1
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Shrestha R, Carpenter TS, Van QN, Agamasu C, Tonelli M, Aydin F, Chen D, Gulten G, Glosli JN, López CA, Oppelstrup T, Neale C, Gnanakaran S, Gillette WK, Ingólfsson HI, Lightstone FC, Stephen AG, Streitz FH, Nissley DV, Turbyville TJ. Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane. Commun Biol 2024; 7:242. [PMID: 38418613 PMCID: PMC10902389 DOI: 10.1038/s42003-024-05916-0] [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] [Received: 07/10/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.
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Affiliation(s)
- Rebika Shrestha
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Que N Van
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Constance Agamasu
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Fikret Aydin
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - De Chen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Gulcin Gulten
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - James N Glosli
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Tomas Oppelstrup
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - William K Gillette
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Felice C Lightstone
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Andrew G Stephen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Frederick H Streitz
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Dwight V Nissley
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Thomas J Turbyville
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA.
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2
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Makkai G, Abraham IM, Barabas K, Godo S, Ernszt D, Kovacs T, Kovacs G, Szocs S, Janosi TZ. Maximum likelihood-based estimation of diffusion coefficient is quick and reliable method for analyzing estradiol actions on surface receptor movements. Front Neuroinform 2023; 17:1005936. [PMID: 36970656 PMCID: PMC10031098 DOI: 10.3389/fninf.2023.1005936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
The rapid effects of estradiol on membrane receptors are in the focus of the estradiol research field, however, the molecular mechanisms of these non-classical estradiol actions are poorly understood. Since the lateral diffusion of membrane receptors is an important indicator of their function, a deeper understanding of the underlying mechanisms of non-classical estradiol actions can be achieved by investigating receptor dynamics. Diffusion coefficient is a crucial and widely used parameter to characterize the movement of receptors in the cell membrane. The aim of this study was to investigate the differences between maximum likelihood-based estimation (MLE) and mean square displacement (MSD) based calculation of diffusion coefficients. In this work we applied both MSD and MLE to calculate diffusion coefficients. Single particle trajectories were extracted from simulation as well as from α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor tracking in live estradiol-treated differentiated PC12 (dPC12) cells. The comparison of the obtained diffusion coefficients revealed the superiority of MLE over the generally used MSD analysis. Our results suggest the use of the MLE of diffusion coefficients because as it has a better performance, especially for large localization errors or slow receptor movements.
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Affiliation(s)
- Geza Makkai
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Nano-Bio-Imaging Core Facility at the Szentágothai Research Centre of the University of Pécs, Pécs, Hungary
| | - Istvan M. Abraham
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Klaudia Barabas
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Soma Godo
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - David Ernszt
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Tamas Kovacs
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gergely Kovacs
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Szilard Szocs
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
| | - Tibor Z. Janosi
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Nano-Bio-Imaging Core Facility at the Szentágothai Research Centre of the University of Pécs, Pécs, Hungary
- *Correspondence: Tibor Z. Janosi,
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3
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López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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4
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Maris JJE, Rabouw FT, Weckhuysen BM, Meirer F. Classification-based motion analysis of single-molecule trajectories using DiffusionLab. Sci Rep 2022; 12:9595. [PMID: 35689015 PMCID: PMC9187757 DOI: 10.1038/s41598-022-13446-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022] Open
Abstract
Single-particle tracking is a powerful approach to study the motion of individual molecules and particles. It can uncover heterogeneities that are invisible to ensemble techniques, which places it uniquely among techniques to study mass transport. Analysis of the trajectories obtained with single-particle tracking in inorganic porous hosts is often challenging, because trajectories are short and/or motion is heterogeneous. We present the DiffusionLab software package for motion analysis of such challenging data sets. Trajectories are first classified into populations with similar characteristics to which the motion analysis is tailored in a second step. DiffusionLab provides tools to classify trajectories based on the motion type either with machine learning or manually. It also offers quantitative mean squared displacement analysis of the trajectories. The software can compute the diffusion constant for an individual trajectory if it is sufficiently long, or the average diffusion constant for multiple shorter trajectories. We demonstrate the DiffusionLab approach via the analysis of a simulated data set with motion types frequently observed in inorganic porous hosts, such as zeolites. The software package with graphical user interface and its documentation are freely available.
