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Kalinichenko L, Kornhuber J, Sinning S, Haase J, Müller CP. Serotonin Signaling through Lipid Membranes. ACS Chem Neurosci 2024; 15:1298-1320. [PMID: 38499042 PMCID: PMC10995955 DOI: 10.1021/acschemneuro.3c00823] [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: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Serotonin (5-HT) is a vital modulatory neurotransmitter responsible for regulating most behaviors in the brain. An inefficient 5-HT synaptic function is often linked to various mental disorders. Primarily, membrane proteins controlling the expression and activity of 5-HT synthesis, storage, release, receptor activation, and inactivation are critical to 5-HT signaling in synaptic and extra-synaptic sites. Moreover, these signals represent information transmission across membranes. Although the lipid membrane environment is often viewed as fairly stable, emerging research suggests significant functional lipid-protein interactions with many synaptic 5-HT proteins. These protein-lipid interactions extend to almost all the primary lipid classes that form the plasma membrane. Collectively, these lipid classes and lipid-protein interactions affect 5-HT synaptic efficacy at the synapse. The highly dynamic lipid composition of synaptic membranes suggests that these lipids and their interactions with proteins may contribute to the plasticity of the 5-HT synapse. Therefore, this broader protein-lipid model of the 5-HT synapse necessitates a reconsideration of 5-HT's role in various associated mental disorders.
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Affiliation(s)
- Liubov
S. Kalinichenko
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Johannes Kornhuber
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Steffen Sinning
- Department
of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Jana Haase
- School
of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Christian P. Müller
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
- Institute
of Psychopharmacology, Central Institute of Mental Health, Medical
Faculty Mannheim, Heidelberg University, 69047, Mannheim, Germany
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2
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Li L, Gao J, Milewski Ł, Hu J, Różycki B. Lattice-based mesoscale simulations and mean-field theory of cell membrane adhesion. Methods Enzymol 2024; 701:425-455. [PMID: 39025578 DOI: 10.1016/bs.mie.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Adhesion of cell membranes involves multi-scale phenomena, ranging from specific molecular binding at Angstrom scale all the way up to membrane deformations and phase separation at micrometer scale. Consequently, theory and simulations of cell membrane adhesion require multi-scale modeling and suitable approximations that capture the essential physics of these phenomena. Here, we present a mesoscale model for membrane adhesion which we have employed in a series of our recent studies. This model quantifies, in particular, how nanoscale lipid clusters physically affect and respond to the intercellular receptor-ligand binding that mediates membrane adhesion. The goal of this Chapter is to present all details and subtleties of the mean-field theory and Monte Carlo simulations of this mesoscale model, which can be used to further explore physical phenomena related to cell membrane adhesion.
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Affiliation(s)
- Long Li
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China; State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jie Gao
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Łukasz Milewski
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China.
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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3
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Bernard C, Carotenuto AR, Pugno NM, Fraldi M, Deseri L. Modelling lipid rafts formation through chemo-mechanical interplay triggered by receptor-ligand binding. Biomech Model Mechanobiol 2024; 23:485-505. [PMID: 38060155 PMCID: PMC10963483 DOI: 10.1007/s10237-023-01787-2] [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: 07/28/2023] [Accepted: 10/21/2023] [Indexed: 12/08/2023]
Abstract
Cell membranes, mediator of many biological mechanisms from adhesion and metabolism up to mutation and infection, are highly dynamic and heterogeneous environments exhibiting a strong coupling between biochemical events and structural re-organisation. This involves conformational changes induced, at lower scales, by lipid order transitions and by the micro-mechanical interplay of lipids with transmembrane proteins and molecular diffusion. Particular attention is focused on lipid rafts, ordered lipid microdomains rich of signalling proteins, that co-localise to enhance substance trafficking and activate different intracellular biochemical pathways. In this framework, the theoretical modelling of the dynamic clustering of lipid rafts implies a full multiphysics coupling between the kinetics of phase changes and the mechanical work performed by transmembrane proteins on lipids, involving the bilayer elasticity. This mechanism produces complex interspecific dynamics in which membrane stresses and chemical potentials do compete by determining different morphological arrangements, alteration in diffusive walkways and coalescence phenomena, with a consequent influence on both signalling potential and intracellular processes. Therefore, after identifying the leading chemo-mechanical interactions, the present work investigates from a modelling perspective the spatio-temporal evolution of raft domains to theoretically explain co-localisation and synergy between proteins' activation and raft formation, by coupling diffusive and mechanical phenomena to observe different morphological patterns and clustering of ordered lipids. This could help to gain new insights into the remodelling of cell membranes and could potentially suggest mechanically based strategies to control their selectivity, by orienting intracellular functions and mechanotransduction.
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Affiliation(s)
- Chiara Bernard
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy
| | - Angelo Rosario Carotenuto
- Department of Structures for Engineering and Architecture, University of Naples "Federico II", Naples, Italy
- Laboratory of Integrated Mechanics and Imaging for Testing and Simulation (LIMITS), University of Naples "Federico II", Naples, Italy
| | - Nicola Maria Pugno
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy
- Laboratory for Bioinspired, Bionic, Nano, Meta Materials and Mechanics, University of Trento, Trento, Italy
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Massimiliano Fraldi
- Department of Structures for Engineering and Architecture, University of Naples "Federico II", Naples, Italy
- Laboratory of Integrated Mechanics and Imaging for Testing and Simulation (LIMITS), University of Naples "Federico II", Naples, Italy
- Département de Physique, LPENS, École Normale Supérieure-PSL, Paris, France
| | - Luca Deseri
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy.
- Department of Mechanical Engineering and Material Sciences, MEMS-SSoE, University of Pittsburgh, Pittsburgh, USA.
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, USA.
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, USA.
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4
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Niu Y, Chen SJ, Klauda JB. Simulations of naïve and KLA-activated macrophage plasma membrane models. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184242. [PMID: 37866689 DOI: 10.1016/j.bbamem.2023.184242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Macrophages (MAs), which play vital roles in human immune responses and lipid metabolisms, are implicated in the development and progression of atherosclerosis, a major contributor to cardiovascular diseases. Specifically, the abnormal lipid metabolism of oxidized low-density lipids (oxLDLs) in MAs is believed to be a crucial factor. However, the precise mechanism by which the MA membrane contributes to this altered lipid metabolism remains unclear. Lipidomic studies have revealed significant differences in membrane composition between various MA phenotypes. This study serves to provide and characterize complex realistic computational models for naïve (M0) and Kdo2-lipid A-activated (M1) state MA. Analyses of surface area per lipid (SA/lip), area compressibility modulus (KA), carbon‑hydrogen order parameter (SCH), electron density profile (EDP), tilt angles, two-dimension radial distribution functions (2D RDFs), mean squared displacement (MSD), hydrogen bonds (H-bonds), lipid clustering, and lipid wobble were conducted for both models. Results indicate that the M1 state MA membrane is more tightly packed, with increased chain order across lipid species, and forms PSM-DOPG-CHOL and PSM-SLPC-CHOL clusters. Importantly, the bilayer thicknesses reported for the models are in good agreement with experimental data for the thicknesses of transmembrane regions for MA integral proteins. These findings validate the described models as physiologically accurate for future computational studies of MA membranes and their residing proteins.
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Affiliation(s)
- Yueqi Niu
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Si Jia Chen
- Medical Scientist Training Program, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, MD 20742, USA.
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5
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Sphingolipid control of cognitive functions in health and disease. Prog Lipid Res 2022; 86:101162. [DOI: 10.1016/j.plipres.2022.101162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 12/14/2022]
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Park S, Kim J, Choi J, Lee C, Lee W, Park S, Park Z, Baek J, Nam J. Lipid raft-disrupting miltefosine preferentially induces the death of colorectal cancer stem-like cells. Clin Transl Med 2021; 11:e552. [PMID: 34841679 PMCID: PMC8567043 DOI: 10.1002/ctm2.552] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Lipid rafts (LRs), cholesterol-enriched microdomains on cell membranes, are increasingly viewed as signalling platforms governing critical facets of cancer progression. The phenotype of cancer stem-like cells (CSCs) presents significant hurdles for successful cancer treatment, and the expression of several CSC markers is associated with LR integrity. However, LR implications in CSCs remain unclear. METHODS This study evaluated the biological and molecular functions of LRs in colorectal cancer (CRC) by using an LR-disrupting alkylphospholipid (APL) drug, miltefosine. The mechanistic role of miltefosine in CSC inhibition was examined through normal or tumour intestinal mouse organoid, human CRC cell, CRC xenograft and miltefosine treatment gene expression profile analyses. RESULTS Miltefosine suppresses CSC populations and their self-renewal activities in CRC cells, a CSC-targeting effect leading to irreversible disruption of tumour-initiating potential in vivo. Mechanistically, miltefosine reduced the expression of a set of genes, leading to stem cell death. Among them, miltefosine transcriptionally inhibited checkpoint kinase 1 (CHEK1), indicating that LR integrity is essential for CHEK1 expression regulation. In isolated CD44high CSCs, we found that CSCs exhibited stronger therapy resistance than non-CSC counterparts by preventing cell death through CHEK1-mediated cell cycle checkpoints. However, inhibition of the LR/CHEK1 axis by miltefosine released cell cycle checkpoints, forcing CSCs to enter inappropriate mitosis with accumulated DNA damage and resulting in catastrophic cell death. CONCLUSION Our findings underscore the therapeutic potential of LR-targeting APLs for CRC treatment that overcomes the therapy-resistant phenotype of CSCs, highlighting the importance of the LR/CHEK1 axis as a novel mechanism of APLs.
