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Latypova AA, Yaremenko AV, Pechnikova NA, Minin AS, Zubarev IV. Magnetogenetics as a promising tool for controlling cellular signaling pathways. J Nanobiotechnology 2024; 22:327. [PMID: 38858689 PMCID: PMC11163773 DOI: 10.1186/s12951-024-02616-z] [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: 03/28/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024] Open
Abstract
Magnetogenetics emerges as a transformative approach for modulating cellular signaling pathways through the strategic application of magnetic fields and nanoparticles. This technique leverages the unique properties of magnetic nanoparticles (MNPs) to induce mechanical or thermal stimuli within cells, facilitating the activation of mechano- and thermosensitive proteins without the need for traditional ligand-receptor interactions. Unlike traditional modalities that often require invasive interventions and lack precision in targeting specific cellular functions, magnetogenetics offers a non-invasive alternative with the capacity for deep tissue penetration and the potential for targeting a broad spectrum of cellular processes. This review underscores magnetogenetics' broad applicability, from steering stem cell differentiation to manipulating neuronal activity and immune responses, highlighting its potential in regenerative medicine, neuroscience, and cancer therapy. Furthermore, the review explores the challenges and future directions of magnetogenetics, including the development of genetically programmed magnetic nanoparticles and the integration of magnetic field-sensitive cells for in vivo applications. Magnetogenetics stands at the forefront of cellular manipulation technologies, offering novel insights into cellular signaling and opening new avenues for therapeutic interventions.
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Affiliation(s)
- Anastasiia A Latypova
- Institute of Future Biophysics, Dolgoprudny, 141701, Russia
- Moscow Center for Advanced Studies, Moscow, 123592, Russia
| | - Alexey V Yaremenko
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Nadezhda A Pechnikova
- Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
- Saint Petersburg Pasteur Institute, Saint Petersburg, 197101, Russia
| | - Artem S Minin
- M.N. Mikheev Institute of Metal Physics of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, 620108, Russia
| | - Ilya V Zubarev
- Institute of Future Biophysics, Dolgoprudny, 141701, Russia.
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2
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Liang J, Smith AW. The Oligomeric State of Vasorin in the Plasma Membrane Measured Non-Invasively by Quantitative Fluorescence Fluctuation Spectroscopy. Int J Mol Sci 2024; 25:4115. [PMID: 38612924 PMCID: PMC11012933 DOI: 10.3390/ijms25074115] [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] [Received: 03/04/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Vasorin (VASN), a transmembrane protein heavily expressed in endothelial cells, has garnered recent interest due to its key role in vascular development and pathology. The oligomeric state of VASN is a crucial piece of knowledge given that receptor clustering is a frequent regulatory mechanism in downstream signaling activation and amplification. However, documentation of VASN oligomerization is currently absent. In this brief report, we describe the measurement of VASN oligomerization in its native membranous environment, leveraging a class of fluorescence fluctuation spectroscopy. Our investigation revealed that the majority of VASN resides in a monomeric state, while a minority of VASN forms homodimers in the cellular membrane. This result raises the intriguing possibility that ligand-independent clustering of VASN may play a role in transforming growth factor signaling.
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Affiliation(s)
- Junyi Liang
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Adam W. Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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3
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Cheng YW, Anzell AR, Morosky SA, Schwartze TA, Hinck CS, Hinck AP, Roman BL, Davidson LA. Shear Stress and Sub-Femtomolar Levels of Ligand Synergize to Activate ALK1 Signaling in Endothelial Cells. Cells 2024; 13:285. [PMID: 38334677 PMCID: PMC10854672 DOI: 10.3390/cells13030285] [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: 10/25/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Endothelial cells (ECs) respond to concurrent stimulation by biochemical factors and wall shear stress (SS) exerted by blood flow. Disruptions in flow-induced responses can result in remodeling issues and cardiovascular diseases, but the detailed mechanisms linking flow-mechanical cues and biochemical signaling remain unclear. Activin receptor-like kinase 1 (ALK1) integrates SS and ALK1-ligand cues in ECs; ALK1 mutations cause hereditary hemorrhagic telangiectasia (HHT), marked by arteriovenous malformation (AVM) development. However, the mechanistic underpinnings of ALK1 signaling modulation by fluid flow and the link to AVMs remain uncertain. We recorded EC responses under varying SS magnitudes and ALK1 ligand concentrations by assaying pSMAD1/5/9 nuclear localization using a custom multi-SS microfluidic device and a custom image analysis pipeline. We extended the previously reported synergy between SS and BMP9 to include BMP10 and BMP9/10. Moreover, we demonstrated that this synergy is effective even at extremely low SS magnitudes (0.4 dyn/cm2) and ALK1 ligand range (femtogram/mL). The synergistic response to ALK1 ligands and SS requires the kinase activity of ALK1. Moreover, ALK1's basal activity and response to minimal ligand levels depend on endocytosis, distinct from cell-cell junctions, cytoskeleton-mediated mechanosensing, or cholesterol-enriched microdomains. However, an in-depth analysis of ALK1 receptor trafficking's molecular mechanisms requires further investigation.
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Affiliation(s)
- Ya-Wen Cheng
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Anthony R. Anzell
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Stefanie A. Morosky
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tristin A. Schwartze
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Cynthia S. Hinck
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Andrew P. Hinck
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Beth L. Roman
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lance A. Davidson
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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4
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Gormal RS, Martinez-Marmol R, Brooks AJ, Meunier FA. Location, location, location: Protein kinase nanoclustering for optimised signalling output. eLife 2024; 13:e93902. [PMID: 38206309 PMCID: PMC10783869 DOI: 10.7554/elife.93902] [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: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Protein kinases (PKs) are proteins at the core of cellular signalling and are thereby responsible for most cellular physiological processes and their regulations. As for all intracellular proteins, PKs are subjected to Brownian thermal energy that tends to homogenise their distribution throughout the volume of the cell. To access their substrates and perform their critical functions, PK localisation is therefore tightly regulated in space and time, relying upon a range of clustering mechanisms. These include post-translational modifications, protein-protein and protein-lipid interactions, as well as liquid-liquid phase separation, allowing spatial restriction and ultimately regulating access to their substrates. In this review, we will focus on key mechanisms mediating PK nanoclustering in physiological and pathophysiological processes. We propose that PK nanoclusters act as a cellular quantal unit of signalling output capable of integration and regulation in space and time. We will specifically outline the various super-resolution microscopy approaches currently used to elucidate the composition and mechanisms driving PK nanoscale clustering and explore the pathological consequences of altered kinase clustering in the context of neurodegenerative disorders, inflammation, and cancer.
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Affiliation(s)
- Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Ramon Martinez-Marmol
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Andrew J Brooks
- Frazer Institute, The University of QueenslandWoolloongabbaAustralia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
- School of Biomedical Sciences, The University of QueenslandSt LuciaAustralia
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5
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Tripathi R, Guglani A, Ghorpade R, Wang B. Biotin conjugates in targeted drug delivery: is it mediated by a biotin transporter, a yet to be identified receptor, or (an)other unknown mechanism(s)? J Enzyme Inhib Med Chem 2023; 38:2276663. [PMID: 37955285 PMCID: PMC10653662 DOI: 10.1080/14756366.2023.2276663] [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: 08/08/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Conjugation of drugs with biotin is a widely studied strategy for targeted drug delivery. The structure-activity relationship (SAR) studies through H3-biotin competition experiments conclude with the presence of a free carboxylic acid being essential for its uptake via the sodium-dependent multivitamin transporter (SMVT, the major biotin transporter). However, biotin conjugation with a payload requires modification of the carboxylic acid to an amide or ester group. Then, there is the question as to how/whether the uptake of biotin conjugates goes through the SMVT. If not, then what is the mechanism? Herein, we present known uptake mechanisms of biotin and its applications reported in the literature. We also critically analyse possible uptake mechanism(s) of biotin conjugates to address the disconnect between the results from SMVT-based SAR and "biotin-facilitated" targeted drug delivery. We believe understanding the uptake mechanism of biotin conjugates is critical for their future applications and further development.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Anchala Guglani
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Rujuta Ghorpade
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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6
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Sonnino S. The relationship between depletion of brain GM1 ganglioside and Parkinson's disease. FEBS Open Bio 2023; 13:1548-1557. [PMID: 36638010 PMCID: PMC10476573 DOI: 10.1002/2211-5463.13554] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
GM1 is one of the main gangliosides of the nervous system, and it exerts neurotrophic and neuroprotective properties in neurons. It is involved in many processes necessary for the correct physiology of neuronal cells. In particular, it is necessary for the activity of neuronal receptors that control processes such as differentiation, survival, and mitochondrial activity. A shortage of GM1 in the substantia nigra is potentially responsible for the neurodegeneration present in Parkinson's disease patients. In this review, I report on the role played by GM1 in neurons and how its genetic shortage may be responsible for the onset of Parkinson's disease.