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Affiliation(s)
- J J Erik Maris
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Freddy T Rabouw
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CG, Utrecht, The Netherlands.,Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC, Utrecht, The Netherlands
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Florian Meirer
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CG, Utrecht, The Netherlands.
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5
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Gabriel L, Almeida H, Avelar M, Sarmento B, das Neves J. MPTHub: An Open-Source Software for Characterizing the Transport of Particles in Biorelevant Media. NANOMATERIALS 2022; 12:nano12111899. [PMID: 35683754 PMCID: PMC9182034 DOI: 10.3390/nano12111899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/04/2023]
Abstract
The study of particle transport in different environments plays an essential role in understanding interactions with humans and other living organisms. Importantly, obtained data can be directly used for multiple applications in fields such as fundamental biology, toxicology, or medicine. Particle movement in biorelevant media can be readily monitored using microscopy and converted into time-resolved trajectories using freely available tracking software. However, translation into tangible and meaningful parameters is time consuming and not always intuitive. We developed new software—MPTHub—as an open-access, standalone, user-friendly tool for the rapid and reliable analysis of particle trajectories extracted from video microscopy. The software was programmed using Python and allowed to import and analyze trajectory data, as well as to export relevant data such as individual and ensemble time-averaged mean square displacements and effective diffusivity, and anomalous transport exponent. Data processing was reliable, fast (total processing time of less than 10 s), and required minimal memory resources (up to a maximum of around 150 MB in random access memory). Demonstration of software applicability was conducted by studying the transport of different polystyrene nanoparticles (100–200 nm) in mucus surrogates. Overall, MPTHub represents a freely available software tool that can be used even by inexperienced users for studying the transport of particles in biorelevant media.
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Affiliation(s)
- Leandro Gabriel
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- FEUP—Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
| | - Helena Almeida
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Marta Avelar
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- FEUP—Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Bruno Sarmento
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- IUCS—Instituto Universitário de Ciências da Saúde, CESPU, 4585-116 Gandra, Portugal
| | - José das Neves
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (L.G.); (H.A.); (M.A.); (B.S.)
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- IUCS—Instituto Universitário de Ciências da Saúde, CESPU, 4585-116 Gandra, Portugal
- Correspondence: ; Tel.: +351-220-408-800
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6
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Shrestha R, Chen D, Frank P, Nissley DV, Turbyville TJ. Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes. iScience 2022; 25:103608. [PMID: 35106460 PMCID: PMC8786645 DOI: 10.1016/j.isci.2021.103608] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/30/2021] [Accepted: 12/08/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the spatiotemporal distribution and dynamics of RAS on the plasma membrane (PM) is the key for elucidating the molecular mechanisms of the RAS signaling pathway. Single particle tracking (SPT) experiments show that in cells, KRAS diffuses in at least three interchanging states on the cellular PM; however, KRAS remains monomeric and always shows homogeneous diffusion on artificial membranes. Here, we show for the first time on a supported lipid bilayer composed of heterogeneous lipid components that we can recapitulate the three-state diffusion of KRAS seen in cells. The use of a biologically relevant eight-lipid system opens a new frontier in the biophysical studies of RAS and other membrane associated proteins on a biomimetic system that recapitulates the complexity of a cellular PM. KRAS4b shows homogeneous diffusion on simple 2-lipids bilayer KRAS4b shows a cell-like, three-state diffusion on a complex 8-lipid bilayer Phase separation in lipids favors the multi-state diffusion of KRAS4b The complex lipid composition favors RAS nanoclustering irrespective of nucleotide state