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Affiliation(s)
- So‐Yeon Park
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
- Cell Logistics Research CenterGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Jee‐Heun Kim
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Jang‐Hyun Choi
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Choong‐Jae Lee
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Won‐Jae Lee
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Sehoon Park
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Zee‐Yong Park
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Jeong‐Heum Baek
- Division of Colon and Rectal SurgeryDepartment of SurgeryGil Medical CenterGachon University College of MedicineIncheonRepublic of Korea
| | - Jeong‐Seok Nam
- School of Life SciencesGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
- Cell Logistics Research CenterGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
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7
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Lee D, Green A, Wu H, Kwon JS. Hybrid
PDE‐kMC
modeling approach to simulate multivalent lectin‐glycan binding process. AIChE J 2021. [DOI: 10.1002/aic.17453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dongheon Lee
- Department of Biomedical Engineering Duke University Durham North Carolina USA
| | - Aaron Green
- Artie McFerrin Department of Chemical Engineering Texas A&M University Texas USA
| | - Hung‐Jen Wu
- Artie McFerrin Department of Chemical Engineering Texas A&M University Texas USA
| | - Joseph Sang‐Il Kwon
- Artie McFerrin Department of Chemical Engineering Texas A&M University Texas USA
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8
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Haack F, Köster T, Uhrmacher AM. Receptor/Raft Ratio Is a Determinant for LRP6 Phosphorylation and WNT/β-Catenin Signaling. Front Cell Dev Biol 2021; 9:706731. [PMID: 34485292 PMCID: PMC8416303 DOI: 10.3389/fcell.2021.706731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
Microdomains or lipid rafts greatly affect the distribution of proteins and peptides in the membrane and play a vital role in the formation and activation of receptor/protein complexes. A prominent example for the decisive impact of lipid rafts on signaling is LRP6, whose localization to the same lipid rafts domain as the kinase CK1γ is crucial for its successful phosphorylation and the subsequent activation of the signalosome, hence WNT/β-catenin signaling. However, according to various experimental measurements, approximately 25 to 35 % of the cell plasma membrane is covered by nanoscopic raft domains with diameters ranging between 10 to 200 nm. Extrapolating/Translating these values to the membrane of a “normal sized” cell yields a raft abundance, that, by far, outnumbers the membrane-associated pathway components of most individual signaling pathway, such as receptor and kinases. To analyze whether and how the quantitative ratio between receptor and rafts affects LRP6 phosphorylation and WNT/β-catenin pathway activation, we present a computational modeling study, that for the first time employs realistic raft numbers in a compartment-based pathway model. Our simulation experiments indicate, that for receptor/raft ratios smaller than 1, i.e., when the number of raft compartments clearly exceeds the number of pathway specific membrane proteins, we observe significant decrease in LRP6 phosphorylation and downstream pathway activity. Our results suggest that pathway specific targeting and sorting mechanism are required to significantly narrow down the receptor/raft ratio and to enable the formation of the LRP6 signalosome, hence signaling.
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Affiliation(s)
- Fiete Haack
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, Institute of Electric Engineering and Computer Science, University of Rostock, Rostock, Germany
| | - Till Köster
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, Institute of Electric Engineering and Computer Science, University of Rostock, Rostock, Germany
| | - Adelinde M Uhrmacher
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, Institute of Electric Engineering and Computer Science, University of Rostock, Rostock, Germany
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9
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COVID-19 Pathogenesis: From Molecular Pathway to Vaccine Administration. Biomedicines 2021; 9:biomedicines9080903. [PMID: 34440107 PMCID: PMC8389702 DOI: 10.3390/biomedicines9080903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
The Coronavirus 2 (SARS-CoV-2) infection is a global pandemic that has affected millions of people worldwide. The advent of vaccines has permitted some restitution. Aside from the respiratory complications of the infection, there is also a thrombotic risk attributed to both the disease and the vaccine. There are no reliable data for the risk of thromboembolism in SARS-CoV-2 infection in patients managed out of the hospital setting. A literature review was performed to identify the pathophysiological mechanism of thrombosis from the SARS-CoV-2 infection including the role of Angiotensin-Converting Enzyme receptors. The impact of the vaccine and likely mechanisms of thrombosis following vaccination were also clarified. Finally, the utility of the vaccines available against the multiple variants is also highlighted. The systemic response to SARS-CoV-2 infection is still relatively poorly understood, but several risk factors have been identified. The roll-out of the vaccines worldwide has also allowed the lifting of lockdown measures and a reduction in the spread of the disease. The experience of the SARS-CoV-2 infection, however, has highlighted the crucial role of epidemiological research and the need for ongoing studies within this field.
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10
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Dielectric Spectroscopy Based Detection of Specific and Nonspecific Cellular Mechanisms. SENSORS 2021; 21:s21093177. [PMID: 34063599 PMCID: PMC8124793 DOI: 10.3390/s21093177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022]
Abstract
Using radiofrequency dielectric spectroscopy, we have investigated the impact of the interaction between a G protein-coupled receptor (GPCR), the sterile2 α-factor receptor protein (Ste2), and its cognate agonist ligand, the α-factor pheromone, on the dielectric properties of the plasma membrane in living yeast cells (Saccharomyces cerevisiae). The dielectric properties of a cell suspension containing a saturating concentration of α-factor were measured over the frequency range 40Hz–110 MHz and compared to the behavior of a similarly prepared suspension of cells in the absence of α-factor. A spherical three-shell model was used to determine the electrical phase parameters for the yeast cells in both types of suspensions. The relative permittivity of the plasma membrane showed a significant increase after exposure to α-factor (by 0.06 ± 0.05). The equivalent experiment performed on yeast cells lacking the ability to express Ste2 showed no change in plasma membrane permittivity. Interestingly, a large change also occurred to the electrical properties of the cellular interior after the addition of α-factor to the cell suspending medium, whether or not the cells were expressing Ste2. We present a number of different complementary experiments performed on the yeast to support these dielectric data and interpret the results in terms of specific cellular reactions to the presence of α-factor.
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11
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Hernández-Adame PL, Meza U, Rodríguez-Menchaca AA, Sánchez-Armass S, Ruiz-García J, Gomez E. Determination of the size of lipid rafts studied through single-molecule FRET simulations. Biophys J 2021; 120:2287-2295. [PMID: 33864789 DOI: 10.1016/j.bpj.2021.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/16/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
Fluorescence resonance energy transfer (FRET) is a high-resolution technique that allows the characterization of spatial and temporal properties of biological structures and mechanisms. In this work, we developed an in silico single-molecule FRET methodology to study the dynamics of fluorophores inside lipid rafts. We monitored the fluorescence of a single acceptor molecule in the presence of several donor molecules. By looking at the average fluorescence, we selected events with single acceptor and donor molecules, and we used them to determine the raft size in the range of 5-16 nm. We conclude that our method is robust and insensitive to variations in the diffusion coefficient, donor density, or selected fluorescence threshold.
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Affiliation(s)
| | - Ulises Meza
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Aldo A Rodríguez-Menchaca
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Sergio Sánchez-Armass
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Jaime Ruiz-García
- Biological Physics Laboratory, Physics Institute, San Luis Potosí, Mexico.
| | - Eduardo Gomez
- Biological Physics Laboratory, Physics Institute, San Luis Potosí, Mexico.
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12
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Li L, Wang X, Wu H, Shao Y, Wu H, Song F. Interplay Between Receptor-Ligand Binding and Lipid Domain Formation Depends on the Mobility of Ligands in Cell-Substrate Adhesion. Front Mol Biosci 2021; 8:655662. [PMID: 33987204 PMCID: PMC8112205 DOI: 10.3389/fmolb.2021.655662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022] Open
Abstract
Cell-cell adhesion and the adhesion of cells to extracellular matrix are mediated by the specific binding of receptors on the cell membrane to their cognate ligands on the opposing surface. The adhesion receptors can exhibit affinity for nanoscale lipid clusters that form in the cell membrane. Experimental studies of such adhesion systems often involve a cell adhering either to a solid surface with immobile ligands or a supported lipid bilayer with mobile ligands. A central question in these cell-substrate adhesions is how the mobility of the ligands physically affects their binding to the adhesion receptors and thereby the behavior of the nanoscale lipid clusters associated with the receptors. Using a statistical mechanical model and Monte Carlo simulations for the adhesion of cells to substrates with ligands, we find that, for mobile ligands, binding to adhesion receptors can promote the formation of mesoscale lipid domains, which in turn enhances the receptor-ligand binding. However, in the case of immobile ligands, the receptor-ligand binding and the tendency for the nanoscale lipid clusters to further coalesce depend on the distribution of the ligands on the substrate. Our findings help to explain why different adhesion experiments for identifying the interplay between receptor-ligand binding and heterogeneities in cell membranes led to contradictory results.
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Affiliation(s)
- Long Li
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Xiaohuan Wang
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Helong Wu
- College of Mechanical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yingfeng Shao
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Huaping Wu
- College of Mechanical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
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13
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Polit A, Mystek P, Błasiak E. Every Detail Matters. That Is, How the Interaction between Gα Proteins and Membrane Affects Their Function. MEMBRANES 2021; 11:222. [PMID: 33804791 PMCID: PMC8003949 DOI: 10.3390/membranes11030222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/16/2022]
Abstract
In highly organized multicellular organisms such as humans, the functions of an individual cell are dependent on signal transduction through G protein-coupled receptors (GPCRs) and subsequently heterotrimeric G proteins. As most of the elements belonging to the signal transduction system are bound to lipid membranes, researchers are showing increasing interest in studying the accompanying protein-lipid interactions, which have been demonstrated to not only provide the environment but also regulate proper and efficient signal transduction. The mode of interaction between the cell membrane and G proteins is well known. Despite this, the recognition mechanisms at the molecular level and how the individual G protein-membrane attachment signals are interrelated in the process of the complex control of membrane targeting of G proteins remain unelucidated. This review focuses on the mechanisms by which mammalian Gα subunits of G proteins interact with lipids and the factors responsible for the specificity of membrane association. We summarize recent data on how these signaling proteins are precisely targeted to a specific site in the membrane region by introducing well-defined modifications as well as through the presence of polybasic regions within these proteins and interactions with other components of the heterocomplex.
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Affiliation(s)
- Agnieszka Polit
- Department of Physical Biochemistry, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; (P.M.); (E.B.)
