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Skóra T. On the importance of the diffusivity gradient term in Brownian dynamics simulations. Biophys J 2024:S0006-3495(24)00383-7. [PMID: 38897204 DOI: 10.1016/j.bpj.2024.05.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
In a recent study, Garner et al. investigated diffusion in the cytoplasm of fission yeasts, revealing vast heterogeneity in intracellular viscosity. Their conclusion was based on a combination of single-particle-tracking experiments and Brownian dynamics simulations. However, in their simulations, the diffusivity gradient term has been neglected-an assumption common in some biophysical applications but unjustified in this particular case due to spatial variations in diffusivity. Here, we aim to comment on the importance of the diffusivity gradient term and the physical consequences of not including it. We also demonstrate that omitting this term likely leads to overestimating fission yeast intracellular viscosity variance and underestimating its mean. Additionally, we propose modifications to the simulations to incorporate the gradient term.
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Affiliation(s)
- Tomasz Skóra
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah.
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2
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Waszkiewicz R, Michaś A, Białobrzewski MK, Klepka BP, Cieplak-Rotowska MK, Staszałek Z, Cichocki B, Lisicki M, Szymczak P, Niedzwiecka A. Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation. J Phys Chem Lett 2024; 15:5024-5033. [PMID: 38696815 PMCID: PMC11103702 DOI: 10.1021/acs.jpclett.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024]
Abstract
The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.
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Affiliation(s)
- Radost Waszkiewicz
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Agnieszka Michaś
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Michał K. Białobrzewski
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Barbara P. Klepka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | | | - Zuzanna Staszałek
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Bogdan Cichocki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Maciej Lisicki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Piotr Szymczak
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Anna Niedzwiecka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
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3
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Długosz M, Cichocki B, Szymczak P. First coarse grain then scale: How to estimate diffusion coefficients of confined molecules. J Chem Phys 2023; 159:214101. [PMID: 38038202 DOI: 10.1063/5.0175501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
An approach for approximating position and orientation dependent translational and rotational diffusion coefficients of rigid molecules of any shape suspended in a viscous fluid under geometric confinement is proposed. It is an extension of the previously developed scheme for evaluating near-wall diffusion of macromolecules, now applied to any geometry of boundaries. The method relies on shape based coarse-graining combined with scaling of mobility matrix components by factors derived based on energy dissipation arguments for Stokes flows. Tests performed for a capsule shaped molecule and its coarse-grained model, a dumbbell, for three different types of boundaries (a sphere, an open cylinder, and two parallel planes) are described. An almost perfect agreement between mobility functions of the detailed and coarse-grained models, even close to boundary surfaces, is obtained. The proposed method can be used to simplify hydrodynamic calculations and reduce errors introduced due to coarse-graining of molecular shapes.
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Affiliation(s)
- Maciej Długosz
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
| | - Bogdan Cichocki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
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4
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Lee JG, Thome CP, Cruse ZA, Ganguly A, Gupta A, Shields CW. Magnetically locked Janus particle clusters with orientation-dependent motion in AC electric fields. NANOSCALE 2023; 15:16268-16276. [PMID: 37800377 PMCID: PMC10598768 DOI: 10.1039/d3nr03744d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Active particles, or micromotors, locally dissipate energy to drive locomotion at small length scales. The type of trajectory is generally fixed and dictated by the geometry and composition of the particle, which can be challenging to tune using conventional fabrication procedures. Here, we report a simple, bottom-up method to magnetically assemble gold-coated polystyrene Janus particles into "locked" clusters that display diverse trajectories when stimulated by AC electric fields. The orientation of particles within each cluster gives rise to distinct modes of locomotion, including translational, rotational, trochoidal, helical, and orbital. We model this system using a simplified rigid beads model and demonstrate qualitative agreement between the predicted and experimentally observed cluster trajectories. Overall, this system provides a facile means to scalably create micromotors with a range of well-defined motions from discrete building blocks.
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Affiliation(s)
- Jin Gyun Lee
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - Cooper P Thome
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - Zoe A Cruse
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - Arkava Ganguly
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - Ankur Gupta
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - C Wyatt Shields
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA.