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Affiliation(s)
- Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Peter Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
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7
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Plaza-Oliver M, Cano EL, Arroyo-Jimenez MM, Gámez M, Lozano-López MV, Santander-Ortega MJ. Taking Particle Tracking into Practice by Novel Software and Screening Approach: Case-Study of Oral Lipid Nanocarriers. Pharmaceutics 2021; 13:370. [PMID: 33802226 PMCID: PMC8001040 DOI: 10.3390/pharmaceutics13030370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
The success on the design of new oral nanocarriers greatly depends on the identification of the best physicochemical properties that would allow their diffusion across the mucus layer that protects the intestinal epithelium. In this context, particle tracking (PT) has arisen in the pharmaceutical field as an excellent tool to evaluate the diffusion of individual particles across the intestinal mucus. In PT, the trajectories of individual particles are characterized by the mean square displacement (MSD), which is used to calculate the coefficient of diffusion (D) and the anomalous diffusion parameter (α) as MSD=4Dτα. Unfortunately, there is no stablished criteria to evaluate the goodness-of-fit of the experimental data to the mathematical model. This work shows that the commonly used R2 parameter may lead to an overestimation of the diffusion capacity of oral nanocarriers. We propose a screening approach based on a combination of R2 with further statistical parameters. We have analyzed the effect of this approach to study the intestinal mucodiffusion of lipid oral nanocarriers, compared to the conventional screening approach. Last, we have developed software able to perform the whole PT analysis in a time-saving, user-friendly, and rational fashion.
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Affiliation(s)
- María Plaza-Oliver
- Cellular Neurobiology and Molecular Chemistry of the Central Nervous System Group, Faculty of Pharmacy, University of Castilla-La Mancha (UCLM), 02071 Albacete, Spain; (M.P.-O.); (M.M.A.-J.); (M.V.L.-L.)
- Regional Centre of Biomedical Research (CRIB), University of Castilla-La Mancha (UCLM), 02008 Albacete, Spain
| | - Emilio L. Cano
- Quantitative Methods and Socio-economic Development Group, Institute for Regional Development (IDR), University of Castilla-La Mancha (UCLM), 02006 Albacete, Spain;
- Data Science laboratory, Rey Juan Carlos University, 28933 Madrid, Spain
| | - María Mar Arroyo-Jimenez
- Cellular Neurobiology and Molecular Chemistry of the Central Nervous System Group, Faculty of Pharmacy, University of Castilla-La Mancha (UCLM), 02071 Albacete, Spain; (M.P.-O.); (M.M.A.-J.); (M.V.L.-L.)
- Regional Centre of Biomedical Research (CRIB), University of Castilla-La Mancha (UCLM), 02008 Albacete, Spain
| | - Matías Gámez
- Quantitative Methods and Socio-economic Development Group, Institute for Regional Development (IDR), University of Castilla-La Mancha (UCLM), 02006 Albacete, Spain;
| | - María Victoria Lozano-López
- Cellular Neurobiology and Molecular Chemistry of the Central Nervous System Group, Faculty of Pharmacy, University of Castilla-La Mancha (UCLM), 02071 Albacete, Spain; (M.P.-O.); (M.M.A.-J.); (M.V.L.-L.)
- Regional Centre of Biomedical Research (CRIB), University of Castilla-La Mancha (UCLM), 02008 Albacete, Spain
| | - Manuel J. Santander-Ortega
- Cellular Neurobiology and Molecular Chemistry of the Central Nervous System Group, Faculty of Pharmacy, University of Castilla-La Mancha (UCLM), 02071 Albacete, Spain; (M.P.-O.); (M.M.A.-J.); (M.V.L.-L.)
