
- Instituto de Investigaciones
Biológicas y Tecnológicas (IIByT), CONICET - Facultad
de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield
1611, X5016GCA Córdoba, Argentina
| | - Ana K. Chattah
- Facultad de Matemática
Astronomía y Física, Universidad Nacional de Córdoba, IFEG-CONICET, X5016LAE Córdoba,
Argentina
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129
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Nam W, Epureanu BI. The effects of viscoelastic fluid on kinesin transport. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:375103. [PMID: 22842317 DOI: 10.1088/0953-8984/24/37/375103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Kinesins are molecular motors which transport various cargoes in the cytoplasm of cells and are involved in cell division. Previous models for kinesins have only targeted their in vitro motion. Thus, their applicability is limited to kinesin moving in a fluid with low viscosity. However, highly viscoelastic fluids have considerable effects on the movement of kinesin. For example, the high viscosity modifies the relation between the load and the speed of kinesin. While the velocity of kinesin has a nonlinear dependence with respect to the load in environments with low viscosity, highly viscous forces change that behavior. Also, the elastic nature of the fluid changes the velocity of kinesin. The new mechanistic model described in this paper considers the viscoelasticity of the fluid using subdiffusion. The approach is based on a generalized Langevin equation and fractional Brownian motion. Results show that a single kinesin has a maximum velocity when the ratio between the viscosity and elasticity is about 0.5. Additionally, the new model is able to capture the transient dynamics, which allows the prediction of the motion of kinesin under time varying loads.
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Affiliation(s)
- Woochul Nam
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
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130
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Kalwarczyk T, Tabaka M, Holyst R. Biologistics--diffusion coefficients for complete proteome of Escherichia coli. ACTA ACUST UNITED AC 2012; 28:2971-8. [PMID: 22942021 PMCID: PMC3496334 DOI: 10.1093/bioinformatics/bts537] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Motivation: Biologistics provides data for quantitative analysis of transport (diffusion) processes and their spatio-temporal correlations in cells. Mobility of proteins is one of the few parameters necessary to describe reaction rates for gene regulation. Although understanding of diffusion-limited biochemical reactions in vivo requires mobility data for the largest possible number of proteins in their native forms, currently, there is no database that would contain the complete information about the diffusion coefficients (DCs) of proteins in a given cell type. Results: We demonstrate a method for the determination of in vivo DCs for any molecule—regardless of its molecular weight, size and structure—in any type of cell. We exemplify the method with the database of in vivo DC for all proteins (4302 records) from the proteome of K12 strain of Escherichia coli, together with examples of DC of amino acids, sugars, RNA and DNA. The database follows from the scale-dependent viscosity reference curve (sdVRC). Construction of sdVRC for prokaryotic or eukaryotic cell requires ~20 in vivo measurements using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), nuclear magnetic resonance (NMR) or particle tracking. The shape of the sdVRC would be different for each organism, but the mathematical form of the curve remains the same. The presented method has a high predictive power, as the measurements of DCs of several inert, properly chosen probes in a single cell type allows to determine the DCs of thousands of proteins. Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo. Contact:rholyst@ichf.edu.pl Supplementary information:Supplementary data are available at Bioinformatics Online.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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131
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Kohli I, Mukhopadhyay A. Diffusion of Nanoparticles in Semidilute Polymer Solutions: Effect of Different Length Scales. Macromolecules 2012. [DOI: 10.1021/ma301237r] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Indermeet Kohli
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Ashis Mukhopadhyay
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
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132
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Biswas N, Ichikawa M, Datta A, Sato YT, Yanagisawa M, Yoshikawa K. Phase separation in crowded micro-spheroids: DNA–PEG system. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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133
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Krise KM, Milosavljevic BH. Mobility of molecules and ions solubilized in protein gels: diffusion in the thick fraction of hen egg white. Biomacromolecules 2011; 12:2351-6. [PMID: 21548573 DOI: 10.1021/bm200417t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thick fraction of hen egg white is a protein hydrogel with an immeasurably high viscosity composed of ∼90% water that can serve as a model system for mammalian mucous membrane. Measurements of the rate constants of diffusion-controlled reactions occurring within the gel (and corresponding activation energies) and electric conductivity revealed that the thick fraction of egg white can be envisioned as a 3D network comprising hydrated protein molecules (held by intermolecular S-S bridges) surrounded by water pools and channels (of nonuniform diameters) that have a microviscosity that is very similar to that of bulk water. This was corroborated by differential scanning calorimetry measurements that revealed that 16% of water is bound to proteins. The melting kinetics of ice crystallites (produced from the freezable water) indicates nonhomogeneous water pool size.