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14
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Urban JM, Chiang W, Hammond JW, Cogan NMB, Litzburg A, Burke R, Stern HA, Gelbard HA, Nilsson BL, Krauss TD. Quantum Dots for Improved Single-Molecule Localization Microscopy. J Phys Chem B 2021; 125:2566-2576. [PMID: 33683893 PMCID: PMC8080873 DOI: 10.1021/acs.jpcb.0c11545] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Colloidal semiconductor quantum dots (QDs) have long established their versatility and utility for the visualization of biological interactions. On the single-particle level, QDs have demonstrated superior photophysical properties compared to organic dye molecules or fluorescent proteins, but it remains an open question as to which of these fundamental characteristics are most significant with respect to the performance of QDs for imaging beyond the diffraction limit. Here, we demonstrate significant enhancement in achievable localization precision in QD-labeled neurons compared to neurons labeled with an organic fluorophore. Additionally, we identify key photophysical parameters of QDs responsible for this enhancement and compare these parameters to reported values for commonly used fluorophores for super-resolution imaging.
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Affiliation(s)
- Jennifer M Urban
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Wesley Chiang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, United states
| | - Jennetta W Hammond
- Center for Neurotherapeutics Discovery and Department of Neurology, University of Rochester Medical Center, Rochester, New York 14642, United states
| | - Nicole M B Cogan
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Angela Litzburg
- Center for Neurotherapeutics Discovery and Department of Neurology, University of Rochester Medical Center, Rochester, New York 14642, United states
| | - Rebeckah Burke
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Harry A Stern
- Center for Integrated Research and Computing, University of Rochester, Rochester, New York 14627-0216, United States
| | - Harris A Gelbard
- Center for Neurotherapeutics Discovery and Department of Neurology, University of Rochester Medical Center, Rochester, New York 14642, United states
- Departments of Pediatrics, Neuroscience, and Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, United states
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Todd D Krauss
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- The Institute of Optics, University of Rochester, Rochester, New York 14627-0216, United States
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Li L, Hu J, Shi X, Różycki B, Song F. Interplay between cooperativity of intercellular receptor-ligand binding and coalescence of nanoscale lipid clusters in adhering membranes. SOFT MATTER 2021; 17:1912-1920. [PMID: 33416062 DOI: 10.1039/d0sm01904f] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Adhesion of biological cells is mediated by the specific binding of receptors and ligands which are typically large proteins spanning through the plasma membranes of the contacting cells. The receptors and ligands can exhibit affinity for nanoscale lipid clusters that form within the plasma membrane. A central question is how these nanoscale lipid clusters physically affect and respond to the receptor-ligand binding during cell adhesion. Within the framework of classical statistical mechanics we find that the receptor-ligand binding reduces the threshold energy for lipid clusters to coalesce into mesoscale domains by up to ∼50%, and that the formation of these domains induces significant cooperativity of the receptor-ligand binding. The interplay between the receptor-ligand binding cooperativity and the lipid domain formation manifests acute sensitivity of the membrane system to changes in control parameters. This sensitivity can be crucial in cell signaling and immune responses.
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Affiliation(s)
- Long Li
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.
| | - Jinglei Hu
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, Nanjing, China.
| | - Xinghua Shi
- National Center for Nanoscience and Technology of China, Beijing, China
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw, Poland.
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China. and School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
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16
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Koklič T, Hrovat A, Guixà-González R, Rodríguez-Espigares I, Navio D, Frangež R, Uršič M, Kubale V, Plemenitaš A, Selent J, Šentjurc M, Vrecl M. Electron Paramagnetic Resonance Gives Evidence for the Presence of Type 1 Gonadotropin-Releasing Hormone Receptor (GnRH-R) in Subdomains of Lipid Rafts. Molecules 2021; 26:molecules26040973. [PMID: 33673080 PMCID: PMC7918721 DOI: 10.3390/molecules26040973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 11/16/2022] Open
Abstract
This study investigated the effect of type 1 gonadotropin releasing hormone receptor (GnRH-R) localization within lipid rafts on the properties of plasma membrane (PM) nanodomain structure. Confocal microscopy revealed colocalization of PM-localized GnRH-R with GM1-enriched raft-like PM subdomains. Electron paramagnetic resonance spectroscopy (EPR) of a membrane-partitioned spin probe was then used to study PM fluidity of immortalized pituitary gonadotrope cell line αT3-1 and HEK-293 cells stably expressing GnRH-R and compared it with their corresponding controls (αT4 and HEK-293 cells). Computer-assisted interpretation of EPR spectra revealed three modes of spin probe movement reflecting the properties of three types of PM nanodomains. Domains with an intermediate order parameter (domain 2) were the most affected by the presence of the GnRH-Rs, which increased PM ordering (order parameter (S)) and rotational mobility of PM lipids (decreased rotational correlation time (τc)). Depletion of cholesterol by methyl-β-cyclodextrin (methyl-β-CD) inhibited agonist-induced GnRH-R internalization and intracellular Ca2+ activity and resulted in an overall reduction in PM order; an observation further supported by molecular dynamics (MD) simulations of model membrane systems. This study provides evidence that GnRH-R PM localization may be related to a subdomain of lipid rafts that has lower PM ordering, suggesting lateral heterogeneity within lipid raft domains.
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Affiliation(s)
- Tilen Koklič
- Laboratory of Biophysics, Department of Condensed Matter Physics, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; (T.K.); (M.Š.)
| | - Alenka Hrovat
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (A.H.); (R.F.); (M.U.); (V.K.)
| | - Ramon Guixà-González
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (R.G.-G.); (I.R.-E.); (D.N.); (J.S.)
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen, Switzerland
- Condensed Matter Theory Group, PSI, 5232 Villigen, Switzerland
| | - Ismael Rodríguez-Espigares
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (R.G.-G.); (I.R.-E.); (D.N.); (J.S.)
| | - Damaris Navio
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (R.G.-G.); (I.R.-E.); (D.N.); (J.S.)
| | - Robert Frangež
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (A.H.); (R.F.); (M.U.); (V.K.)
| | - Matjaž Uršič
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (A.H.); (R.F.); (M.U.); (V.K.)
| | - Valentina Kubale
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (A.H.); (R.F.); (M.U.); (V.K.)
| | - Ana Plemenitaš
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (R.G.-G.); (I.R.-E.); (D.N.); (J.S.)
| | - Marjeta Šentjurc
- Laboratory of Biophysics, Department of Condensed Matter Physics, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; (T.K.); (M.Š.)
| | - Milka Vrecl
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (A.H.); (R.F.); (M.U.); (V.K.)
- Correspondence: ; Tel.: +386-1-477-9118
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17
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The Gαi protein subclass selectivity to the dopamine D 2 receptor is also decided by their location at the cell membrane. Cell Commun Signal 2020; 18:189. [PMID: 33308256 PMCID: PMC7731117 DOI: 10.1186/s12964-020-00685-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background G protein-coupled receptor (GPCR) signaling via heterotrimeric G proteins plays an important role in the cellular regulation of responses to external stimuli. Despite intensive structural research, the mechanism underlying the receptor–G protein coupling of closely related subtypes of Gαi remains unclear. In addition to the structural changes of interacting proteins, the interactions between lipids and proteins seem to be crucial in GPCR-dependent cell signaling due to their functional organization in specific membrane domains. In previous works, we found that Gαs and Gαi3 subunits prefer distinct types of membrane-anchor lipid domains that also modulate the G protein trimer localization. In the present study, we investigated the functional selectivity of dopamine D2 long receptor isoform (D2R) toward the Gαi1, Gαi2, and Gαi3 subunits, and analyzed whether the organization of Gαi heterotrimers at the plasma membrane affects the signal transduction. Methods We characterized the lateral diffusion and the receptor–G protein spatial distribution in living cells using two assays: fluorescence recovery after photobleaching microscopy and fluorescence resonance energy transfer detected by fluorescence-lifetime imaging microscopy. Depending on distribution of data differences between Gα subunits were investigated using parametric approach–unpaired T-test or nonparametric–Mann–Whitney U test. Results Despite the similarities between the examined subunits, the experiments conducted in the study revealed a significantly faster lateral diffusion of the Gαi2 subunit and the singular distribution of the Gαi1 subunit in the plasma membrane. The cell membrane partitioning of distinct Gαi heterotrimers with dopamine receptor correlated very well with the efficiency of D2R-mediated inhibition the formation of cAMP. Conclusions This study showed that even closely related subunits of Gαi differ in their membrane-trafficking properties that impact on their signaling. The interactions between lipids and proteins seem to be crucial in GPCR-dependent cell signaling due to their functional organization in specific membrane domains, and should therefore be taken into account as one of the selectivity determinants of G protein coupling. Video abstract
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Carotenuto AR, Lunghi L, Piccolo V, Babaei M, Dayal K, Pugno N, Zingales M, Deseri L, Fraldi M. Mechanobiology predicts raft formations triggered by ligand-receptor activity across the cell membrane. JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS 2020; 141:103974. [PMID: 32461703 PMCID: PMC7243794 DOI: 10.1016/j.jmps.2020.103974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 05/05/2023]
Abstract
Clustering of ligand-binding receptors of different types on thickened isles of the cell membrane, namely lipid rafts, is an experimentally observed phenomenon. Although its influence on cell's response is deeply investigated, the role of the coupling between mechanical processes and multiphysics involving the active receptors and the surrounding lipid membrane during ligand-binding has not yet been understood. Specifically, the focus of this work is on G-protein-coupled receptors (GPCRs), the widest group of transmembrane proteins in animals, which regulate specific cell processes through chemical signalling pathways involving a synergistic balance between the cyclic Adenosine Monophosphate (cAMP) produced by active GPCRs in the intracellular environment and its efflux, mediated by the Multidrug Resistance Proteins (MRPs) transporters. This paper develops a multiphysics approach based on the interplay among energetics, multiscale geometrical changes and mass balance of species, i.e. active GPCRs and MRPs, including diffusion and kinetics of binding and unbinding. Because the obtained energy depends upon both the kinematics and the changes of species densities, balance of mass and of linear momentum are coupled and govern the space-time evolution of the cell membrane. The mechanobiology involving remodelling and change of lipid ordering of the cell membrane allows to predict dynamics of transporters and active receptors -in full agreement with experimentally observed cAMP levels- and how the latter trigger rafts formation and cluster on such sites. Within the current scientific debate on Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) and on the basis of the ascertained fact that lipid rafts often serve as an entry port for viruses, it is felt that approaches accounting for strong coupling among mechanobiological aspects could even turn helpful in better understanding membrane-mediated phenomena such as COVID-19 virus-cell interaction.