- Regional Centre of Biomedical Research (CRIB), University of Castilla-La Mancha (UCLM), 02008 Albacete, Spain
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8
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Koch S, Seinen AB, Kamel M, Kuckla D, Monzel C, Kedrov A, Driessen AJM. Single-molecule analysis of dynamics and interactions of the SecYEG translocon. FEBS J 2020; 288:2203-2221. [PMID: 33058437 DOI: 10.1111/febs.15596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/11/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022]
Abstract
Protein translocation and insertion into the bacterial cytoplasmic membrane are the essential processes mediated by the Sec machinery. The core machinery is composed of the membrane-embedded translocon SecYEG that interacts with the secretion-dedicated ATPase SecA and translating ribosomes. Despite the simplicity and the available structural insights on the system, diverse molecular mechanisms and functional dynamics have been proposed. Here, we employ total internal reflection fluorescence microscopy to study the oligomeric state and diffusion of SecYEG translocons in supported lipid bilayers at the single-molecule level. Silane-based coating ensured the mobility of lipids and reconstituted translocons within the bilayer. Brightness analysis suggested that approx. 70% of the translocons were monomeric. The translocons remained in a monomeric form upon ribosome binding, but partial oligomerization occurred in the presence of nucleotide-free SecA. Individual trajectories of SecYEG in the lipid bilayer revealed dynamic heterogeneity of diffusion, as translocons commonly switched between slow and fast mobility modes with corresponding diffusion coefficients of 0.03 and 0.7 µm2 ·s-1 . Interactions with SecA ATPase had a minor effect on the lateral mobility, while bound ribosome:nascent chain complexes substantially hindered the diffusion of single translocons. Notably, the mobility of the translocon:ribosome complexes was not affected by the solvent viscosity or macromolecular crowding modulated by Ficoll PM 70, so it was largely determined by interactions within the lipid bilayer and at the interface. We suggest that the complex mobility of SecYEG arises from the conformational dynamics of the translocon and protein:lipid interactions.
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Affiliation(s)
- Sabrina Koch
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Anne-Bart Seinen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Biophysics, AMOLF, Amsterdam, The Netherlands
| | - Michael Kamel
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Daniel Kuckla
- Experimental Medical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Germany
| | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
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9
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Goswami D, Chen D, Yang Y, Gudla PR, Columbus J, Worthy K, Rigby M, Wheeler M, Mukhopadhyay S, Powell K, Burgan W, Wall V, Esposito D, Simanshu DK, Lightstone FC, Nissley DV, McCormick F, Turbyville T. Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior. eLife 2020; 9:47654. [PMID: 31958057 PMCID: PMC7060043 DOI: 10.7554/elife.47654] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/02/2020] [Indexed: 01/16/2023] Open
Abstract
The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable region side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here, we characterize RAS in live human and mouse cells using single-molecule-tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein’s globular domain. To understand the altered mobility of an oncogenic KRAS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a detailed mechanism.
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Affiliation(s)
- Debanjan Goswami
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Yue Yang
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
| | - Prabhakar R Gudla
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - John Columbus
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Karen Worthy
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Megan Rigby
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Madeline Wheeler
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Suman Mukhopadhyay
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Katie Powell
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - William Burgan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Vanessa Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, San Francisco, United States
| | - Thomas Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
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10
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TCR-pMHC bond conformation controls TCR ligand discrimination. Cell Mol Immunol 2019; 17:203-217. [PMID: 31530899 PMCID: PMC7052167 DOI: 10.1038/s41423-019-0273-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 11/15/2022] Open
Abstract
A major unanswered question is how a TCR discriminates between foreign and self-peptides presented on the APC surface. Here, we used in situ fluorescence resonance energy transfer (FRET) to measure the distances of single TCR–pMHC bonds and the conformations of individual TCR–CD3ζ receptors at the membranes of live primary T cells. We found that a TCR discriminates between closely related peptides by forming single TCR–pMHC bonds with different conformations, and the most potent pMHC forms the shortest bond. The bond conformation is an intrinsic property that is independent of the binding affinity and kinetics, TCR microcluster formation, and CD4 binding. The bond conformation dictates the degree of CD3ζ dissociation from the inner leaflet of the plasma membrane via a positive calcium signaling feedback loop to precisely control the accessibility of CD3ζ ITAMs for phosphorylation. Our data revealed the mechanism by which a TCR deciphers the structural differences among peptides via the TCR–pMHC bond conformation.