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5
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Brookes EH, Rocco M. Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:225-232. [PMID: 36853343 PMCID: PMC10460822 DOI: 10.1007/s00249-023-01636-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/07/2023] [Indexed: 06/13/2023]
Abstract
At the 25th International Analytical Ultracentrifugation Workshop and Symposium, we described the recent implementation of the UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF) database, containing hydrodynamic, structural, CD calculations, and other ancillary information, performed on the entire AF v2 database of predicted protein structures, containing more than 1,000,000 entries. The scope of the US-SOMO-AF database was that of providing direct access to pre-calculated physicochemical parameters for rapid assessment against their experimentally determined counterparts to test the compatibility in solution of predicted AlphaFold structures. In the meantime, the AlphaFold consortium has extended its database of predicted structures to an astonishing > 200 million entries, making it quite impractical for their coverage in the US-SOMO-AF database. Therefore, we have created the US-SOMO-Web site, allowing the rapid calculations of all the properties, as present in the US-SOMO-AF database, on user-supplied PDB and mmCIF structures, as well as allowing direct processing of the latest AlphaFold models. Major features on the website are described, along with current limitations and potential future developments.
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Affiliation(s)
- Emre H Brookes
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, 59812, USA.
| | - Mattia Rocco
- Retired, Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132, Genova, Italy
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6
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Muñiz‐Chicharro A, Votapka LW, Amaro RE, Wade RC. Brownian dynamics simulations of biomolecular diffusional association processes. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Abraham Muñiz‐Chicharro
- Molecular and Cellular Modeling Group Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
- Faculty of Biosciences and Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp) Heidelberg University Heidelberg Germany
| | | | | | - Rebecca C. Wade
- Molecular and Cellular Modeling Group Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
- Center for Molecular Biology (ZMBH), DKFZ‐ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University Heidelberg Germany
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7
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Długosz M, Cichocki B, Szymczak P. Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. Phys Rev E 2022; 106:014407. [PMID: 35974550 DOI: 10.1103/physreve.106.014407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
We developed a computationally efficient approach to approximate near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. The proposed method relies on extremum principles for Stokes flows produced by the motion of rigid bodies. In the presence of the wall, the rate of energy dissipation is decreased relative to the unbounded fluid. In our approach, the position- and orientation-dependent mobility matrix of a body suspended near a no-slip plane is calculated numerically using a coarse-grained molecular model and the Rotne-Prager-Yamakawa description of hydrodynamics. Effects of the boundary are accounted for via Blake's image construction. The matrix components are scaled using ratios of the corresponding bulk values evaluated for the detailed representation of the molecule and its coarse-grained model, leading to accurate values of the near-wall diffusion coefficients. We assess the performance of the approach for two biomolecules at different levels of coarse-graining.
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Affiliation(s)
- Maciej Długosz
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
| | - Bogdan Cichocki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Pasteura 5, Poland
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8
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Karpińska A, Pilz M, Buczkowska J, Żuk PJ, Kucharska K, Magiera G, Kwapiszewska K, Hołyst R. Quantitative analysis of biochemical processes in living cells at a single-molecule level: a case of olaparib-PARP1 (DNA repair protein) interactions. Analyst 2021; 146:7131-7143. [PMID: 34726203 DOI: 10.1039/d1an01769a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Quantitative description of biochemical processes inside living cells and at single-molecule levels remains a challenge at the forefront of modern instrumentation and spectroscopy. This paper demonstrates such single-cell, single-molecule analyses performed to study the mechanism of action of olaparib - an up-to-date, FDA-approved drug for germline-BRCA mutated metastatic breast cancer. We characterized complexes formed with PARPi-FL - fluorescent analog of olaparib in vitro and in cancer cells using the advanced fluorescent-based method: Fluorescence Correlation Spectroscopy (FCS) combined with a length-scale dependent cytoplasmic/nucleoplasmic viscosity model. We determined in vitro olaparib-PARP1 equilibrium constant (6.06 × 108 mol L-1). In the cell nucleus, we distinguished three states of olaparib: freely diffusing drug (24%), olaparib-PARP1 complex (50%), and olaparib-PARP1-RNA complex (26%). We show olaparib accumulation in 3D spheroids, where intracellular concentration is twofold higher than in 2D cells. Moreover, olaparib concentration was tenfold higher (506 nmol L-1vs. 57 nmol L-1) in cervical cancer (BRCA1 high abundance) than in breast cancer cells (BRCA1 low abundance) but with a lower toxic effect. Thus we confirmed that the amount of BRCA1 protein in the cells is a better predictor of the therapeutic effect of olaparib than its penetration into cancer tissue. Our single-molecule and single-cell approach give a new perspective of drug action in living cells. FCS provides a detailed in vivo insight, valuable in drug development and targeting.