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Affiliation(s)
- Sandro Sonnino
- Department of Medical Biotechnology and Translational MedicineUniversity of MilanItaly
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7
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Gambles MT, Yang J, Kopeček J. Multi-targeted immunotherapeutics to treat B cell malignancies. J Control Release 2023; 358:232-258. [PMID: 37121515 PMCID: PMC10330463 DOI: 10.1016/j.jconrel.2023.04.048] [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: 01/05/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
The concept of multi-targeted immunotherapeutic systems has propelled the field of cancer immunotherapy into an exciting new era. Multi-effector molecules can be designed to engage with, and alter, the patient's immune system in a plethora of ways. The outcomes can vary from effector cell recruitment and activation upon recognition of a cancer cell, to a multipronged immune checkpoint blockade strategy disallowing evasion of the cancer cells by immune cells, or to direct cancer cell death upon engaging multiple cell surface receptors simultaneously. Here, we review the field of multi-specific immunotherapeutics implemented to treat B cell malignancies. The mechanistically diverse strategies are outlined and discussed; common B cell receptor antigen targeting strategies are outlined and summarized; and the challenges of the field are presented along with optimistic insights for the future.
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Affiliation(s)
- M Tommy Gambles
- Center for Controlled Chemical Delivery, University of Utah, Salt Lake City, UT 84112, USA; Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT 84112, USA
| | - Jiyuan Yang
- Center for Controlled Chemical Delivery, University of Utah, Salt Lake City, UT 84112, USA; Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT 84112, USA.
| | - Jindřich Kopeček
- Center for Controlled Chemical Delivery, University of Utah, Salt Lake City, UT 84112, USA; Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA.
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8
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The Impact of Membrane Protein Diffusion on GPCR Signaling. Cells 2022; 11:cells11101660. [PMID: 35626696 PMCID: PMC9139411 DOI: 10.3390/cells11101660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 12/10/2022] Open
Abstract
Spatiotemporal signal shaping in G protein-coupled receptor (GPCR) signaling is now a well-established and accepted notion to explain how signaling specificity can be achieved by a superfamily sharing only a handful of downstream second messengers. Dozens of Gs-coupled GPCR signals ultimately converge on the production of cAMP, a ubiquitous second messenger. This idea is almost always framed in terms of local concentrations, the differences in which are maintained by means of spatial separation. However, given the dynamic nature of the reaction-diffusion processes at hand, the dynamics, in particular the local diffusional properties of the receptors and their cognate G proteins, are also important. By combining some first principle considerations, simulated data, and experimental data of the receptors diffusing on the membranes of living cells, we offer a short perspective on the modulatory role of local membrane diffusion in regulating GPCR-mediated cell signaling. Our analysis points to a diffusion-limited regime where the effective production rate of activated G protein scales linearly with the receptor–G protein complex’s relative diffusion rate and to an interesting role played by the membrane geometry in modulating the efficiency of coupling.
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9
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Morzy D, Bastings M. Significance of Receptor Mobility in Multivalent Binding on Lipid Membranes. Angew Chem Int Ed Engl 2022; 61:e202114167. [PMID: 34982497 PMCID: PMC9303963 DOI: 10.1002/anie.202114167] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Indexed: 01/16/2023]
Abstract
Numerous key biological processes rely on the concept of multivalency, where ligands achieve stable binding only upon engaging multiple receptors. These processes, like viral entry or immune synapse formation, occur on the diffusive cellular membrane. One crucial, yet underexplored aspect of multivalent binding is the mobility of coupled receptors. Here, we discuss the consequences of mobility in multivalent processes from four perspectives: (I) The facilitation of receptor recruitment by the multivalent ligand due to their diffusivity prior to binding. (II) The effects of receptor preassembly, which allows their local accumulation. (III) The consequences of changes in mobility upon the formation of receptor/ligand complex. (IV) The changes in the diffusivity of lipid environment surrounding engaged receptors. We demonstrate how understanding mobility is essential for fully unravelling the principles of multivalent membrane processes, leading to further development in studies on receptor interactions, and guide the design of new generations of multivalent ligands.
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Affiliation(s)
- Diana Morzy
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale de Lausanne, Route Cantonale, 1015, Lausanne, Switzerland
| | - Maartje Bastings
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale de Lausanne, Route Cantonale, 1015, Lausanne, Switzerland
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10
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Morzy D, Bastings M. Significance of Receptor Mobility in Multivalent Binding on Lipid Membranes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Diana Morzy
- Programmable Biomaterials Laboratory Institute of Materials School of Engineering École Polytechnique Fédérale de Lausanne Route Cantonale 1015 Lausanne Switzerland
| | - Maartje Bastings
- Programmable Biomaterials Laboratory Institute of Materials School of Engineering École Polytechnique Fédérale de Lausanne Route Cantonale 1015 Lausanne Switzerland
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11
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Nanomedicine in Pancreatic Cancer: Current Status and Future Opportunities for Overcoming Therapy Resistance. Cancers (Basel) 2021; 13:cancers13246175. [PMID: 34944794 PMCID: PMC8699181 DOI: 10.3390/cancers13246175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Despite access to a vast arsenal of anticancer agents, many fail to realise their full therapeutic potential in clinical practice. One key determinant of this is the evolution of multifaceted resistance mechanisms within the tumour that may either pre-exist or develop during the course of therapy. This is particularly evident in pancreatic cancer, where limited responses to treatment underlie dismal survival rates, highlighting the urgent need for new therapeutic approaches. Here, we discuss the major features of pancreatic tumours that contribute to therapy resistance, and how they may be alleviated through exploitation of the mounting and exciting promise of nanomedicines; a unique collection of nanoscale platforms with tunable and multifunctional capabilities that have already elicited a widespread impact on cancer management. Abstract The development of drug resistance remains one of the greatest clinical oncology challenges that can radically dampen the prospect of achieving complete and durable tumour control. Efforts to mitigate drug resistance are therefore of utmost importance, and nanotechnology is rapidly emerging for its potential to overcome such issues. Studies have showcased the ability of nanomedicines to bypass drug efflux pumps, counteract immune suppression, serve as radioenhancers, correct metabolic disturbances and elicit numerous other effects that collectively alleviate various mechanisms of tumour resistance. Much of this progress can be attributed to the remarkable benefits that nanoparticles offer as drug delivery vehicles, such as improvements in pharmacokinetics, protection against degradation and spatiotemporally controlled release kinetics. These attributes provide scope for precision targeting of drugs to tumours that can enhance sensitivity to treatment and have formed the basis for the successful clinical translation of multiple nanoformulations to date. In this review, we focus on the longstanding reputation of pancreatic cancer as one of the most difficult-to-treat malignancies where resistance plays a dominant role in therapy failure. We outline the mechanisms that contribute to the treatment-refractory nature of these tumours, and how they may be effectively addressed by harnessing the unique capabilities of nanomedicines. Moreover, we include a brief perspective on the likely future direction of nanotechnology in pancreatic cancer, discussing how efforts to develop multidrug formulations will guide the field further towards a therapeutic solution for these highly intractable tumours.