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11
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Floc'h K, Lacroix F, Servant P, Wong YS, Kleman JP, Bourgeois D, Timmins J. Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans. Nat Commun 2019; 10:3815. [PMID: 31444361 PMCID: PMC6707255 DOI: 10.1038/s41467-019-11725-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Our knowledge of bacterial nucleoids originates mostly from studies of rod- or crescent-shaped bacteria. Here we reveal that Deinococcus radiodurans, a relatively large spherical bacterium with a multipartite genome, constitutes a valuable system for the study of the nucleoid in cocci. Using advanced microscopy, we show that D. radiodurans undergoes coordinated morphological changes at both the cellular and nucleoid level as it progresses through its cell cycle. The nucleoid is highly condensed, but also surprisingly dynamic, adopting multiple configurations and presenting an unusual arrangement in which oriC loci are radially distributed around clustered ter sites maintained at the cell centre. Single-particle tracking and fluorescence recovery after photobleaching studies of the histone-like HU protein suggest that its loose binding to DNA may contribute to this remarkable plasticity. These findings demonstrate that nucleoid organization is complex and tightly coupled to cell cycle progression in this organism.
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Affiliation(s)
- Kevin Floc'h
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | | | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Yung-Sing Wong
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
| | | | | | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
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12
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Zhu Q, Smith EA. Diaphanous-1 affects the nanoscale clustering and lateral diffusion of receptor for advanced glycation endproducts (RAGE). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:43-49. [PMID: 30401627 DOI: 10.1016/j.bbamem.2018.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 12/22/2022]
Abstract
The interactions between the cytoplasmic protein diaphanous-1 (Diaph1) and the receptor for advanced glycation endproducts (RAGE) drive the negative consequences of RAGE signaling in several disease processes. Reported in this work is how Diaph1 affects the nanoscale clustering and diffusion of RAGE measured using super-resolution stochastic optical reconstruction microscopy (STORM) and single particle tracking (SPT). Altering the Diaph1 binding site has a different impact on RAGE diffusion compared to when Diaph1 expression is reduced in HEK293 cells. In cells with reduced Diaph1 expression (RAGE-Diaph1-/-), the average RAGE diffusion coefficient is increased by 35%. RAGE diffusion is known to be influenced by the dynamics of the actin cytoskeleton. Actin labeling shows that a reduced Diaph1 expression leads to cells with reduced filopodia density and length. In contrast, when two RAGE amino acids that interact with Diaph1 are mutated (RAGERQ/AA), the average RAGE diffusion coefficient is decreased by 16%. Since RAGE diffusion is slowed when the interaction between Diaph1 and RAGE is disrupted, the interaction of the two proteins results in faster RAGE diffusion. In both RAGERQ/AA and RAGE-Diaph1-/- cells the number and size of RAGE clusters are decreased compared to cells expressing RAGE and native concentrations of Diaph1. This work shows that Diaph1 has a role in affecting RAGE clusters and diffusion.
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Affiliation(s)
- Qiaochu Zhu
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States
| | - Emily A Smith
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States.