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Affiliation(s)
- Aneta Karpińska
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Marta Pilz
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Joanna Buczkowska
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Paweł J Żuk
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland. .,Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - Karolina Kucharska
- Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Gaweł Magiera
- Department of Medicine, Poznan University of Medical Sciences, 60-356, Poznan, Poland
| | - Karina Kwapiszewska
- 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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9
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Cichocki B, Szymczak P, Żuk PJ. Generalized Rotne-Prager-Yamakawa approximation for Brownian dynamics in shear flow in bounded, unbounded, and periodic domains. J Chem Phys 2021; 154:124905. [PMID: 33810690 DOI: 10.1063/5.0030175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Inclusion of hydrodynamic interactions is essential for a quantitatively accurate Brownian dynamics simulation of colloidal suspensions or polymer solutions. We use the generalized Rotne-Prager-Yamakawa (GRPY) approximation, which takes into account all long-ranged terms in the hydrodynamic interactions, to derive the complete set of hydrodynamic matrices in different geometries: unbounded space, periodic boundary conditions of Lees-Edwards type, and vicinity of a free surface. The construction is carried out both for non-overlapping as well as for overlapping particles. We include the dipolar degrees of freedom, which allows one to use this formalism to simulate the dynamics of suspensions in a shear flow and to study the evolution of their rheological properties. Finally, we provide an open-source numerical package, which implements the GRPY algorithm in Lees-Edwards periodic boundary conditions.
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Affiliation(s)
- Bogdan Cichocki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Paweł J Żuk
- Department of Biosystems and Soft Matter, Institute of Fundamental and Technological Research, Polish Academy of Sciences, Pawinskiego 5B, 02-106 Warsaw, Poland
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10
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Waszkiewicz R, Lisicki M. Hydrodynamic effects in the capture of rod-like molecules by a nanopore. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:104005. [PMID: 33285536 DOI: 10.1088/1361-648x/abd11b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the approach of biomolecules to a nanopore, it is essential to capture the effects of hydrodynamic anisotropy of the molecules and the near-wall hydrodynamic interactions which hinder their diffusion. We present a detailed theoretical analysis of the behaviour of a rod-like molecule attracted electrostatically by a charged nanopore. We first estimate the time scales corresponding to Brownian and electrostatic translations and reorientation. We find that Brownian motion becomes negligible at distances within the pore capture radius, and numerically determine the trajectories of the nano-rod in this region to explore the effects of anisotropic mobility. This allows us to determine the range of directions from the pore in which hydrodynamic interactions with the boundary shape the approach dynamics and need to be accounted for in detailed modelling.
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Affiliation(s)
- Radost Waszkiewicz
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Poland
| | - Maciej Lisicki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Poland
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García de la Torre J, Hernández Cifre J. Hydrodynamic Properties of Biomacromolecules and Macromolecular Complexes: Concepts and Methods. A Tutorial Mini-review. J Mol Biol 2020; 432:2930-2948. [DOI: 10.1016/j.jmb.2019.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 01/08/2023]
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12
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Camp T, McLean M, Kato M, Cheruzel L, Sligar S. The hydrodynamic motion of Nanodiscs. Chem Phys Lipids 2019; 220:28-35. [PMID: 30802435 DOI: 10.1016/j.chemphyslip.2019.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 02/02/2023]
Abstract
We present a fluorescence-based methodology for monitoring the rotational dynamics of Nanodiscs. Nanodiscs are nano-scale lipid bilayers surrounded by a helical membrane scaffold protein (MSP) that have found considerable use in studying the interactions between membrane proteins and their lipid bilayer environment. Using a long-lifetime Ruthenium label covalently attached to the Nanodiscs, we find that Nanodiscs of increasing diameter, made by varying the number of helical repeats in the MSP, display increasing rotational correlation times. We also model our system using both analytical equations that describe rotating spheroids and numerical calculations performed on atomic models of Nanodiscs. Using these methods, we observe a linear relationship between the experimentally determined rotational correlation times and those calculated from both analytical equations and numerical solutions. This work sets the stage for accurate, label-free quantification of protein-lipid interactions at the membrane surface.
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Affiliation(s)
- Tyler Camp
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 314F Roger Adams Laboratory (MC-712), 600 S Mathews Ave, Urbana, IL, 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, 417 RAL (MC-712), 600 South Mathews Avenue, Urbana, IL, 61801, United States
| | - Mark McLean
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 417 RAL (MC-712), 600 South Mathews Avenue, Urbana, IL, 61801, United States
| | - Mallory Kato
- Department of Chemistry, San Jose State University, San Jose, CA, 95192-0101, United States
| | - Lionel Cheruzel
- Department of Chemistry, San Jose State University, San Jose, CA, 95192-0101, United States
| | - Stephen Sligar
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 314F Roger Adams Laboratory (MC-712), 600 S Mathews Ave, Urbana, IL, 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, 417 RAL (MC-712), 600 South Mathews Avenue, Urbana, IL, 61801, United States.
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