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12
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Tan ZC, Meyer AS. A general model of multivalent binding with ligands of heterotypic subunits and multiple surface receptors. Math Biosci 2021; 342:108714. [PMID: 34637774 PMCID: PMC8612982 DOI: 10.1016/j.mbs.2021.108714] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Multivalent cell surface receptor binding is a ubiquitous biological phenomenon with functional and therapeutic significance. Predicting the amount of ligand binding for a cell remains an important question in computational biology as it can provide great insight into cell-to-cell communication and rational drug design toward specific targets. In this study, we extend a mechanistic, two-step multivalent binding model. This model predicts the behavior of a mixture of different multivalent ligand complexes binding to cells expressing various types of receptors. It accounts for the combinatorially large number of interactions between multiple ligands and receptors, optionally allowing a mixture of complexes with different valencies and complexes that contain heterogeneous ligand units. We derive the macroscopic predictions and demonstrate how this model enables large-scale predictions on mixture binding and the binding space of a ligand. This model thus provides an elegant and computationally efficient framework for analyzing multivalent binding.
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Affiliation(s)
- Zhixin Cyrillus Tan
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, 90095, United States
| | - Aaron S Meyer
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, 90095, United States; Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, 90095, United States; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, 90095, United States; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California, 90095, United States.
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13
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Femminella M, Reali G. A Simple Queuing Model for Molecular Communications Receivers. SENSORS (BASEL, SWITZERLAND) 2021; 21:7664. [PMID: 34833758 PMCID: PMC8625728 DOI: 10.3390/s21227664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022]
Abstract
The complexity of molecular communications system, involving a massive number of interacting entities, makes scalability a fundamental property of simulators and modeling tools. A typical scenario is that of targeted drug delivery systems, which makes use of biological nanomachines close to a biological target, able to release molecules in the diseased area. In this paper, we propose a simple but reliable receiver model for diffusion-based molecular communication systems tackling the time needed for analyzing such a system. The proposed model consists of using an equivalent markovian queuing model, which reproduces the aggregate behavior of thousands of receptors spread over the receiver surface. It takes into account not only the fact that the absorption of molecules can occur only through receptors, but also that absorption is not an instantaneous process and may require a significant time during which the receptor is not available to bind to other molecules. Our results, expressed in terms of number of absorbed molecules and average number of busy receptors, demonstrate that the proposed approach is in good agreement with results obtained through particle-based simulations of a large number of receptors, although the time taken for obtaining the results with the proposed model is an order of magnitudes lower than the simulation time. We believe that this model can be the precursor of novel class of models based on similar principles that allow realizing reliable simulations of much larger systems.
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Affiliation(s)
- Mauro Femminella
- Department of Engineering, University of Perugia, Via G. Duranti 93, 06125 Perugia, Italy;
- Consorzio Nazionale Interuniversitario per le Telecomunicazioni (CNIT), 43124 Parma, Italy
| | - Gianluca Reali
- Department of Engineering, University of Perugia, Via G. Duranti 93, 06125 Perugia, Italy;
- Consorzio Nazionale Interuniversitario per le Telecomunicazioni (CNIT), 43124 Parma, Italy
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14
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Kalwarczyk T, Bielec K, Burdzy K, Holyst R. Influence of molecular rebinding on the reaction rate of complex formation. Phys Chem Chem Phys 2021; 23:19343-19351. [PMID: 34524310 DOI: 10.1039/d1cp02820k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We simulated Brownian diffusion and reaction-diffusion processes to study the influence of molecular rebinding on the reaction rates of bimolecular reactions. We found that the number of rebinding events, Nreb, is proportional to the target's size and inversely proportional to the diffusion coefficient D and simulation time-step Δt. We found the proportionality constant close to π-1/2. We confirmed that Nreb is defined as a ratio of the activation-limited rate constant ka to the diffusion-limited rate constant, kD. We provide the formula describing the reactivity coefficient κ, modelling the transient-native complex transition for the activation-controlled reaction rates. We show that κ is proportional to (D/Δt)1/2. Finally, we apply our rebinding-including reaction rate model to the real reactions of photoacid dissociation and protein association. Based on literature data for both types of reactions, we found the Δt time-scale. We show that for the photodissociation of a proton, the Δt is equal to 171 ± 18 fs and the average number of rebinding events is approximately equal to 40. For proteins, Δt is of the order of 100 ps with around 20 rebinding events. In both cases the timescale is similar to the timescale of fluctuation of the solvent molecules surrounding the reactants; vibrations and bending in the case of photoacid dissociation and diffusional motion for proteins.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Burdzy
- Department of Mathematics, Box 354350, University of Washington, Seattle, WA 98195, USA
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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15
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Stimulus-specific responses in innate immunity: Multilayered regulatory circuits. Immunity 2021; 54:1915-1932. [PMID: 34525335 DOI: 10.1016/j.immuni.2021.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/07/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
Immune sentinel cells initiate immune responses to pathogens and tissue injury and are capable of producing highly stimulus-specific responses. Insight into the mechanisms underlying such specificity has come from the identification of regulatory factors and biochemical pathways, as well as the definition of signaling circuits that enable combinatorial and temporal coding of information. Here, we review the multi-layered molecular mechanisms that underlie stimulus-specific gene expression in macrophages. We categorize components of inflammatory and anti-pathogenic signaling pathways into five layers of regulatory control and discuss unifying mechanisms determining signaling characteristics at each layer. In this context, we review mechanisms that enable combinatorial and temporal encoding of information, identify recurring regulatory motifs and principles, and present strategies for integrating experimental and computational approaches toward the understanding of signaling specificity in innate immunity.
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16
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Janssen M, Stenmark H, Carlson A. Divalent ligand-monovalent molecule binding. SOFT MATTER 2021; 17:5375-5383. [PMID: 33961000 PMCID: PMC8691183 DOI: 10.1039/d1sm00070e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Simultaneous binding of a divalent ligand to two identical monovalent molecules is a widespread phenomenon in biology and chemistry. Here, we describe how two such monovalent molecules B bind to a divalent ligand AA to form the intermediate and final complexes AA·B and AA·B2. Cases wherein the total concentration [AA]T is either much larger or much smaller than the total concentration [B]T have been studied earlier, but a systematic description of comparable concentrations [AA]T and [B]T is missing. Here, we present numerical and analytical results for the concentrations [AA·B] and [AA·B2] for the entire range 0 < [B]T/[AA]T < ∞. Specifically, we theoretically study three types of experimental procedures: dilution of AA and B at fixed [B]T/[AA]T, addition of AA at fixed [B]T, and addition of B at fixed [AA]T. When [AA]T and [B]T are comparable, the concentrations of free ligands and molecules both decrease upon binding. Such depletion is expected to be important in cellular contexts, e.g., in antigen detection and in coincidence detection of proteins or lipids.
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Affiliation(s)
- Mathijs Janssen
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
| | - Andreas Carlson
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway.
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17
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Sánchez MF, Els-Heindl S, Beck-Sickinger AG, Wieneke R, Tampé R. Photoinduced receptor confinement drives ligand-independent GPCR signaling. Science 2021; 371:science.abb7657. [PMID: 33632896 DOI: 10.1126/science.abb7657] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022]
Abstract
Cell-cell communication relies on the assembly of receptor-ligand complexes at the plasma membrane. The spatiotemporal receptor organization has a pivotal role in evoking cellular responses. We studied the clustering of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) and established a photoinstructive matrix with ultrasmall lock-and-key interaction pairs to control lateral membrane organization of hormone neuropeptide Y2 receptors in living cells by light. Within seconds, receptor clustering was modulated in size, location, and density. After in situ confinement, changes in cellular morphology, motility, and calcium signaling revealed ligand-independent receptor activation. This approach may enhance the exploration of mechanisms in cell signaling and mechanotransduction.