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Affiliation(s)
- Angelo R. Carotenuto
- Department of Structures for Engineering and Architecture, University of Napoli “Federico II”, Italy
| | - Laura Lunghi
- Smiling International School, formerly at the Department of Life Sciences and Biotech., University of Ferrara, Italy
| | - Valentina Piccolo
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Italy
| | - Mahnoush Babaei
- Department of Civil and Environmental Engineering, Department of Mechanical Engineering, Carnegie Mellon, USA
| | - Kaushik Dayal
- Department of Civil and Environmental Engineering, Department of Mechanical Engineering, Carnegie Mellon, USA
| | - Nicola Pugno
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Italy
- Laboratory of Bio-inspired, Bionic, Nano, Meta Materials & Mechanics, Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano, 77, Trento 38123, Italy
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Massimiliano Zingales
- Dipartimento di Ingegneria, Universitàdi Palermo, viale delle Scienze ed.8, 90128 Palermo, Italy
| | - Luca Deseri
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Italy
- Department of Civil and Environmental Engineering, Department of Mechanical Engineering, Carnegie Mellon, USA
- Department of Mechanical Engineering and Material Sciences, SSoE, University of Pittsburgh USA
- Department of Nanomedicine, The Houston Methodist Research Institute, USA
| | - Massimiliano Fraldi
- Department of Structures for Engineering and Architecture, University of Napoli “Federico II”, Italy
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Garzon Dasgupta AK, Martyanov AA, Filkova AA, Panteleev MA, Sveshnikova AN. Development of a Simple Kinetic Mathematical Model of Aggregation of Particles or Clustering of Receptors. Life (Basel) 2020; 10:E97. [PMID: 32604803 PMCID: PMC7345685 DOI: 10.3390/life10060097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
The process of clustering of plasma membrane receptors in response to their agonist is the first step in signal transduction. The rate of the clustering process and the size of the clusters determine further cell responses. Here we aim to demonstrate that a simple 2-differential equation mathematical model is capable of quantitative description of the kinetics of 2D or 3D cluster formation in various processes. Three mathematical models based on mass action kinetics were considered and compared with each other by their ability to describe experimental data on GPVI or CR3 receptor clustering (2D) and albumin or platelet aggregation (3D) in response to activation. The models were able to successfully describe experimental data without losing accuracy after switching between complex and simple models. However, additional restrictions on parameter values are required to match a single set of parameters for the given experimental data. The extended clustering model captured several properties of the kinetics of cluster formation, such as the existence of only three typical steady states for this system: unclustered receptors, receptor dimers, and clusters. Therefore, a simple kinetic mass-action-law-based model could be utilized to adequately describe clustering in response to activation both in 2D and in 3D.
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Affiliation(s)
- Andrei K. Garzon Dasgupta
- Faculty of Physics, Lomonosov Moscow State University, 1/2 Leninskie gory, 119991 Moscow, Russia; (A.K.G.D.); (A.A.M.); (A.A.F.); (M.A.P.)
- National Medical Research Centеr of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, 1 Samory Mashela St, 117198 Moscow, Russia
| | - Alexey A. Martyanov
- Faculty of Physics, Lomonosov Moscow State University, 1/2 Leninskie gory, 119991 Moscow, Russia; (A.K.G.D.); (A.A.M.); (A.A.F.); (M.A.P.)
- National Medical Research Centеr of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, 1 Samory Mashela St, 117198 Moscow, Russia
- Institute for Biochemical Physics (IBCP), Russian Academy of Sciences (RAS), Russian Federation, Kosyigina 4, 119334 Moscow, Russia
- Center for Theoretical Problems of Physico-Сhemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya str., 109029 Moscow, Russia
| | - Aleksandra A. Filkova
- Faculty of Physics, Lomonosov Moscow State University, 1/2 Leninskie gory, 119991 Moscow, Russia; (A.K.G.D.); (A.A.M.); (A.A.F.); (M.A.P.)
- National Medical Research Centеr of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, 1 Samory Mashela St, 117198 Moscow, Russia
- Center for Theoretical Problems of Physico-Сhemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya str., 109029 Moscow, Russia
| | - Mikhail A. Panteleev
- Faculty of Physics, Lomonosov Moscow State University, 1/2 Leninskie gory, 119991 Moscow, Russia; (A.K.G.D.); (A.A.M.); (A.A.F.); (M.A.P.)
- National Medical Research Centеr of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, 1 Samory Mashela St, 117198 Moscow, Russia
- Center for Theoretical Problems of Physico-Сhemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya str., 109029 Moscow, Russia
- Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology, 9 Institutskii per., 141700 Dolgoprudnyi, Russia
| | - Anastasia N. Sveshnikova
- Faculty of Physics, Lomonosov Moscow State University, 1/2 Leninskie gory, 119991 Moscow, Russia; (A.K.G.D.); (A.A.M.); (A.A.F.); (M.A.P.)
- National Medical Research Centеr of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, 1 Samory Mashela St, 117198 Moscow, Russia
- Center for Theoretical Problems of Physico-Сhemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya str., 109029 Moscow, Russia
- Department of Normal Physiology, Sechenov First Moscow State Medical University, 8/2 Trubetskaya St., 119991 Moscow, Russia
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20
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Function-based high-throughput screening for antibody antagonists and agonists against G protein-coupled receptors. Commun Biol 2020; 3:146. [PMID: 32218528 PMCID: PMC7099005 DOI: 10.1038/s42003-020-0867-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Hybridoma and phage display are two powerful technologies for isolating target-specific monoclonal antibodies based on the binding. However, for complex membrane proteins, such as G protein-coupled receptors (GPCRs), binding-based screening rarely results in functional antibodies. Here we describe a function-based high-throughput screening method for quickly identifying antibody antagonists and agonists against GPCRs by combining glycosylphosphatidylinositol-anchored antibody cell display with β-arrestin recruitment-based cell sorting and screening. This method links antibody genotype with phenotype and is applicable to all GPCR targets. We validated this method by identifying a panel of antibody antagonists and an antibody agonist to the human apelin receptor from an immune antibody repertoire. In contrast, we obtained only neutral binders and antibody antagonists from the same repertoire by phage display, suggesting that the new approach described here is more efficient than traditional methods in isolating functional antibodies. This new method may create a new paradigm in antibody drug discovery. Ren et al. develop a function-based high-throughput screening method for identifying antibody antagonists and agonists against GPCRs by combining GPI-anchored antibody cell surface display and β-arrestin recruitment reporter assay. They identify a panel of antibody antagonists and an agonist to the human apelin receptor, which is not obtainable from phage display technology.
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21
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Li L, Hu J, Różycki B, Song F. Intercellular Receptor-Ligand Binding and Thermal Fluctuations Facilitate Receptor Aggregation in Adhering Membranes. NANO LETTERS 2020; 20:722-728. [PMID: 31858798 PMCID: PMC7751893 DOI: 10.1021/acs.nanolett.9b04596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/15/2019] [Indexed: 05/28/2023]
Abstract
Nanoscale molecular clusters in cell membranes can serve as platforms to recruit membrane proteins for various biological functions. A central question is how these nanoclusters respond to physical contacts between cells. Using a statistical mechanics model and Monte Carlo simulations, we explore how the adhesion of cell membranes affects the stability and coalescence of clusters enriched in receptor proteins. Our results show that intercellular receptor-ligand binding and membrane shape fluctuations can lead to receptor aggregation within the adhering membranes even if large-scale clusters are thermodynamically unstable in nonadhering membranes.
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Affiliation(s)
- Long Li
- State
Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of
Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jinglei Hu
- Kuang
Yaming Honors School & Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - Bartosz Różycki
- Institute
of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Fan Song
- State
Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of
Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School
of Engineering Science, University of Chinese
Academy of Sciences, Beijing 100049, China
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Choi HK, Lee D, Singla A, Kwon JSI, Wu HJ. The influence of heteromultivalency on lectin-glycan binding behavior. Glycobiology 2019; 29:397-408. [PMID: 30824941 DOI: 10.1093/glycob/cwz010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023] Open
Abstract
We recently discovered that the nature of lectin multivalency and glycolipid diffusion on cell membranes could lead to the heteromultivalent binding (i.e., a single lectin simultaneously binding to different types of glycolipid ligands). This heteromultivalent binding may even govern the lectin-glycan recognition process. To investigate this, we developed a kinetic Monte Carlo simulation, which only considers the fundamental physics/chemistry principles, to model the process of lectin binding to glycans on cell surfaces. We found that the high-affinity glycan ligands could facilitate lectin binding to other low-affinity glycan ligands, even though these low-affinity ligands are barely detectable in microarrays with immobilized glycan ligands. Such heteromultivalent binding processes significantly change lectin binding behaviors. We hypothesize that living organisms probably utilize this mechanism to regulate the downstream lectin functions. Our finding not only offers a mechanism to describe the concept that lectins are pattern recognition molecules, but also suggests that the two overlooked parameters, surface diffusion of glycan ligand and lectin binding kinetics, can play important roles in glycobiology processes. In this paper, we identified the critical parameters that influence the heteromultivalent binding process. We also discussed how our discovery can impact the current lectin-glycan analysis.