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13
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Floc'h K, Lacroix F, Barbieri L, Servant P, Galland R, Butler C, Sibarita JB, Bourgeois D, Timmins J. Bacterial cell wall nanoimaging by autoblinking microscopy. Sci Rep 2018; 8:14038. [PMID: 30232348 PMCID: PMC6145920 DOI: 10.1038/s41598-018-32335-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/06/2018] [Indexed: 01/02/2023] Open
Abstract
Spurious blinking fluorescent spots are often seen in bacteria during single-molecule localization microscopy experiments. Although this 'autoblinking' phenomenon is widespread, its origin remains unclear. In Deinococcus strains, we observed particularly strong autoblinking at the periphery of the bacteria, facilitating its comprehensive characterization. A systematic evaluation of the contributions of different components of the sample environment to autoblinking levels and the in-depth analysis of the photophysical properties of autoblinking molecules indicate that the phenomenon results from transient binding of fluorophores originating mostly from the growth medium to the bacterial cell wall, which produces single-molecule fluorescence through a Point Accumulation for Imaging in Nanoscale Topography (PAINT) mechanism. Our data suggest that the autoblinking molecules preferentially bind to the plasma membrane of bacterial cells. Autoblinking microscopy was used to acquire nanoscale images of live, unlabeled D. radiodurans and could be combined with PALM imaging of PAmCherry-labeled bacteria in two-color experiments. Autoblinking-based super-resolved images provided insight into the formation of septa in dividing bacteria and revealed heterogeneities in the distribution and dynamics of autoblinking molecules within the cell wall.
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Affiliation(s)
- Kevin Floc'h
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | | | | | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Remi Galland
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | - Corey Butler
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | - Jean-Baptiste Sibarita
- Institut Interdisciplinaire de Neurosciences, University of Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique, UMR5297, Bordeaux, France
| | | | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
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14
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Sharma KK, Marzinek JK, Tantirimudalige SN, Bond PJ, Wohland T. Single-molecule studies of flavivirus envelope dynamics: Experiment and computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:38-51. [PMID: 30223001 DOI: 10.1016/j.pbiomolbio.2018.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022]
Abstract
Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that are employed to investigate flaviviruses. In particular, we review how (i) time-resolved Förster resonance energy transfer (trFRET) was applied to probe dengue envelope conformations; (ii) FRET-fluorescence correlation spectroscopy to investigate dengue envelope intrinsic dynamics and (iii) single particle tracking to follow the path of dengue viruses in cells. We also discuss how such methods may be supported by molecular dynamics (MD) simulations over a range of spatio-temporal scales, to provide complementary data on the structure and dynamics of flaviviral systems. We describe recent improvements in multiscale MD approaches that allowed the simulation of dengue particle envelopes in near-atomic resolution. We hope this review is an incentive for setting up and applying similar single-molecule studies and combine them with MD simulations to investigate structural dynamics of entire flavivirus particles over the nanosecond-to-millisecond time-scale and follow viruses during infection in cells over milliseconds to minutes.
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Affiliation(s)
- Kamal Kant Sharma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Jan K Marzinek
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Sarala Neomi Tantirimudalige
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.
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15
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Yousefpour A, Modarress H, Goharpey F, Amjad-Iranagh S. Combination of anti-hypertensive drugs: a molecular dynamics simulation study. J Mol Model 2017; 23:158. [DOI: 10.1007/s00894-017-3333-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/27/2017] [Indexed: 01/03/2023]
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16
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Shi X, Kohram M, Zhuang X, Smith AW. Interactions and Translational Dynamics of Phosphatidylinositol Bisphosphate (PIP2) Lipids in Asymmetric Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1732-1741. [PMID: 26829708 DOI: 10.1021/acs.langmuir.5b02814] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phosphatidylinositol phosphate (PIP) lipids are critical to many cell signaling pathways, in part by acting as molecular beacons that recruit peripheral membrane proteins to specific locations within the plasma membrane. Understanding the biophysics of PIP-protein interactions is critical to developing a chemically detailed model of cell communication. Resolving such interactions is challenging, even in model membrane systems, because of the difficulty in preparing PIP-containing membranes with high fluidity and integrity. Here we report on a simple, vesicle-based protocol for preparing asymmetric supported lipid bilayers in which fluorescent PIP lipid analogues are found only on the top leaflet of the supported membrane facing the bulk solution. With this asymmetric distribution of lipids between the leaflets, the fluorescent signal from the PIP lipid analogue reports directly on interactions between the peripheral molecules and the top leaflet of the membrane. Asymmetric PIP-containing bilayers are an ideal platform to investigate the interaction of PIP with peripheral membrane proteins using fluorescence-based imaging approaches. We demonstrate their usefulness here with a combined fluorescence correlation spectroscopy and single particle tracking study of the interaction between PIP2 lipids and a polycationic polymer, quaternized polyvinylpyridine (QPVP). With this approach we are able to quantify the microscopic features of the mobility coupling between PIP2 lipids and polybasic QPVP. With single particle tracking we observe individual PIP2 lipids switch from Brownian to intermittent motion as they become transiently trapped by QPVP.