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Affiliation(s)
- M Florencia Sánchez
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sylvia Els-Heindl
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, 04109 Leipzig, Germany
| | | | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
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18
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Erlendsson S, Teilum K. Binding Revisited-Avidity in Cellular Function and Signaling. Front Mol Biosci 2021; 7:615565. [PMID: 33521057 PMCID: PMC7841115 DOI: 10.3389/fmolb.2020.615565] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
When characterizing biomolecular interactions, avidity, is an umbrella term used to describe the accumulated strength of multiple specific and unspecific interactions between two or more interaction partners. In contrast to the affinity, which is often sufficient to describe monovalent interactions in solution and where the binding strength can be accurately determined by considering only the relationship between the microscopic association and dissociation rates, the avidity is a phenomenological macroscopic parameter linked to several microscopic events. Avidity also covers potential effects of reduced dimensionality and/or hindered diffusion observed at or near surfaces e.g., at the cell membrane. Avidity is often used to describe the discrepancy or the "extra on top" when cellular interactions display binding that are several orders of magnitude stronger than those estimated in vitro. Here we review the principles and theoretical frameworks governing avidity in biological systems and the methods for predicting and simulating avidity. While the avidity and effects thereof are well-understood for extracellular biomolecular interactions, we present here examples of, and discuss how, avidity and the underlying kinetics influences intracellular signaling processes.
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Affiliation(s)
- Simon Erlendsson
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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19
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Sivaram AJ, Wardiana A, Alcantara S, Sonderegger SE, Fletcher NL, Houston ZH, Howard CB, Mahler SM, Alexander C, Kent SJ, Bell CA, Thurecht KJ. Controlling the Biological Fate of Micellar Nanoparticles: Balancing Stealth and Targeting. ACS NANO 2020; 14:13739-13753. [PMID: 32936613 DOI: 10.1021/acsnano.0c06033] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Integrating nanomaterials with biological entities has led to the development of diagnostic tools and biotechnology-derived therapeutic products. However, to optimize the design of these hybrid bionanomaterials, it is essential to understand how controlling the biological interactions will influence desired outcomes. Ultimately, this knowledge will allow more rapid translation from the bench to the clinic. In this paper, we developed a micellar system that was assembled using modular antibody-polymer amphiphilic materials. The amphiphilic nature was established using either poly(ethylene glycol) (PEG) or a single-chain variable fragment (scFv) from an antibody as the hydrophile and a thermoresponsive polymer (poly(oligoethylene glycol) methyl ether methacrylate) as the hydrophobe. By varying the ratios of these components, a series of nanoparticles with different antibody content was self-assembled, where the surface presentation of targeting ligand was carefully controlled. In vitro and in vivo analysis of these systems identified a mismatch between the optimal targeting ligand density to achieve maximum cell association in vitro compared to tumor accumulation in vivo. For this system, we determined an optimum antibody density for both longer circulation and enhanced targeting to tumors that balanced stealthiness of the particle (to evade immune recognition as determined in both mouse models and in whole human blood) with enhanced accumulation achieved through receptor binding on tumor cells in solid tumors. This approach provides fundamental insights into how different antibody densities affect the interaction of designed nanoparticles with both target cells and immune cells, thereby offering a method to probe the intricate interplay between increased targeting efficiency and the subsequent immune response to nanoparticles.
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Affiliation(s)
- Amal J Sivaram
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Andri Wardiana
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Sheilajen Alcantara
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Stefan E Sonderegger
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nicholas L Fletcher
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zachary H Houston
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Cameron Alexander
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Stephen J Kent
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Craig A Bell
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kristofer J Thurecht
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St Lucia, QLD 4072, Australia
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20
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Wang L, DeRose PC, Inwood SL, Gaigalas AK. Stochastic Reaction-Diffusion Model of the Binding of Monoclonal Antibodies to CD4 Receptors on the Surface of T Cells. Int J Mol Sci 2020; 21:E6086. [PMID: 32846978 PMCID: PMC7504294 DOI: 10.3390/ijms21176086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 11/16/2022] Open
Abstract
A stochastic reaction-diffusion model was developed to describe the binding of labeled monoclonal antibodies (mAbs) to CD4 receptors on the surface of T cells. The mAbs diffused to, adsorbed on, and underwent monovalent and bivalent binding to CD4 receptors on the cell surface. The model predicted the time-dependent nature of all populations involved in the labeling process. At large time, the populations reached equilibrium values, giving the number of antibodies bound to the T cell (ABC) defined as the sum of monovalently and bivalently bound mAbs. The predicted coefficient of variation (CV%) of the (ABC) values translated directly to a corresponding CV% of the measured mean fluorescence intensity (MFI). The predicted CV% was about 0.2% from the intrinsic fluctuations of the stochastic reaction process, about 5% after inclusion of the known fluctuations in the number of available CD4 receptors, and about 11% when fluctuations in bivalent binding affinity were included. The fluorescence detection process is expected to contribute approximately 7%. The abovementioned contributions to CV% sum up to approximately 13%. Work is underway to reconcile the predicted values and the measured values of 17% to 22%.
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Affiliation(s)
- Lili Wang
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (L.W.); (P.C.D.); (S.L.I.)
| | - Paul C. DeRose
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (L.W.); (P.C.D.); (S.L.I.)
| | - Sarah L. Inwood
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (L.W.); (P.C.D.); (S.L.I.)
| | - Adolfas K. Gaigalas
- Fluorescence Spectroscopy Consultant, 2650 Lake Shore Drive, Riviera Beach, FL 33404, USA
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21
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Lawley SD, Lindsay AE, Miles CE. Receptor Organization Determines the Limits of Single-Cell Source Location Detection. PHYSICAL REVIEW LETTERS 2020; 125:018102. [PMID: 32678664 DOI: 10.1103/physrevlett.125.018102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Many types of cells require the ability to pinpoint the location of an external stimulus from the arrival of diffusing signaling molecules at cell-surface receptors. How does the organization (number and spatial configuration) of these receptors shape the limit of a cell's ability to infer the source location? In the idealized scenario of a spherical cell, we apply asymptotic analysis to compute splitting probabilities between individual receptors and formulate an information-theoretic framework to quantify the role of receptor organization. Clustered configurations of receptors provide an advantage in detecting sources aligned with the clusters, suggesting a possible multiscale mechanism for single-cell source inference.
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Affiliation(s)
- Sean D Lawley
- Department of Mathematics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Alan E Lindsay
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, South Bend, Indiana 46556, USA
| | - Christopher E Miles
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10005, USA
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22
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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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23
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Evidence for an effect of receptor density on ligand occupancy and agonist EC 50. Sci Rep 2019; 9:19111. [PMID: 31836743 PMCID: PMC6910986 DOI: 10.1038/s41598-019-55361-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/21/2019] [Indexed: 01/16/2023] Open
Abstract
Drug-receptor interaction theory predicts that proportional receptor occupancy is a function of ligand concentration as defined by a ligand-receptor affinity constant, and is independent of receptor density. However, we previously observed that the EC50 of 5-HT reduced as the density of 5-HT3 receptors increased, suggesting an effect of receptor density on occupancy. The current study was designed to maximise variability in experimentally observed currents and confirm this apparent contradiction prospectively. Xenopus oocytes were injected with RNA encoding 5-HT3A receptors under conditions designed to achieve varying receptor expression levels and 5-HT-evoked currents measured using two electrode voltage clamp. Results from 99 oocytes showed that as the maximal peak current increased from 0.05 µA to 12.1 µA there was a 3.7-fold reduction in EC50. Since occupancy and conductance are directly related in this system, this indicates that for a given concentration of 5-HT, proportional occupancy increases with increased receptor density. We conclude that normalising data masks this correlation, and can result in reduced accuracy of pharmacological measurements. We propose a mechanistic explanation for our observations.