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Affiliation(s)
- Hyun-Kyu Choi
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Dongheon Lee
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Akshi Singla
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Joseph Sang-Il Kwon
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Hung-Jen Wu
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
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Spinosa PC, Humphries BA, Lewin Mejia D, Buschhaus JM, Linderman JJ, Luker GD, Luker KE. Short-term cellular memory tunes the signaling responses of the chemokine receptor CXCR4. Sci Signal 2019; 12:eaaw4204. [PMID: 31289212 PMCID: PMC7059217 DOI: 10.1126/scisignal.aaw4204] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The chemokine receptor CXCR4 regulates fundamental processes in development, normal physiology, and diseases, including cancer. Small subpopulations of CXCR4-positive cells drive the local invasion and dissemination of malignant cells during metastasis, emphasizing the need to understand the mechanisms controlling responses at the single-cell level to receptor activation by the chemokine ligand CXCL12. Using single-cell imaging, we discovered that short-term cellular memory of changes in environmental conditions tuned CXCR4 signaling to Akt and ERK, two kinases activated by this receptor. Conditioning cells with growth stimuli before CXCL12 exposure increased the number of cells that initiated CXCR4 signaling and the amplitude of Akt and ERK activation. Data-driven, single-cell computational modeling revealed that growth factor conditioning modulated CXCR4-dependent activation of Akt and ERK by decreasing extrinsic noise (preexisting cell-to-cell differences in kinase activity) in PI3K and mTORC1. Modeling established mTORC1 as critical for tuning single-cell responses to CXCL12-CXCR4 signaling. Our single-cell model predicted how combinations of extrinsic noise in PI3K, Ras, and mTORC1 superimposed on different driver mutations in the ERK and/or Akt pathways to bias CXCR4 signaling. Computational experiments correctly predicted that selected kinase inhibitors used for cancer therapy shifted subsets of cells to states that were more permissive to CXCR4 activation, suggesting that such drugs may inadvertently potentiate pro-metastatic CXCR4 signaling. Our work establishes how changing environmental inputs modulate CXCR4 signaling in single cells and provides a framework to optimize the development and use of drugs targeting this signaling pathway.
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Affiliation(s)
- Phillip C Spinosa
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brock A Humphries
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Daniela Lewin Mejia
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Johanna M Buschhaus
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gary D Luker
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kathryn E Luker
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Norris JW, Watson JL, Tablin F, Kozikowski TA, Knych HK. Pharmacokinetics and competitive pharmacodynamics of ADP-induced platelet activation after oral administration of clopidogrel to horses. Am J Vet Res 2019; 80:505-512. [PMID: 31034271 DOI: 10.2460/ajvr.80.5.505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine pharmacokinetics and pharmacodynamics after oral administration of a single dose of clopidogrel to horses. ANIMALS 6 healthy adult horses. PROCEDURES Blood samples were collected before and at various times up to 24 hours after oral administration of clopidogrel (2 mg/kg). Reactivity of platelets from each blood sample was determined by optical aggregometry and phosphorylation of vasodilator-stimulated phosphoprotein (VASP). Concentrations of clopidogrel and the clopidogrel active metabolite derivative (CAMD) were measured in each blood sample by use of liquid chromatography-tandem mass spectrometry, and pharmacokinetic parameters were determined with a noncompartmental model. RESULTS Compared with results for preadministration samples, platelet aggregation in response to 12.5μM ADP decreased significantly within 4 hours after clopidogrel administration for 5 of 6 horses. After 24 hours, platelet aggregation was identical to that measured before administration. Platelet aggregation in response to 25μM ADP was identical between samples obtained before and after administration. Phosphorylation of VASP in response to ADP (20μM) and prostaglandin E1 (3.3μM) was also unchanged by administration of clopidogrel. Time to maximum concentration of clopidogrel and CAMD was 0.54 and 0.71 hours, respectively, and calculated terminal-phase half-life of clopidogrel and CAMD was 1.81 and 0.97 hours, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Clopidogrel or CAMD caused competitive inhibition of ADP-induced platelet aggregation during the first 24 hours after clopidogrel administration. Because CAMD was rapidly eliminated from horses, clopidogrel administration may be needed more frequently than in other species in which clopidogrel causes irreversible platelet inhibition. (Am J Vet Res 2019;80:505-512).
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Gutierrez MG, Deyell J, White KL, Dalle Ore LC, Cherezov V, Stevens RC, Malmstadt N. The lipid phase preference of the adenosine A 2A receptor depends on its ligand binding state. Chem Commun (Camb) 2019; 55:5724-5727. [PMID: 31038495 PMCID: PMC6561478 DOI: 10.1039/c8cc10130b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Giant unilamellar protein vesicles (GUPs) were formed with the adenosine A2A receptor (A2AR) incorporated in the lipid bilayer and protein partitioning into the liquid ordered and liquid disordered phases was observed. When no ligand is bound, A2AR partitions preferentially into the liquid disordered phase of GUPs, while ligand-bound A2AR partitions into the liquid ordered phase.
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Affiliation(s)
- M Gertrude Gutierrez
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA.
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26
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Bieberich E. Sphingolipids and lipid rafts: Novel concepts and methods of analysis. Chem Phys Lipids 2018; 216:114-131. [PMID: 30194926 PMCID: PMC6196108 DOI: 10.1016/j.chemphyslip.2018.08.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/20/2018] [Accepted: 08/25/2018] [Indexed: 12/12/2022]
Abstract
About twenty years ago, the functional lipid raft model of the plasma membrane was published. It took into account decades of research showing that cellular membranes are not just homogenous mixtures of lipids and proteins. Lateral anisotropy leads to assembly of membrane domains with specific lipid and protein composition regulating vesicular traffic, cell polarity, and cell signaling pathways in a plethora of biological processes. However, what appeared to be a clearly defined entity of clustered raft lipids and proteins became increasingly fluid over the years, and many of the fundamental questions about biogenesis and structure of lipid rafts remained unanswered. Experimental obstacles in visualizing lipids and their interactions hampered progress in understanding just how big rafts are, where and when they are formed, and with which proteins raft lipids interact. In recent years, we have begun to answer some of these questions and sphingolipids may take center stage in re-defining the meaning and functional significance of lipid rafts. In addition to the archetypical cholesterol-sphingomyelin raft with liquid ordered (Lo) phase and the liquid-disordered (Ld) non-raft regions of cellular membranes, a third type of microdomains termed ceramide-rich platforms (CRPs) with gel-like structure has been identified. CRPs are "ceramide rafts" that may offer some fresh view on the membrane mesostructure and answer several critical questions for our understanding of lipid rafts.
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Affiliation(s)
- Erhard Bieberich
- Department of Physiology at the University of Kentucky, Lexington, KY, United States.
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Jaykumar AB, Caceres PS, Ortiz PA. Single-molecule labeling for studying trafficking of renal transporters. Am J Physiol Renal Physiol 2018; 315:F1243-F1249. [PMID: 30043625 DOI: 10.1152/ajprenal.00082.2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The ability to detect and track single molecules presents the advantage of visualizing the complex behavior of transmembrane proteins with a time and space resolution that would otherwise be lost with traditional labeling and biochemical techniques. Development of new imaging probes has provided a robust method to study their trafficking and surface dynamics. This mini-review focuses on the current technology available for single-molecule labeling of transmembrane proteins, their advantages, and limitations. We also discuss the application of these techniques to the study of renal transporter trafficking in light of recent research.
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Affiliation(s)
- Ankita Bachhawat Jaykumar
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital , Detroit, Michigan.,Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan
| | - Paulo S Caceres
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital , Detroit, Michigan
| | - Pablo A Ortiz
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital , Detroit, Michigan.,Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan
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Romay-Tallon R, Kulhawy E, Brymer KJ, Allen J, Rivera-Baltanas T, Olivares JM, Kalynchuk LE, Caruncho HJ. Changes in Membrane Protein Clustering in Peripheral Lymphocytes in an Animal Model of Depression Parallel Those Observed in Naïve Depression Patients: Implications for the Development of Novel Biomarkers of Depression. Front Pharmacol 2018; 9:1149. [PMID: 30374301 PMCID: PMC6196231 DOI: 10.3389/fphar.2018.01149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/24/2018] [Indexed: 12/27/2022] Open
Abstract
Naïve depression patients show alterations in serotonin transporter (SERT) and serotonin 2A (5HT2A) receptor clustering in peripheral lymphocytes, and these alterations have been proposed as a biomarker of therapeutic efficacy in major depression. Repeated corticosterone (CORT) induces a consistent depression-like phenotype and has been widely used as an animal model to study neurobiological alterations underlying the depressive symptoms. In this experiment, we used the CORT paradigm to evaluate whether depression-like behavior is associated with similar changes in the pattern of SERT and 5HT2A membrane protein clustering as those observed in depression patients. We also analyzed the clustering of other proteins expressed in lipid rafts in lymphocytes. Rats received daily CORT or vehicle injections for 21 consecutive days. Afterward they underwent the forced swim test to evaluate depression-like behavior, and isolated lymphocytes were analyzed by immunocytochemistry coupled to image-analysis to study clustering parameters of the SERT, 5HT2A receptor, dopamine transporter (DAT), Beta2 adrenergic receptor (β2AR), NMDA 2B receptor (NR2B), Pannexin 1 (Pnx1), and prion cellular protein (PrPc). Our results showed that CORT increases the size of protein clusters for all proteins with the exception of β 2AR, which is decreased. CORT also increased the number of clusters for Pnx1 and PrPc only. Overall, these results indicate that alterations in SERT and 5HT2A protein clustering in naïve depression patients are paralleled by changes seen in an animal model of depression. The CORT paradigm may be a useful screen for examining additional proteins in lymphocytes as a preliminary step prior to their analysis as biomarkers of depression in human blood samples.
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Affiliation(s)
| | - Erin Kulhawy
- Innovate-Calgary, University of Calgary, Calgary, AB, Canada
| | - Kyle J Brymer
- Department of Psychology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Josh Allen
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Jose M Olivares
- Division of Psychiatry, Hospital Alvaro Cunqueiro, CHUVI, Vigo, Spain
| | - Lisa E Kalynchuk
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Hector J Caruncho
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
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Li L, Hu J, Xu G, Song F. Binding constant of cell adhesion receptors and substrate-immobilized ligands depends on the distribution of ligands. Phys Rev E 2018; 97:012405. [PMID: 29448355 DOI: 10.1103/physreve.97.012405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 12/16/2022]
Abstract
Cell-cell adhesion and the adhesion of cells to tissues and extracellular matrix, which are pivotal for immune response, tissue development, and cell locomotion, depend sensitively on the binding constant of receptor and ligand molecules anchored on the apposing surfaces. An important question remains of whether the immobilization of ligands affects the affinity of binding with cell adhesion receptors. We have investigated the adhesion of multicomponent membranes to a flat substrate coated with immobile ligands using Monte Carlo simulations of a statistical mesoscopic model with biologically relevant parameters. We find that the binding of the adhesion receptors to ligands immobilized on the substrate is strongly affected by the ligand distribution. In the case of ligand clusters, the receptor-ligand binding constant can be significantly enhanced due to the less translational entropy loss of lipid-raft domains in the model cell membranes upon the formation of additional complexes. For ligands randomly or uniformly immobilized on the substrate, the binding constant is rather decreased since the receptors localized in lipid-raft domains have to pay an energetic penalty in order to bind ligands. Our findings help to understand why cell-substrate adhesion experiments for measuring the impact of lipid rafts on the receptor-ligand interactions led to contradictory results.