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Affiliation(s)
- Keith M Krise
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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134
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Kalwarczyk T, Ziebacz N, Bielejewska A, Zaboklicka E, Koynov K, Szymański J, Wilk A, Patkowski A, Gapiński J, Butt HJ, Hołyst R. Comparative analysis of viscosity of complex liquids and cytoplasm of mammalian cells at the nanoscale. NANO LETTERS 2011; 11:2157-63. [PMID: 21513331 DOI: 10.1021/nl2008218] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells. This analysis unveils in the cytoplasm two length scales: (i) the correlation length ξ (approximately 5 nm in HeLa and 7 nm in Swiss 3T3 cells) and (ii) the limiting length scale that marks the crossover between nano- and macroscale viscosity (approximately 86 nm in HeLa and 30 nm in Swiss 3T3 cells). During motion, probes smaller than ξ experienced matrix viscosity: η(matrix) ≈ 2.0 mPa·s for HeLa and 0.88 mPa·s for Swiss 3T3 cells. Probes much larger than the limiting length scale experienced macroscopic viscosity, η(macro) ≈ 4.4 × 10(-2) and 2.4 × 10(-2) Pa·s for HeLa and Swiss 3T3 cells, respectively. Our results are persistent for the lengths scales from 0.14 nm to a few hundred nanometers.
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Affiliation(s)
- Tomasz Kalwarczyk
- Department of Soft Condensed Matter, Institute of Physical Chemistry PAS, Kasprzaka 44/52 01-224 Warsaw, Poland
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135
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Krise KM, Hwang AA, Sovic DM, Milosavljevic BH. Macro- and Microscale Rheological Properties of Poly(vinyl alcohol) Aqueous Solutions. J Phys Chem B 2011; 115:2759-64. [DOI: 10.1021/jp109451d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keith M. Krise
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Research Building, University Park, Pennsylvania 16802, United States
| | - Angela A. Hwang
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Research Building, University Park, Pennsylvania 16802, United States
| | - David M. Sovic
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
| | - Bratoljub H. Milosavljevic
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Research Building, University Park, Pennsylvania 16802, United States
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States
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136
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Egorov SA. Anomalous nanoparticle diffusion in polymer solutions and melts: A mode-coupling theory study. J Chem Phys 2011; 134:084903. [DOI: 10.1063/1.3556749] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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137
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Gapiński J, Szymański J, Wilk A, Kohlbrecher J, Patkowski A, Hołyst R. Size and shape of micelles studied by means of SANS, PCS, and FCS. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:9304-9314. [PMID: 20345164 DOI: 10.1021/la100181d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The hexaethylene glycol monododecyl ether (C(12)E(6)) micelles at concentrations up to 10% have been studied in their isotropic phase (10-48 degrees C) by means of small angle neutron scattering (SANS) and photon correlation spectroscopy (PCS). The SANS data obtained at low temperatures could be unequivocally interpreted as a result of scattering from a suspension of compact globular micelles with the shape of a triaxial ellipsoid or a short end-capped elliptical rod. Different models have been applied to analyze the SANS data obtained at higher temperatures: (i) elongated rod-like micelles with purely sterical interactions, (ii) compact globular micelles with a weak attractive potential, and (iii) globular micelles influenced by the critical phenomena in the whole temperature range studied. The good quality of the experimental data indicated model (i) as the best fit for our data. The diffusion coefficients obtained from the PCS measurements have been compared to the diffusion coefficients calculated for the rod-like micelles--results of the SANS data analysis. A good agreement was achieved using the solvent viscosity, in agreement with the theoretical predictions for sterically interacting globular colloidal particles. Finally, the SANS results obtained at 24 degrees C were compared to the micelle self-diffusion coefficients previously measured by means of fluorescence correlation spectroscopy (FCS) at this temperature. The good agreement obtained after scaling the data with solution viscosity supports the validity of the generalized Stokes-Einstein relation in sterically interacting systems: the product of the colloidal particle self-diffusion coefficient and the macroscopic viscosity remains constant in a broad range of concentrations. It has been concluded that the FCS technique in combination with simple viscosity measurements might serve as a tool for estimating the micellar size and shape.
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Affiliation(s)
- Jacek Gapiński
- Faculty of Physics, A. Mickiewicz University, Umultowska 85 61-614 Poznań, Poland.
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