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24
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Zhang S, Reinhard BM. Characterizing Large-Scale Receptor Clustering on the Single Cell Level: A Comparative Plasmon Coupling and Fluorescence Superresolution Microscopy Study. J Phys Chem B 2019; 123:5494-5505. [PMID: 31244098 DOI: 10.1021/acs.jpcb.9b05176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Spatial clustering of cell membrane receptors has been indicated to play a regulatory role in signal initiation, and the distribution of receptors on the cell surface may represent a potential biomarker. To realize its potential for diagnostic purposes, scalable assays capable of mapping spatial receptor heterogeneity with high throughput are needed. In this work, we use gold nanoparticle (NP) labels with an average diameter of 72.17 ± 2.16 nm as bright markers for large-scale epidermal growth factor receptor (EGFR) clustering in hyperspectral plasmon coupling microscopy and compare the obtained clustering maps with those obtained through fluorescence superresolution microscopy (direct stochastic optical reconstruction microscopy, dSTORM). Our dSTORM experiments reveal average EGFR cluster sizes of 172 ± 99 and 150 ± 90 nm for MDA-MB-468 and HeLa, respectively. The cluster sizes decrease after EGFR activation. Hyperspectral imaging of the NP labels shows that differences in the EGFR cluster sizes are accompanied by differences in the average separations between electromagnetically coupled NPs. Because of the distance dependence of plasmon coupling, changes in the average interparticle separation result in significant spectral shifts. For the experimental conditions investigated in this work, hyperspectral plasmon coupling microscopy of NP labels identified the same trends in large-scale EGFR clustering as dSTORM, but the NP imaging approach provided the information in a fraction of the time. Both dSTORM and hyperspectral plasmon coupling microscopy confirm the cortical actin network as one structural component that determines the average size of EGFR clusters.
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Affiliation(s)
- Sandy Zhang
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Björn M Reinhard
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
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25
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Multivalent Binding of a Ligand-Coated Particle: Role of Shape, Size, and Ligand Heterogeneity. Biophys J 2019; 114:1830-1846. [PMID: 29694862 DOI: 10.1016/j.bpj.2018.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 01/18/2023] Open
Abstract
We utilize a multiscale modeling framework to study the effect of shape, size, and ligand composition on the efficacy of binding of a ligand-coated particle to a substrate functionalized with the target receptors. First, we show how molecular dynamics along with steered molecular dynamics calculations can be used to accurately parameterize the molecular-binding free energy and the effective spring constant for a receptor-ligand pair. We demonstrate this for two ligands that bind to the α5β1-domain of integrin. Next, we show how these effective potentials can be used to build computational models at the meso- and continuum-scales. These models incorporate the molecular nature of the receptor-ligand interactions and yet provide an inexpensive route to study the multivalent interaction of receptors and ligands through the construction of Bell potentials customized to the molecular identities. We quantify the binding efficacy of the ligand-coated-particle in terms of its multivalency, binding free-energy landscape, and the losses in the configurational entropies. We show that 1) the binding avidity for particle sizes less than 350 nm is set by the competition between the enthalpic and entropic contributions, whereas that for sizes above 350 nm is dominated by the enthalpy of binding; 2) anisotropic particles display higher levels of multivalent binding compared to those of spherical particles; and 3) variations in ligand composition can alter binding avidity without altering the average multivalency. The methods and results presented here have wide applications in the rational design of functionalized carriers and also in understanding cell adhesion.
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26
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Single-Cell Receptor Quantification of an In Vitro Coculture Angiogenesis Model Reveals VEGFR, NRP1, Tie2, and PDGFR Regulation and Endothelial Heterogeneity. Processes (Basel) 2019. [DOI: 10.3390/pr7060356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Angiogenesis, the formation of new blood vessels from pre-existing ones, is essential for both normal development and numerous pathologies. Systems biology has offered a unique approach to study angiogenesis by profiling tyrosine kinase receptors (RTKs) that regulate angiogenic processes and computationally modeling RTK signaling pathways. Historically, this systems biology approach has been applied on ex vivo angiogenesis assays, however, these assays are difficult to quantify and limited in their potential of temporal analysis. In this study, we adopted a simple two-dimensional angiogenesis assay comprised of human umbilical vein endothelial cells (HUVECs) and human dermal fibroblasts (HDFs) and examined temporal dynamics of a panel of six RTKs and cell heterogeneity up to 17 days. We observed ~2700 VEGFR1 (vascular endothelial growth factor receptor 1) per cell on 24-h-old cocultured HDF plasma membranes, which do not express VEGFR when cultured alone. We observed 4000–8100 VEGFR2 per cell on cocultured HUVEC plasma membranes throughout endothelial tube formation. We showed steady increase of platelet-derived growth factor receptors (PDGFRs) on cocultured HDF plasma membranes, and more interestingly, 1900–2900 PDGFRβ per plasma membrane were found on HUVECs within the first six hours of coculturing. These quantitative findings will offer us insights into molecular regulation during angiogenesis and help assess in vitro tube formation models and their physiological relevance.
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27
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Chen S, Imoukhuede PI. Multiplexing Angiogenic Receptor Quantification via Quantum Dots. Anal Chem 2019; 91:7603-7612. [DOI: 10.1021/acs.analchem.9b00238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Si Chen
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, Missouri 63130, United States
| | - P. I. Imoukhuede
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, Missouri 63130, United States
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28
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Lieser RM, Chen W, Sullivan MO. Controlled Epidermal Growth Factor Receptor Ligand Display on Cancer Suicide Enzymes via Unnatural Amino Acid Engineering for Enhanced Intracellular Delivery in Breast Cancer Cells. Bioconjug Chem 2019; 30:432-442. [PMID: 30615416 DOI: 10.1021/acs.bioconjchem.8b00783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteins are ideal candidates for disease treatment because of their high specificity and potency. Despite this potential, delivery of proteins remains a significant challenge due to the intrinsic size, charge, and stability of proteins. Attempts to overcome these challenges have most commonly relied on direct conjugation of polymers and peptides to proteins via reactive groups on naturally occurring residues. While such approaches have shown some success, they allow limited control of the spacing and number of moieties coupled to proteins, which can hinder bioactivity and delivery capabilities of the therapeutic. Here, we describe a strategy to site-specifically conjugate delivery moieties to therapeutic proteins through unnatural amino acid (UAA) incorporation, in order to explore the effect of epidermal growth factor receptor (EGFR)-targeted ligand valency and spacing on internalization of proteins in EGFR-overexpressing inflammatory breast cancer (IBC) cells. Our results demonstrate the ability to enhance targeted protein delivery by tuning a small number of EGFR ligands per protein and clustering these ligands to promote multivalent ligand-receptor interactions. Furthermore, the tailorability of this simple approach was demonstrated through IBC-targeted cell death via the delivery of yeast cytosine deaminase (yCD), a prodrug converting enzyme.
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Affiliation(s)
- Rachel M Lieser
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering , University of Delaware , 150 Academy Street , Newark , Delaware 19716 , United States
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29
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Large DE, Soucy JR, Hebert J, Auguste DT. Advances in Receptor-Mediated, Tumor-Targeted Drug Delivery. ADVANCED THERAPEUTICS 2019; 2:1800091. [PMID: 38699509 PMCID: PMC11064891 DOI: 10.1002/adtp.201800091] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Receptor-mediated drug delivery presents an opportunity to enhance therapeutic efficiency by accumulating drug within the tissue of interest and reducing undesired, off-target effects. In cancer, receptor overexpression is a platform for binding and inhibiting pathways that shape biodistribution, toxicity, cell binding and uptake, and therapeutic function. This review will identify tumor-targeted drug delivery vehicles and receptors that show promise for clinical translation based on quantitative in vitro and in vivo data. The authors describe the rationale to engineer a targeted drug delivery vehicle based on the ligand, chemical conjugation method, and type of drug delivery vehicle. Recent advances in multivalent targeting and ligand organization on tumor accumulation are discussed. Revolutionizing receptor-mediated drug delivery may be leveraged in the therapeutic delivery of chemotherapy, gene editing tools, and epigenetic drugs.