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Affiliation(s)
| | | | - Xiaodong Zhuang
- Institute of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , 315 Jiangong Building, 800 Dongchuan Road, Shanghai 200240, China
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17
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Chew SC, Rice SA, Kjelleberg S, Yang L. In Situ Mapping of the Mechanical Properties of Biofilms by Particle-tracking Microrheology. J Vis Exp 2015:e53093. [PMID: 26709625 PMCID: PMC4692780 DOI: 10.3791/53093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Bacterial cells are able to form surface-attached biofilm communities known as biofilms by encasing themselves in extracellular polymeric substances (EPS). The EPS serves as a physical and protective scaffold that houses the bacterial cells and consists of a variety of materials that includes proteins, exopolysaccharides and DNA. The composition of the EPS may change, which remodels the mechanic properties of the biofilm to further develop or support alternative biofilm structures, such as streamers, as a response to environmental cues. Despite this, there are little quantitative descriptions on how EPS components contribute to the mechanical properties and function of biofilms. Rheology, the study of the flow of matter, is of particular relevance to biofilms as many biofilms grow in flow conditions and are constantly exposed to shear stress. It also provides measurement and insight on the spreading of the biofilm on a surface. Here, particle-tracking microrheology is used to examine the viscoelasticity and effective crosslinking roles of different matrix components in various parts of the biofilm during development. This approach allows researchers to measure mechanic properties of biofilms at the micro-scale, which might provide useful information for controlling and engineering biofilms.
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Affiliation(s)
- Su C Chew
- Interdisciplinary Graduate School, Nanyang Technological University; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University
| | - Scott A Rice
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University; School of Biological Sciences, Nanyang Technological University; Centre for Marine Bio-Innovation, University of New South Wales; School of Biological, Earth and Environmental Sciences, University of New South Wales
| | - Staffan Kjelleberg
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University; School of Biological Sciences, Nanyang Technological University; Centre for Marine Bio-Innovation, University of New South Wales; School of Biotechnology and Biomolecular Sciences Sciences, University of New South Wales
| | - Liang Yang
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University; School of Biological Sciences, Nanyang Technological University;
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18
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Hinks J, Wang Y, Matysik A, Kraut R, Kjelleberg S, Mu Y, Bazan GC, Wuertz S, Seviour T. Increased Microbial Butanol Tolerance by Exogenous Membrane Insertion Molecules. CHEMSUSCHEM 2015; 8:3718-3726. [PMID: 26404512 DOI: 10.1002/cssc.201500194] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/13/2015] [Indexed: 06/05/2023]
Abstract
Butanol is an ideal biofuel, although poor titers lead to high recovery costs by distillation. Fluidization of microbial membranes by butanol is one of the major factors limiting titers in butanol-producing bioprocesses. Starting with the hypothesis that certain membrane insertion molecules would stabilize the lipid bilayer in the presence of butanol, we applied a combination of in vivo and in vitro techniques within an in silico framework to describe a new approach to achieve solvent tolerance in bacteria. Single-molecule tracking of a model supported bilayer showed that COE1-5C, a five-ringed oligo-polyphenylenevinylene conjugated oligoelectrolyte (COE), reduced the diffusion rate of phospholipids in a microbially derived lipid bilayer to a greater extent than three-ringed and four-ringed COEs. Furthermore, COE1-5C treatment increased the specific growth rate of E. coli K12 relative to a control at inhibitory butanol concentrations. Consequently, to confer butanol tolerance to microbes by exogenous means is complementary to genetic modification of strains in industrial bioprocesses, extends the physiological range of microbes to match favorable bioprocess conditions, and is amenable with complex and undefined microbial consortia for biobutanol production. Molecular dynamics simulations indicated that the π-conjugated aromatic backbone of COE1-5C likely acts as a hydrophobic tether for glycerophospholipid acyl chains by enhancing bilayer integrity in the presence of high butanol concentrations, which thereby counters membrane fluidization. COE1-5C-mitigated E. coli K12 membrane depolarization by butanol is consistent with the hypothesis that improved growth rates in the presence of butanol are a consequence of improved bilayer stability.