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Affiliation(s)
- Long Li
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China.,Shenzhen Institute of Research, Nanjing University, Shenzhen 518057, China
| | - Guangkui Xu
- School of Aerospace, Xi'an Jiaotong University, Xi'an 710049, China
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing 100049, China
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30
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Evolution and development of model membranes for physicochemical and functional studies of the membrane lateral heterogeneity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2012-2017. [DOI: 10.1016/j.bbamem.2018.03.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/08/2018] [Accepted: 03/11/2018] [Indexed: 12/19/2022]
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31
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Lee D, Mohr A, Kwon JSI, Wu HJ. Kinetic Monte Carlo modeling of multivalent binding of CTB proteins with GM1 receptors. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2018.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Worstell NC, Singla A, Saenkham P, Galbadage T, Sule P, Lee D, Mohr A, Kwon JSI, Cirillo JD, Wu HJ. Hetero-Multivalency of Pseudomonas aeruginosa Lectin LecA Binding to Model Membranes. Sci Rep 2018; 8:8419. [PMID: 29849092 PMCID: PMC5976636 DOI: 10.1038/s41598-018-26643-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/16/2018] [Indexed: 12/29/2022] Open
Abstract
A single glycan-lectin interaction is often weak and semi-specific. Multiple binding domains in a single lectin can bind with multiple glycan molecules simultaneously, making it difficult for the classic “lock-and-key” model to explain these interactions. We demonstrated that hetero-multivalency, a homo-oligomeric protein simultaneously binding to at least two types of ligands, influences LecA (a Pseudomonas aeruginosa adhesin)-glycolipid recognition. We also observed enhanced binding between P. aeruginosa and mixed glycolipid liposomes. Interestingly, strong ligands could activate weaker binding ligands leading to higher LecA binding capacity. This hetero-multivalency is probably mediated via a simple mechanism, Reduction of Dimensionality (RD). To understand the influence of RD, we also modeled LecA’s two-step binding process with membranes using a kinetic Monte Carlo simulation. The simulation identified the frequency of low-affinity ligand encounters with bound LecA and the bound LecA’s retention of the low-affinity ligand as essential parameters for triggering hetero-multivalent binding, agreeing with experimental observations. The hetero-multivalency can alter lectin binding properties, including avidities, capacities, and kinetics, and therefore, it likely occurs in various multivalent binding systems. Using hetero-multivalency concept, we also offered a new strategy to design high-affinity drug carriers for targeted drug delivery.
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Affiliation(s)
- Nolan C Worstell
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Akshi Singla
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Panatda Saenkham
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Thushara Galbadage
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Preeti Sule
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Dongheon Lee
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Alec Mohr
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Joseph Sang-Il Kwon
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Jeffrey D Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Hung-Jen Wu
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA.
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Deci MB, Liu M, Dinh QT, Nguyen J. Precision engineering of targeted nanocarriers. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1511. [PMID: 29436157 DOI: 10.1002/wnan.1511] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/11/2017] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Since their introduction in 1980, the number of advanced targeted nanocarrier systems has grown considerably. Nanocarriers capable of targeting single receptors, multiple receptors, or multiple epitopes have all been used to enhance delivery efficiency and selectivity. Despite tremendous progress, preclinical studies and clinically translatable nanotechnology remain disconnected. The disconnect in targeting efficacy may stem from poorly-understood factors such as receptor clustering, spatial control of targeting ligands, ligand mobility, and ligand architecture. Further, the relationship between receptor distribution and ligand architecture remains elusive. Traditionally, targeted nanocarriers were engineered assuming a "static" target. However, it is becoming increasingly clear that receptor expression patterns change in response to external stimuli and disease progression. Here, we discuss how cutting-edge technologies will enable a better characterization of the spatiotemporal distribution of membrane receptors and their clustering. We further describe how this will enable the design of new nanocarriers that selectively target the site of disease. Ultimately, we explore how the precision engineering of targeted nanocarriers that adapt to receptor dynamics will have the potential to drive nanotechnology to the forefront of therapy and make targeted nanomedicine a clinical reality. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Michael B Deci
- Department of Pharmaceutical Sciences, School of Pharmacy, University at Buffalo, The State University of New York, Buffalo, New York
| | - Maixian Liu
- Department of Pharmaceutical Sciences, School of Pharmacy, University at Buffalo, The State University of New York, Buffalo, New York
| | - Quoc Thai Dinh
- Department of Experimental Pneumology and Allergology, Saarland University Faculty of Medicine, Homburg/Saar, Germany
| | - Juliane Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University at Buffalo, The State University of New York, Buffalo, New York
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34
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Cheng B, Lin M, Huang G, Li Y, Ji B, Genin GM, Deshpande VS, Lu TJ, Xu F. Cellular mechanosensing of the biophysical microenvironment: A review of mathematical models of biophysical regulation of cell responses. Phys Life Rev 2017; 22-23:88-119. [PMID: 28688729 PMCID: PMC5712490 DOI: 10.1016/j.plrev.2017.06.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 12/11/2022]
Abstract
Cells in vivo reside within complex microenvironments composed of both biochemical and biophysical cues. The dynamic feedback between cells and their microenvironments hinges upon biophysical cues that regulate critical cellular behaviors. Understanding this regulation from sensing to reaction to feedback is therefore critical, and a large effort is afoot to identify and mathematically model the fundamental mechanobiological mechanisms underlying this regulation. This review provides a critical perspective on recent progress in mathematical models for the responses of cells to the biophysical cues in their microenvironments, including dynamic strain, osmotic shock, fluid shear stress, mechanical force, matrix rigidity, porosity, and matrix shape. The review highlights key successes and failings of existing models, and discusses future opportunities and challenges in the field.
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Affiliation(s)
- Bo Cheng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Min Lin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Guoyou Huang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Yuhui Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Baohua Ji
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing, China
| | - Guy M Genin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; Department of Mechanical Engineering & Materials Science, and NSF Science and Technology Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis 63130, MO, USA
| | - Vikram S Deshpande
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - Tian Jian Lu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
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Flierl U, Schäfer A. Fractalkine – a local inflammatory marker aggravating platelet activation at the vulnerable plaque. Thromb Haemost 2017; 108:457-63. [DOI: 10.1160/th12-04-0271] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 05/30/2012] [Indexed: 01/10/2023]
Abstract
SummaryChemokines play an important role in inducing chemotaxis of cells, piloting white blood cells in immune surveillance and are crucial parts in the development and progression of atherosclerosis. Platelets are mandatory players in the initiation of atherosclerotic lesion formation and are susceptible targets for and producers of chemokines. Several chemokine receptors on platelets have been described previously, amongst them CX3CR1, the receptor for fractalkine. The unique chemokine fractalkine (CX3CL1, FKN) exists as a soluble as well as a membrane-anchored glycoprotein. Its essential role in the formation of atherosclerotic lesions and atherosclerosis progression has been impressively described in mouse models. Moreover, fractalkine induces platelet activation and adhesion via a functional fractalkine receptor (CX3CR1) expressed on the platelet surface. Platelet activation via the FKN/CX3CR1-axis triggers leukocyte adhesion to activated endothelium, and fractalkine-induced platelet P-selectin is mandatory for leukocyte recruitment under arterial flow conditions. This review summarises the role of fractalkine as a potential local inflammatory mediator which influences platelet activation in the setting of atherosclerosis. Beyond that, aspects of a potential interaction between fractalkine and platelet responsiveness to antiplatelet drugs are described. Furthermore, the possible impact of high-density lipoprotein cholesterol (HDL-C) on atherosclerosis progression, platelet activation and fractalkine signalling are discussed.
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36
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Li L, Hu J, Shi X, Shao Y, Song F. Lipid rafts enhance the binding constant of membrane-anchored receptors and ligands. SOFT MATTER 2017; 13:4294-4304. [PMID: 28573272 DOI: 10.1039/c7sm00572e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gaining insights into the binding of membrane-anchored receptors and ligands that mediate cell adhesion and signal transduction is of great significance for understanding numerous physiological processes driven by intercellular communication. Lipid rafts, microdomains in cell membranes enriched in cholesterol and saturated lipids such as sphingomyelin, are believed to serve as the essential platforms to recruit protein molecules for biological functions. An important question remains how the lipid rafts affect the binding constant of membrane-anchored receptors and ligands. We have investigated the adhesion of multicomponent membranes by using Monte Carlo simulations of a mesoscopic model with biologically relevant parameters. We find that the preferential partitioning of membrane-anchored receptor and ligand proteins in the lipid rafts significantly increases the binding constant of those proteins, in cooperation with the shape fluctuations of the membranes caused by thermal excitations. The binding constant can even be greater than that of the same receptors and ligands anchored to two apposing supported, planar membranes without shape fluctuations. The membrane shape fluctuations facilitate the binding of the anchored receptors and ligands, in contrast to the case of homogeneous membranes. Our results suggest that cells might regulate the binding of membrane-anchored receptor and ligand proteins by modulating the properties of lipid rafts such as area fraction, size and the affinity of rafts to the proteins.
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Affiliation(s)
- Long Li
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.