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Affiliation(s)
- Danielle E Large
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA
| | - Jonathan R Soucy
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA
| | - Jacob Hebert
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA
| | - Debra T Auguste
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA
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Johnston MC, Scott CJ. Antibody conjugated nanoparticles as a novel form of antibody drug conjugate chemotherapy. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 30:63-69. [PMID: 30553522 DOI: 10.1016/j.ddtec.2018.10.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 06/09/2023]
Abstract
Antibody conjugated nanoparticles (ACNPs) represent a novel strategy for the development of therapies exploiting antibodies to augment the delivery of chemotherapy payloads. Following in the footsteps of the success of antibody drug conjugates (ADCs), ACNPs are only now reaching clinical evaluation. In this review we discuss the success of ADCs and explore the opportunities ACNPs offer, such as broad chemotherapy payload selection, high drug to antibody ratios and the ability to finely tailor drug release in comparison to ADCs. The ability of ACNPs to elicit increased avidity due to multivalent effects and the potential to use these modular platforms in immunotherapeutic approaches is also explored. Through addressing challenges that still remain in bringing these complex formulations to the clinic, ACNPs hold obvious potential for the treatment of a wide range of cancers and other diseases where selective targeting of drug agents is essential.
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Affiliation(s)
- Michael C Johnston
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, United Kingdom
| | - Christopher J Scott
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, United Kingdom.
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31
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Zhang Q, Reinhard BM. Ligand Density and Nanoparticle Clustering Cooperate in the Multivalent Amplification of Epidermal Growth Factor Receptor Activation. ACS NANO 2018; 12:10473-10485. [PMID: 30289688 PMCID: PMC6252274 DOI: 10.1021/acsnano.8b06141] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Multivalent presentation of ligands on nanoparticles (NPs) is considered a general strategy for enhancing receptor binding and activation through amplification of ligand-receptor interactions within the footprint of the individual NPs. The spatial clustering of ligand-functionalized NPs represents an additional, less well understood mechanism for increasing local ligand-receptor interactions, especially for receptors that form higher-order assemblies, such as the epidermal growth factor (EGF) receptor (EGFR). To shed light on the interplay between ligand density ( i.e., multivalency) and NP clustering in signal amplification, we apply EGF-functionalized 72 ± 1 nm gold nanoparticles (NP-EGF) with known ligand loading (10-200 EGF/NP) as quantifiable and experimentally tractable units of EGFR activation and characterize the NP-mediated amplification of EGFR phosphorylation as a function of both EGF surface density and NP-EGF clustering for two cancer cell lines (HeLa and MDA-MB-468). The measurements confirm a strong multivalent amplification of EGFR phosphorylation through NP-EGF on the cellular level that results in EGF-loading-dependent maximum EGFR phosphorylation levels. A microscopic analysis of NP-EGF-induced EGFR phosphorylation reveals a heterogeneous spatial distribution of EGFR activation across the cell surface. Clustering of multivalent NP-EGF on sub-diffraction-limited length scales is found to result in a local enhancement of EGFR phosphorylation in signaling "hot spots" from where the signal can spread laterally in an EGF-independent fashion. Increasing EGF loadings of the NP enhances NP-EGF clustering and intensifies EGFR phosphorylation. These observations suggest that NP-EGF clustering and the associated local enhancement of ligand-receptor interactions are intrinsic components of the multivalent amplification of phosphorylation for the heterogeneously distributed EGFR through NP-EGF.
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Affiliation(s)
- Qianyun Zhang
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Björn M Reinhard
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
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32
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Lee D, Singla A, Wu HJ, Kwon JSI. An integrated numerical and experimental framework for modeling of CTB and GD1b ganglioside binding kinetics. AIChE J 2018. [DOI: 10.1002/aic.16209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dongheon Lee
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; College Station TX 77840
| | - Akshi Singla
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; College Station TX 77840
| | - Hung-Jen Wu
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; College Station TX 77840
| | - Joseph Sang-Il Kwon
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; College Station TX 77840
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Lowry P, Woods R. The placenta controls the physiology of pregnancy by increasing the half-life in blood and receptor activity of its secreted peptide hormones. J Mol Endocrinol 2018; 60:R23-R30. [PMID: 29212865 DOI: 10.1530/jme-17-0275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 11/24/2017] [Indexed: 11/08/2022]
Abstract
An efficient functioning placenta is essential for a healthy pregnancy and yet the way this is achieved has been the subject of much discussion and confusion, particularly with the occurrence of pathological conditions such as preeclampsia, morning sickness and hyperemesis/ptyalism gravidarum. We will attempt to explain the underlying physiology and the potential roles played by the placental tachykinins, neurokinin B and endokinin.
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Affiliation(s)
- Philip Lowry
- School of Biological SciencesUniversity of Reading, Reading, UK
| | - Russell Woods
- School of Biological SciencesUniversity of Reading, Reading, UK
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Abraham V, Parambath A, Joe DS, DeLisser HM. Influence of PECAM-1 ligand interactions on PECAM-1-dependent cell motility and filopodia extension. Physiol Rep 2017; 4:4/22/e13030. [PMID: 27895229 PMCID: PMC5358002 DOI: 10.14814/phy2.13030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 10/16/2016] [Accepted: 10/17/2016] [Indexed: 01/31/2023] Open
Abstract
Platelet endothelial cell adhesion molecule (PECAM‐1) has been implicated in angiogenesis through processes that involve stimulation of endothelial cell motility. Previous studies suggest that PECAM‐1 tyrosine phosphorylation mediates the recruitment and then activation of the tyrosine phosphatase SHP‐2, which in turn promotes the turnover of focal adhesions and the extension of filopodia, processes critical to cell motility. While these studies have implicated PECAM‐1‐dependent signaling in PECAM‐1‐mediated cell motility, the involvement of PECAM‐1 ligand binding in cell migration is undefined. Therefore to investigate the role of PECAM‐1 binding interactions in cell motility, mutants of PECAM‐1 were generated in which either homophilic or heparin/glycosaminoglycan (GAG)‐mediated heterophilic binding had been disabled and then expressed in an endothelial cell surrogate. We found that the ability of PECAM‐1 to stimulate cell migration, promote filopodia formation and trigger Cdc42 activation were lost if PECAM‐1‐dependent homophilic or heparin/GAG‐dependent heterophilic ligand binding was disabled. We further observed that PECAM‐1 concentrated at the tips of extended filopodia, an activity that was diminished if homophilic, but not heparin/GAG‐mediated heterophilic binding had been disrupted. Similar patterns of activities were seen in mouse endothelial cells treated with antibodies that specifically block PECAM‐1‐dependent homophilic or heterophilic adhesion. Together these data provide evidence for the differential involvement of PECAM‐1‐ligand interactions in PECAM‐1‐dependent motility and the extension of filopodia.