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Affiliation(s)
- Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore.
| | - Yaofeng Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Artur Matysik
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Rachel Kraut
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- Centre for Marine BioInnovation and School of Biotechnology and Bimolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Guillermo C Bazan
- Department of Chemistry & Biochemistry and Materials, Center for Polymers and Organic Solids, University of California, Santa Barbara, California, 93106, USA
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
- Department of Civil and Environmental Engineering, University of California, Davis, California, 95616, USA
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore.
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19
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Fluorescence methods for analysis of interactions between Ca(2+) signaling, lysosomes, and endoplasmic reticulum. Methods Cell Biol 2015. [PMID: 25665449 DOI: 10.1016/bs.mcb.2014.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The endoplasmic reticulum (ER) is both the major source of intracellular Ca(2+) for cell signaling and the organelle that forms the most extensive contacts with the plasma membrane and other organelles. Lysosomes fulfill important roles in degrading cellular materials and in cholesterol handling, but they also contribute to Ca(2+) signaling by both releasing and sequestering Ca(2+). Interactions between ER and other Ca(2+)-transporting membranes, notably mitochondria and the plasma membrane, often occur at sites where the two membranes are closely apposed, allowing local Ca(2+) signaling between them. These interactions are often facilitated by scaffold proteins. Recent evidence suggests similar local interactions between ER and lysosomes. We describe simple fluorescence-based methods that allow the interplay between Ca(2+) signals, the ER, and lysosomes to be examined.
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20
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Matysik A, Kraut RS. Preparation of mica supported lipid bilayers for high resolution optical microscopy imaging. J Vis Exp 2014. [PMID: 24961277 DOI: 10.3791/52054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Supported lipid bilayers (SLBs) are widely used as a model for studying membrane properties (phase separation, clustering, dynamics) and its interaction with other compounds, such as drugs or peptides. However SLB characteristics differ depending on the support used. Commonly used techniques for SLB imaging and measurements are single molecule fluorescence microscopy, FCS and atomic force microscopy (AFM). Because most optical imaging studies are carried out on a glass support, while AFM requires an extremely flat surface (generally mica), results from these techniques cannot be compared directly, since the charge and smoothness properties of these materials strongly influence diffusion. Unfortunately, the high level of manual dexterity required for the cutting and gluing thin slices of mica to the glass slide presents a hurdle to routine use of mica for SLB preparation. Although this would be the method of choice, such prepared mica surfaces often end up being uneven (wavy) and difficult to image, especially with small working distance, high numerical aperture lenses. Here we present a simple and reproducible method for preparing thin, flat mica surfaces for lipid vesicle deposition and SLB preparation. Additionally, our custom made chamber requires only very small volumes of vesicles for SLB formation. The overall procedure results in the efficient, simple and inexpensive production of high quality lipid bilayer surfaces that are directly comparable to those used in AFM studies.
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Affiliation(s)
- Artur Matysik
- School of Biological Sciences, Nanyang Technological University;
| | - Rachel S Kraut
- School of Biological Sciences, Nanyang Technological University
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