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37
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Deshpande SA, Pawar AB, Dighe A, Athale CA, Sengupta D. Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association–diffusion models. Phys Biol 2017; 14:036002. [DOI: 10.1088/1478-3975/aa6b68] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Li L, Xu GK, Song F. Impact of lipid rafts on the T-cell-receptor and peptide-major-histocompatibility-complex interactions under different measurement conditions. Phys Rev E 2017; 95:012403. [PMID: 28208397 DOI: 10.1103/physreve.95.012403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Indexed: 01/02/2023]
Abstract
The interactions between T-cell receptor (TCR) and peptide-major-histocompatibility complex (pMHC), which enable T-cell development and initiate adaptive immune responses, have been intensively studied. However, a central issue of how lipid rafts affect the TCR-pMHC interactions remains unclear. Here, by using a statistical-mechanical membrane model, we show that the binding affinity of TCR and pMHC anchored on two apposing cell membranes is significantly enhanced because of the lipid raft-induced signaling protein aggregation. This finding may provide an alternative insight into the mechanism of T-cell activation triggered by very low densities of pMHC. In the case of cell-substrate adhesion, our results indicate that the loss of lateral mobility of the proteins on the solid substrate leads to the inhibitory effect of lipid rafts on TCR-pMHC interactions. Our findings help to understand why different experimental methods for measuring the impact of lipid rafts on the receptor-ligand interactions have led to contradictory conclusions.
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Affiliation(s)
- Long Li
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Guang-Kui Xu
- International Center for Applied Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing 100049, China
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SNAP23-Dependent Surface Translocation of Leukotriene B4 (LTB4) Receptor 1 Is Essential for NOX2-Mediated Exocytotic Degranulation in Human Mast Cells Induced by Trichomonas vaginalis-Secreted LTB4. Infect Immun 2016; 85:IAI.00526-16. [PMID: 27795355 DOI: 10.1128/iai.00526-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/16/2016] [Indexed: 11/20/2022] Open
Abstract
Trichomonas vaginalis is a sexually transmitted parasite that causes vaginitis in women and itself secretes lipid mediator leukotriene B4 (LTB4). Mast cells are important effector cells of tissue inflammation during infection with parasites. Membrane-bridging SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complexes are critical for fusion during exocytosis. Although T. vaginalis-derived secretory products (TvSP) have been shown to induce exocytosis in mast cells, information regarding the signaling mechanisms between mast cell activation and TvSP is limited. In this study, we found that SNAP23-dependent surface trafficking of LTB4 receptor 1 (BLT1) is required for nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2)-mediated exocytotic degranulation of mast cells induced by TvSP. First, stimulation with TvSP induced exocytotic degranulation and reactive oxygen species (ROS) generation in HMC-1 cells. Next, TvSP-induced ROS generation and exocytosis were strongly inhibited by transfection of BLT1 small interfering RNA (siRNA). TvSP induced trafficking of BLT1 from the cytosol to the plasma membrane. We also found that knockdown of SNAP23 abrogated TvSP-induced ROS generation, exocytosis, and surface trafficking of BLT1 in HMC-1 cells. By coimmunoprecipitation, there was a physical interaction between BLT1 and SNAP23 in TvSP-stimulated HMC-1 cells. Taken together, our results suggest that SNAP23-dependent surface trafficking of BLT1 is essential for exocytosis in human mast cells induced by T. vaginalis-secreted LTB4 Our data collectively demonstrate a novel regulatory mechanism for SNAP23-dependent mast cell activation of T. vaginalis-secreted LTB4 involving surface trafficking of BLT1. These results can help to explain how the cross talk mechanism between parasite and host can govern deliberately tissue inflammatory responses.
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40
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Gahbauer S, Böckmann RA. Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function. Front Physiol 2016; 7:494. [PMID: 27826255 PMCID: PMC5078798 DOI: 10.3389/fphys.2016.00494] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/11/2016] [Indexed: 12/18/2022] Open
Abstract
The dimerization or even oligomerization of G protein coupled receptors (GPCRs) causes ongoing, controversial debates about its functional role and the coupled biophysical, biochemical or biomedical implications. A continously growing number of studies hints to a relation between oligomerization and function of GPCRs and strengthens the assumption that receptor assembly plays a key role in the regulation of protein function. Additionally, progress in the structural analysis of GPCR-G protein and GPCR-ligand interactions allows to distinguish between actively functional and non-signaling complexes. Recent findings further suggest that the surrounding membrane, i.e., its lipid composition may modulate the preferred dimerization interface and as a result the abundance of distinct dimeric conformations. In this review, the association of GPCRs and the role of the membrane in oligomerization will be discussed. An overview of the different reported oligomeric interfaces is provided and their capability for signaling discussed. The currently available data is summarized with regard to the formation of GPCR oligomers, their structures and dependency on the membrane microenvironment as well as the coupling of oligomerization to receptor function.
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Affiliation(s)
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-NürnbergErlangen, Germany
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Berger M, Manghi M, Destainville N. Nanodomains in Biomembranes with Recycling. J Phys Chem B 2016; 120:10588-10602. [PMID: 27654087 DOI: 10.1021/acs.jpcb.6b07631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cell membranes are out of thermodynamic equilibrium notably because of membrane recycling, i.e., active exchange of material with the cytosol. We propose an analytically tractable model of biomembrane predicting the effects of recycling on the size of protein nanodomains also called protein clusters. The model includes a short-range attraction between proteins and a weaker long-range repulsion which ensures the existence of so-called cluster phases in equilibrium, where monomeric proteins coexist with finite-size domains. Our main finding is that, when taking recycling into account, the typical cluster size at steady state increases logarithmically with the recycling rate at fixed protein concentration. Using physically realistic model parameters, the predicted 2-fold increase due to recycling in living cells is most likely experimentally measurable with the help of super-resolution microscopy.
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Affiliation(s)
- Mareike Berger
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, F-31062 Toulouse, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, F-31062 Toulouse, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, F-31062 Toulouse, France
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Sengupta D, Joshi M, Athale CA, Chattopadhyay A. What can simulations tell us about GPCRs. Methods Cell Biol 2016; 132:429-52. [DOI: 10.1016/bs.mcb.2015.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Rodríguez-Frade JM, Martínez-Muñoz L, Villares R, Cascio G, Lucas P, Gomariz RP, Mellado M. Chemokine Detection Using Receptors Immobilized on an SPR Sensor Surface. Methods Enzymol 2015; 570:1-18. [PMID: 26921939 DOI: 10.1016/bs.mie.2015.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Chemokines and their receptors take part in many physiological and pathological processes, and their dysregulated expression is linked to chronic inflammatory and autoimmune diseases, immunodeficiencies, and cancer. The chemokine receptors, members of the G protein-coupled receptor family, are integral membrane proteins, with seven-transmembrane domains that bind the chemokines and transmit signals through GTP-binding proteins. Many assays used to study the structure, conformation, or activation mechanism of these receptors are based on ligand-binding measurement, as are techniques to detect new agonists and antagonists that modulate chemokine function. Such methods require labeling of the chemokine and/or its receptor, which can alter their binding characteristics. Surface plasmon resonance (SPR) is a powerful technique for analysis of the interaction between immobilized receptors and ligands in solution, in real time, and without labeling. SPR measurements nonetheless require expression and purification steps that can alter the conformation, stability, and function of the chemokine and/or the chemokine receptor. In this review, we focus on distinct methods to immobilize chemokine receptors on the surface of an optical biosensor. We expose the advantages and disadvantages of different protocols used and describe in detail the method to retain viral particles as receptor carriers that can be used for SPR determinations.
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Affiliation(s)
| | - Laura Martínez-Muñoz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Madrid, Spain
| | - Ricardo Villares
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Madrid, Spain
| | - Graciela Cascio
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Madrid, Spain
| | - Pilar Lucas
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Madrid, Spain
| | - Rosa P Gomariz
- Department of Cell Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Mario Mellado
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Madrid, Spain.
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Is membrane homeostasis the missing link between inflammation and neurodegenerative diseases? Cell Mol Life Sci 2015; 72:4795-805. [PMID: 26403788 PMCID: PMC5005413 DOI: 10.1007/s00018-015-2038-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/16/2015] [Accepted: 09/03/2015] [Indexed: 12/14/2022]
Abstract
Systemic inflammation and infections are associated with neurodegenerative diseases. Unfortunately, the molecular bases of this link are still largely undiscovered. We, therefore, review how inflammatory processes can imbalance membrane homeostasis and theorize how this may have an effect on the aggregation behavior of the proteins implicated in such diseases. Specifically, we describe the processes that generate such imbalances at the molecular level, and try to understand how they affect protein folding and localization. Overall, current knowledge suggests that microglia pro-inflammatory mediators can generate membrane damage, which may have an impact in terms of triggering or accelerating disease manifestation.