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Affiliation(s)
- Valsamma Abraham
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, Perelman School of School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew Parambath
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, Perelman School of School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Debria S Joe
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, Perelman School of School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Horace M DeLisser
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, Perelman School of School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Chen J, Almo SC, Wu Y. General principles of binding between cell surface receptors and multi-specific ligands: A computational study. PLoS Comput Biol 2017; 13:e1005805. [PMID: 29016600 PMCID: PMC5654264 DOI: 10.1371/journal.pcbi.1005805] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/20/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022] Open
Abstract
The interactions between membrane receptors and extracellular ligands control cell-cell and cell-substrate adhesion, and environmental responsiveness by representing the initial steps of cell signaling pathways. These interactions can be spatial-temporally regulated when different extracellular ligands are tethered. The detailed mechanisms of this spatial-temporal regulation, including the competition between distinct ligands with overlapping binding sites and the conformational flexibility in multi-specific ligand assemblies have not been quantitatively evaluated. We present a new coarse-grained model to realistically simulate the binding process between multi-specific ligands and membrane receptors on cell surfaces. The model simplifies each receptor and each binding site in a multi-specific ligand as a rigid body. Different numbers or types of ligands are spatially organized together in the simulation. These designs were used to test the relation between the overall binding of a multi-specific ligand and the affinity of its cognate binding site. When a variety of ligands are exposed to cells expressing different densities of surface receptors, we demonstrated that ligands with reduced affinities have higher specificity to distinguish cells based on the relative concentrations of their receptors. Finally, modification of intramolecular flexibility was shown to play a role in optimizing the binding between receptors and ligands. In summary, our studies bring new insights to the general principles of ligand-receptor interactions. Future applications of our method will pave the way for new strategies to generate next-generation biologics. In order to adapt to surrounding environments, multiple signaling pathways have been evolved in cells. The first step of these pathways is to detect external stimuli, which is conducted by the dynamic interactions between cell surface receptors and extracellular ligands. As a result, recognition of extracellular ligands by cell surface receptors is an indispensable component of many physiological or pathological activities. In both natural selection and drug design, the presence of multiple binding sites in extracellular ligand complexes (so-called multi-specific ligands) is a common strategy to target different receptors on surface of the same cell. Such spatial organization of ligand binding sites can elaborately modulate the downstream signaling pathways. However, our understanding to the interactions between multi-specific ligands and membrane receptors is largely limited by the fact that these interactions are difficult to quantify and they have only been successfully measured in a very small number of cases in vivo. Using a simple computational model, we can realistically simulate the binding process between specially designed multi-specific ligands and membrane receptors on cell surfaces. This study therefore provides a useful pathway to unravel basic mechanisms of ligand-receptor interactions and design principles for new drug candidates.
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Affiliation(s)
- Jiawen Chen
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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36
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Hudson SV, Dolin CE, Poole LG, Massey VL, Wilkey D, Beier JI, Merchant ML, Frieboes HB, Arteel GE. Modeling the Kinetics of Integrin Receptor Binding to Hepatic Extracellular Matrix Proteins. Sci Rep 2017; 7:12444. [PMID: 28963535 PMCID: PMC5622105 DOI: 10.1038/s41598-017-12691-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023] Open
Abstract
The composition of the extracellular matrix (ECM) proteins and the expression of their cognate receptors dictate cell behavior and dynamics. In particular, the interactions of ECM proteins with integrin receptors are key mediators of these cellular processes, playing a crucial role in the progression of several diseases of the liver, including inflammation, fibrosis/cirrhosis and cancer. This study establishes a modeling approach combining computation and experiments to evaluate the kinetics of integrin receptor binding to hepatic ECM proteins. ECM ligand concentration was derived from LC-MS/MS quantification of the hepatic ECM from mice exposed to chronic carbon tetrachloride (CCl4); receptor density was derived from published literature. Mathematical models for ECM-integrin binding kinetics that were developed incorporate receptor divalence and an aggregation scheme to represent clustering. The computer simulations reproduced positive cooperativity in the receptor aggregation model when the aggregation equilibrium constant (Ka) was positive and greater than Keq for divalent complex formation. Importantly, the modeling projected an increase in integrin binding for several receptors for which signaling is known to be increased after CCl4 exposure in the liver. The proposed modeling approach may be of use to elucidate the kinetics of integrin receptor binding to ECM proteins for homeostatic and diseased livers.
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Affiliation(s)
- Shanice V Hudson
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
- Department of Bioengineering, University of Louisville, Louisville, KY, 40208, USA
| | - Christine E Dolin
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Lauren G Poole
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Veronica L Massey
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Daniel Wilkey
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Juliane I Beier
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Michael L Merchant
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Hermann B Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
- Department of Bioengineering, University of Louisville, Louisville, KY, 40208, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA
| | - Gavin E Arteel
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA.
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, 40202, KY, USA.
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37
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Kinnear C, Moore TL, Rodriguez-Lorenzo L, Rothen-Rutishauser B, Petri-Fink A. Form Follows Function: Nanoparticle Shape and Its Implications for Nanomedicine. Chem Rev 2017; 117:11476-11521. [DOI: 10.1021/acs.chemrev.7b00194] [Citation(s) in RCA: 342] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Calum Kinnear
- Bio21 Institute & School of Chemistry, University of Melbourne, Parkville 3010, Australia
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38
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A model of dynamic stability of H3K9me3 heterochromatin to explain the resistance to reprogramming of differentiated cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:184-195. [DOI: 10.1016/j.bbagrm.2016.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 12/16/2022]
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Abstract
In this paper we construct and analyze a model of cell receptor aggregation. Experiments have shown that receptors in an aggregated state have greatly reduced mobility. We model the effects of this reduced mobility with a density dependent diffusion and study the impact of density dependent diffusion on aggregate formation in a one-dimensional domain. Critical values of receptor diffusivity and receptor activation are found and compared with numerical simulations. We find that the role of density dependant diffusion is quite limited in the formation of aggregate structures. In the case of receptor activation, the analytical results agree very well with the numerical calculations. Finally, we consider our model in higher dimensional domains. In this case our analysis is primarily numerical.
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40
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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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41
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Dong X, Yu Y, Wang Q, Xi Y, Liu Y. Interaction Mechanism and Clustering among RGD Peptides and Integrins. Mol Inform 2016; 36. [DOI: 10.1002/minf.201600069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/27/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Xiuli Dong
- Soft Matter Research Center; Department of Chemistry; Zhejiang University; Hangzhou 310027 PR China
- College of Pharmacy; Binzhou Medical University; Yantai 264003 PR China
| | - Yuping Yu
- Soft Matter Research Center; Department of Chemistry; Zhejiang University; Hangzhou 310027 PR China
| | - Qi Wang
- Soft Matter Research Center; Department of Chemistry; Zhejiang University; Hangzhou 310027 PR China
| | - Ying Xi
- Department of Pharmaceutics; Peking University; Beijing 100191 PR China
| | - Yingchun Liu
- Soft Matter Research Center; Department of Chemistry; Zhejiang University; Hangzhou 310027 PR China
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Peck EM, Battles PM, Rice DR, Roland FM, Norquest KA, Smith BD. Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging. Bioconjug Chem 2016; 27:1400-10. [PMID: 27088305 DOI: 10.1021/acs.bioconjchem.6b00173] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.
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Affiliation(s)
- Evan M Peck
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Paul M Battles
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Douglas R Rice
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Felicia M Roland
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Kathryn A Norquest
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame , Notre Dame, Indiana 46556, United States
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One-pot system for synthesis, assembly, and display of functional single-span membrane proteins on oil-water interfaces. Proc Natl Acad Sci U S A 2015; 113:608-13. [PMID: 26721399 DOI: 10.1073/pnas.1504992113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-span membrane proteins (ssMPs) represent approximately one-half of all membrane proteins and play important roles in cellular communications. However, like all membrane proteins, ssMPs are prone to misfolding and aggregation because of the hydrophobicity of transmembrane helices, making them difficult to study using common aqueous solution-based approaches. Detergents and membrane mimetics can solubilize membrane proteins but do not always result in proper folding and functionality. Here, we use cell-free protein synthesis in the presence of oil drops to create a one-pot system for the synthesis, assembly, and display of functional ssMPs. Our studies suggest that oil drops prevent aggregation of some in vitro-synthesized ssMPs by allowing these ssMPs to localize on oil surfaces. We speculate that oil drops may provide a hydrophobic interior for cotranslational insertion of the transmembrane helices and a fluidic surface for proper assembly and display of the ectodomains. These functionalized oil drop surfaces could mimic cell surfaces and allow ssMPs to interact with cell surface receptors under an environment closest to cell-cell communication. Using this approach, we showed that apoptosis-inducing human transmembrane proteins, FasL and TRAIL, synthesized and displayed on oil drops induce apoptosis of cultured tumor cells. In addition, we take advantage of hydrophobic interactions of transmembrane helices to manipulate the assembly of ssMPs and create artificial clusters on oil drop surfaces. Thus, by coupling protein synthesis with self-assembly at the water-oil interface, we create a platform that can use recombinant ssMPs to communicate with cells.
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Walker MA, Kohl T, Lehnart SE, Greenstein JL, Lederer WJ, Winslow RL. On the Adjacency Matrix of RyR2 Cluster Structures. PLoS Comput Biol 2015; 11:e1004521. [PMID: 26545234 PMCID: PMC4636394 DOI: 10.1371/journal.pcbi.1004521] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023] Open
Abstract
In the heart, electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells. This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors (RyR2). Their openings cause cell-wide release of Ca2+, which in turn causes muscle contraction and the generation of the mechanical force required to pump blood. In resting myocytes, RyR2s can also open spontaneously giving rise to spatially-confined Ca2+ release events known as "sparks." RyR2s are organized in a lattice to form clusters in the junctional sarcoplasmic reticulum membrane. Our recent work has shown that the spatial arrangement of RyR2s within clusters strongly influences the frequency of Ca2+ sparks. We showed that the probability of a Ca2+ spark occurring when a single RyR2 in the cluster opens spontaneously can be predicted from the precise spatial arrangements of the RyR2s. Thus, "function" follows from "structure." This probability is related to the maximum eigenvalue (λ1) of the adjacency matrix of the RyR2 cluster lattice. In this work, we develop a theoretical framework for understanding this relationship. We present a stochastic contact network model of the Ca2+ spark initiation process. We show that λ1 determines a stability threshold for the formation of Ca2+ sparks in terms of the RyR2 gating transition rates. We recapitulate these results by applying the model to realistic RyR2 cluster structures informed by super-resolution stimulated emission depletion (STED) microscopy. Eigendecomposition of the linearized mean-field contact network model reveals functional subdomains within RyR2 clusters with distinct sensitivities to Ca2+. This work provides novel perspectives on the cardiac Ca2+ release process and a general method for inferring the functional properties of transmembrane receptor clusters from their structure.
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Affiliation(s)
- Mark A. Walker
- Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tobias Kohl
- Heart Research Center Göttingen, Clinic of Cardiology and Pulmonology, University Medical Center Göttingen, Göttingen, Germany
| | - Stephan E. Lehnart
- Heart Research Center Göttingen, Clinic of Cardiology and Pulmonology, University Medical Center Göttingen, Göttingen, Germany
- German Center for Cardiovascular Research site Göttingen, Germany
| | - Joseph L. Greenstein
- Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - W. J. Lederer
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Raimond L. Winslow
- Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Liu Z, Legant WR, Chen BC, Li L, Grimm JB, Lavis LD, Betzig E, Tjian R. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. eLife 2014; 3:e04236. [PMID: 25537195 PMCID: PMC4381973 DOI: 10.7554/elife.04236] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 11/26/2014] [Indexed: 12/19/2022] Open
Abstract
Combinatorial cis-regulatory networks encoded in animal genomes represent the foundational gene expression mechanism for directing cell-fate commitment and maintenance of cell identity by transcription factors (TFs). However, the 3D spatial organization of cis-elements and how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, and ChIP-exo mapping to localize and functionally probe Sox2 enhancer-organization in living embryonic stem cells. Sox2 enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset of Pol II enriched regions. Sox2 searches for specific binding targets via a 3D-diffusion dominant mode when shuttling long-distances between clusters while chromatin-bound states predominate within individual clusters. Thus, enhancer clustering may reduce global search efficiency but enables rapid local fine-tuning of TF search parameters. Our results suggest an integrated model linking cis-element 3D spatial distribution to local-versus-global target search modalities essential for regulating eukaryotic gene transcription.
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Affiliation(s)
- Zhe Liu
- Junior Fellow Program, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Wesley R Legant
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Bi-Chang Chen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Li Li
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Jonathan B Grimm
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Luke D Lavis
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Eric Betzig
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Robert Tjian
- Transcription Imaging Consortium, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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Van AL, Soula HA, Berry H. Space-induced bifurcation in repression-based transcriptional circuits. BMC SYSTEMS BIOLOGY 2014; 8:125. [PMID: 25387605 PMCID: PMC4233083 DOI: 10.1186/s12918-014-0125-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 09/25/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Albeit the molecular mechanisms of gene expression are well documented, our understanding of their dynamics is much less advanced. Recent experimental evidence has revealed that gene expression might be accurately organized in space, with several molecular actors localized to specific positions in the cell. However, the influence of this spatial localization on the dynamics of gene expression is unclear. This issue is also central in synthetic biology, where one usually considers the spatial localization in the cell of the genes of the inserted synthetic construct as irrelevant for its temporal dynamics. RESULTS Here, we assessed the influence of the spatial distribution of the genes on the dynamics of 3-gene transcriptional ring networks regulated by repression, i.e. repressilator circuits, using individual-based modelling to simulate their dynamics in two and three space dimensions. Our simulations suggest that variations of spatial parameters - namely the degree of demixing of the positions of the gene or the spatial range of the mRNA and proteins (i.e. the typical distance they travel before degradation) - have dramatic effects by switching the dynamical regime from spontaneous oscillations to a stationary state where each species fluctuates around a constant value. By analogy with the bifurcations arising from the variation of kinetic parameters, we referred to those transitions as space-induced bifurcations. CONCLUSIONS Taken together, our results strongly support the idea that the spatial organization of the molecular actors of transcriptional networks is crucial for the dynamics of gene expression and suggest that the spatial localization of the synthetic genes in the cell could be used as an additional toggle to control the dynamics of the inserted construct in synthetic biology experiments.
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Affiliation(s)
- Amanda Lo Van
- INRIA, 56 Blvd Niels Bohr, Villeurbanne, 69603, France. .,LIRIS, Université de Lyon, UMR 5205 CNRS-INSA, Villeurbanne, 69621, France.
| | - Hedi A Soula
- INRIA, 56 Blvd Niels Bohr, Villeurbanne, 69603, France. .,Université de Lyon, Inserm UMR1060, Villeurbanne, 69621, France.
| | - Hugues Berry
- INRIA, 56 Blvd Niels Bohr, Villeurbanne, 69603, France. .,LIRIS, Université de Lyon, UMR 5205 CNRS-INSA, Villeurbanne, 69621, France.
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Wang X, Li S, Shi Y, Chuan X, Li J, Zhong T, Zhang H, Dai W, He B, Zhang Q. The development of site-specific drug delivery nanocarriers based on receptor mediation. J Control Release 2014; 193:139-53. [DOI: 10.1016/j.jconrel.2014.05.028] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/13/2014] [Accepted: 05/17/2014] [Indexed: 01/28/2023]
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Schöneberg J, Ullrich A, Noé F. Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC BIOPHYSICS 2014; 7:11. [PMID: 25737778 PMCID: PMC4347613 DOI: 10.1186/s13628-014-0011-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/29/2014] [Indexed: 11/17/2022]
Abstract
Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics.
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Affiliation(s)
- Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| | - Alexander Ullrich
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
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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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Targeting efficiency of RGD-modified nanocarriers with different ligand intervals in response to integrin αvβ3 clustering. Biomaterials 2014; 35:6106-17. [DOI: 10.1016/j.biomaterials.2014.04.031] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/10/2014] [Indexed: 02/06/2023]
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