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Haack F, Lemcke H, Ewald R, Rharass T, Uhrmacher AM. Spatio-temporal model of endogenous ROS and raft-dependent WNT/beta-catenin signaling driving cell fate commitment in human neural progenitor cells. PLoS Comput Biol 2015; 11:e1004106. [PMID: 25793621 PMCID: PMC4368204 DOI: 10.1371/journal.pcbi.1004106] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 12/31/2014] [Indexed: 02/03/2023] Open
Abstract
Canonical WNT/β-catenin signaling is a central pathway in embryonic development, but it is also connected to a number of cancers and developmental disorders. Here we apply a combined in-vitro and in-silico approach to investigate the spatio-temporal regulation of WNT/β-catenin signaling during the early neural differentiation process of human neural progenitors cells (hNPCs), which form a new prospect for replacement therapies in the context of neurodegenerative diseases. Experimental measurements indicate a second signal mechanism, in addition to canonical WNT signaling, being involved in the regulation of nuclear β-catenin levels during the cell fate commitment phase of neural differentiation. We find that the biphasic activation of β-catenin signaling observed experimentally can only be explained through a model that combines Reactive Oxygen Species (ROS) and raft dependent WNT/β-catenin signaling. Accordingly after initiation of differentiation endogenous ROS activates DVL in a redox-dependent manner leading to a transient activation of down-stream β-catenin signaling, followed by continuous auto/paracrine WNT signaling, which crucially depends on lipid rafts. Our simulation studies further illustrate the elaborate spatio-temporal regulation of DVL, which, depending on its concentration and localization, may either act as direct inducer of the transient ROS/β-catenin signal or as amplifier during continuous auto-/parcrine WNT/β-catenin signaling. In addition we provide the first stochastic computational model of WNT/β-catenin signaling that combines membrane-related and intracellular processes, including lipid rafts/receptor dynamics as well as WNT- and ROS-dependent β-catenin activation. The model’s predictive ability is demonstrated under a wide range of varying conditions for in-vitro and in-silico reference data sets. Our in-silico approach is realized in a multi-level rule-based language, that facilitates the extension and modification of the model. Thus, our results provide both new insights and means to further our understanding of canonical WNT/β-catenin signaling and the role of ROS as intracellular signaling mediator. Human neural progenitor cells offer the promising perspective of using in-vitro grown neural cell populations for replacement therapies in the context of neurodegenerative diseases, such as Parkinson’s or Huntington’s disease. However, to control hNPC differentiation within the scope of stem cell engineering, a thorough understanding of cell fate determination and its endogenous regulation is required. Here we investigate the spatio-temporal regulation of WNT/β-catenin signaling in the process of cell fate commitment in hNPCs, which has been reported to play a crucial role for the differentiation process of hNPCs. Based on a combined in-vitro and in-silico approach we demonstrate an elaborate interplay between endogenous ROS and lipid raft dependent WNT/beta-catenin signaling controlling the nuclear beta-catenin levels throughout the initial phase of neural differentiation. The stochastic multi-level computational model we derive from our experimental measurements adds to the family of existing WNT models, addressing major biochemical and spatial aspects of WNT/beta-catenin signaling that have not been considered in existing models so far. Cross validation studies manifest its predictive capability for other cells and cell lines rendering the model a suitable basis for further studies also in the context of embryonic development, developmental disorders and cancers.
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Affiliation(s)
- Fiete Haack
- Modeling and Simulation Group, Institute of Computer Science, University of Rostock, Rostock, Germany
- * E-mail:
| | - Heiko Lemcke
- Live Cell Imaging Center, Institute of Biological Sciences, University of Rostock, Rostock, Germany
- Reference and Translation Center for Cardiac Stem Cell Therapy (RTC), University Medical Center Rostock, Rostock, Germany
| | - Roland Ewald
- Modeling and Simulation Group, Institute of Computer Science, University of Rostock, Rostock, Germany
| | - Tareck Rharass
- Live Cell Imaging Center, Institute of Biological Sciences, University of Rostock, Rostock, Germany
- Electrochemical Signaling in Development and Disease, Max-Delbrück-Center for Molecular Medicine (MDC) Berlin-Buch, Berlin-Buch, Germany
| | - Adelinde M. Uhrmacher
- Modeling and Simulation Group, Institute of Computer Science, University of Rostock, Rostock, Germany
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Martínez-Muñoz L, Barroso R, Paredes AG, Mellado M, Rodríguez-Frade JM. Methods to immobilize GPCR on the surface of SPR sensors. Methods Mol Biol 2015; 1272:173-188. [PMID: 25563184 DOI: 10.1007/978-1-4939-2336-6_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The G protein-coupled receptors (GPCRs) form one of the largest membrane receptor families. The nature of the ligands that interact with these receptors is highly diverse; they include light, peptides and hormones, neurotransmitters, and small molecular weight compounds. The GPCRs are involved in a wide variety of physiological processes and thus hold considerable therapeutic potential.GPCR function is usually determined in cell-based assays, whose complexity nonetheless limits their use. The use of alternative, cell-free assays is hampered by the difficulties in purifying these seven-transmembrane domain receptors without altering their functional properties. Several methods have been proposed to immobilize GPCR on biosensor surfaces which use antibodies or avidin-/biotin-based capture procedures, alone or with reconstitution of the GPCR physiological microenvironment. Here we propose a method for GPCR immobilization in their native membrane microenvironment that requires no manipulation of the target receptor and maintains the many conformations GPCR can adopt in the cell membrane.
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Affiliation(s)
- Laura Martínez-Muñoz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain
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Abstract
The publication of high-resolution structures for all of the opioid receptor subfamilies has unveiled exciting opportunities for mechanistic insight into the molecular mechanisms underlying the biology of nociception, reward, and higher cognitive functions, as well as promises for progress in several clinical areas such as pain management, physiological dependence, addiction, and mood disorders. To turn this promise into novel and improved therapeutic entities, however, this information needs to be supplemented with research strategies that explore the dynamic behavior of the proteins and their interactions with other receptors and ligands in their physiological environment.Here we describe state-of-the-art molecular dynamics computational protocols, based on all-atom and coarse-grained modeling techniques, designed to estimate crucial thermodynamic and kinetic parameters describing the binding of small-molecule ligands and the formation of supramolecular complexes.
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48
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Ge Y, Siegel AP, Jordan R, Naumann CA. Ligand binding alters dimerization and sequestering of urokinase receptors in raft-mimicking lipid mixtures. Biophys J 2014; 107:2101-11. [PMID: 25418095 PMCID: PMC4223190 DOI: 10.1016/j.bpj.2014.09.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/05/2014] [Accepted: 09/19/2014] [Indexed: 11/17/2022] Open
Abstract
Lipid heterogeneities, such as lipid rafts, are widely considered to be important for the sequestering of membrane proteins in plasma membranes, thereby influencing membrane protein functionality. However, the underlying mechanisms of such sequestration processes remain elusive, in part, due to the small size and often transient nature of these functional membrane heterogeneities in cellular membranes. To overcome these challenges, here we report the sequestration behavior of urokinase receptor (uPAR), a glycosylphosphatidylinositol-anchored protein, in a planar model membrane platform with raft-mimicking lipid mixtures of well-defined compositions using a powerful optical imaging platform consisting of confocal spectroscopy XY-scans, photon counting histogram, and fluorescence correlation spectroscopy analyses. This methodology provides parallel information about receptor sequestration, oligomerization state, and lateral mobility with single molecule sensitivity. Most notably, our experiments demonstrate that moderate changes in uPAR sequestration are not only associated with modifications in uPAR dimerization levels, but may also be linked to ligand-mediated allosteric changes of these membrane receptors. Our data show that these modifications in uPAR sequestration can be induced by exposure to specific ligands (urokinase plasminogen activator, vitronectin), but not via adjustment of the cholesterol level in the planar model membrane system. Good agreement of our key findings with published results on cell membranes confirms the validity of our model membrane approach. We hypothesize that the observed mechanism of receptor translocation in the presence of raft-mimicking lipid mixtures is also applicable to other glycosylphosphatidylinositol-anchored proteins.
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Affiliation(s)
- Yifan Ge
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana
| | - Amanda P Siegel
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana; Integrated Nanosystems Development Institute, Indiana University-Purdue University, Indianapolis, Indiana
| | - Rainer Jordan
- Makromolekulare Chemie, TU Dresden, Dresden, Germany
| | - Christoph A Naumann
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana; Integrated Nanosystems Development Institute, Indiana University-Purdue University, Indianapolis, Indiana.
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49
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Szalai B, Hoffmann P, Prokop S, Erdélyi L, Várnai P, Hunyady L. Improved methodical approach for quantitative BRET analysis of G Protein Coupled Receptor dimerization. PLoS One 2014; 9:e109503. [PMID: 25329164 PMCID: PMC4201472 DOI: 10.1371/journal.pone.0109503] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/11/2014] [Indexed: 01/22/2023] Open
Abstract
G Protein Coupled Receptors (GPCR) can form dimers or higher ordered oligomers, the process of which can remarkably influence the physiological and pharmacological function of these receptors. Quantitative Bioluminescence Resonance Energy Transfer (qBRET) measurements are the gold standards to prove the direct physical interaction between the protomers of presumed GPCR dimers. For the correct interpretation of these experiments, the expression of the energy donor Renilla luciferase labeled receptor has to be maintained constant, which is hard to achieve in expression systems. To analyze the effects of non-constant donor expression on qBRET curves, we performed Monte Carlo simulations. Our results show that the decrease of donor expression can lead to saturation qBRET curves even if the interaction between donor and acceptor labeled receptors is non-specific leading to false interpretation of the dimerization state. We suggest here a new approach to the analysis of qBRET data, when the BRET ratio is plotted as a function of the acceptor labeled receptor expression at various donor receptor expression levels. With this method, we were able to distinguish between dimerization and non-specific interaction when the results of classical qBRET experiments were ambiguous. The simulation results were confirmed experimentally using rapamycin inducible heterodimerization system. We used this new method to investigate the dimerization of various GPCRs, and our data have confirmed the homodimerization of V2 vasopressin and CaSR calcium sensing receptors, whereas our data argue against the heterodimerization of these receptors with other studied GPCRs, including type I and II angiotensin, β2 adrenergic and CB1 cannabinoid receptors.
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Affiliation(s)
- Bence Szalai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
| | - Péter Hoffmann
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Susanne Prokop
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - László Erdélyi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
| | - Péter Várnai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
| | - László Hunyady
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
- * E-mail:
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50
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Clancy T, Hovig E. From proteomes to complexomes in the era of systems biology. Proteomics 2014; 14:24-41. [PMID: 24243660 DOI: 10.1002/pmic.201300230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 10/22/2013] [Accepted: 11/06/2013] [Indexed: 01/16/2023]
Abstract
Protein complexes carry out almost the entire signaling and functional processes in the cell. The protein complex complement of a cell, and its network of complex-complex interactions, is referred to here as the complexome. Computational methods to predict protein complexes from proteomics data, resulting in network representations of complexomes, have recently being developed. In addition, key advances have been made toward understanding the network and structural organization of complexomes. We review these bioinformatics advances, and their discovery-potential, as well as the merits of integrating proteomics data with emerging methods in systems biology to study protein complex signaling. It is envisioned that improved integration of proteomics and systems biology, incorporating the dynamics of protein complexes in space and time, may lead to more predictive models of cell signaling networks for effective modulation.
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Affiliation(s)
- Trevor Clancy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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