1
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Woo S, Saka SK, Xuan F, Yin P. Molecular robotic agents that survey molecular landscapes for information retrieval. Nat Commun 2024; 15:3293. [PMID: 38632239 PMCID: PMC11024175 DOI: 10.1038/s41467-024-46978-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-based artificial motors have allowed the recapitulation of biological functions and the creation of new features. Here, we present a molecular robotic system that surveys molecular environments and reports spatial information in an autonomous and repeated manner. A group of molecular agents, termed 'crawlers', roam around and copy information from DNA-labeled targets, generating records that reflect their trajectories. Based on a mechanism that allows random crawling, we show that our system is capable of counting the number of subunits in example molecular complexes. Our system can also detect multivalent proximities by generating concatenated records from multiple local interactions. We demonstrate this capability by distinguishing colocalization patterns of three proteins inside fixed cells under different conditions. These mechanisms for examining molecular landscapes may serve as a basis towards creating large-scale detailed molecular interaction maps inside the cell with nanoscale resolution.
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Affiliation(s)
- Sungwook Woo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Materials Science and Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea.
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- European Molecular Biology Laboratory (EMBL), Heidelberg, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Feng Xuan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Spear Bio Inc., Woburn, MA, 01801, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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2
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Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
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Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
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3
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Jaramillo-Granada AM, Li J, Flores Villarreal A, Lozano O, Ruiz-Suárez JC, Monje-Galvan V, Sierra-Valdez FJ. Modulation of Phospholipase A 2 Membrane Activity by Anti-inflammatory Drugs. Langmuir 2024; 40:7038-7048. [PMID: 38511880 DOI: 10.1021/acs.langmuir.4c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The phospholipase A2 (PLA2) superfamily consists of lipolytic enzymes that hydrolyze specific cell membrane phospholipids and have long been considered a central hub of biosynthetic pathways, where their lipid metabolites exert a variety of physiological roles. A misregulated PLA2 activity is associated with mainly inflammatory-derived pathologies and thus has shown relevant therapeutic potential. Many natural and synthetic anti-inflammatory drugs (AIDs) have been proposed as direct modulators of PLA2 activity. However, despite the specific chemical properties that these drugs share in common, little is known about the indirect modulation able to finely tune membrane structural changes at the precise lipid-binding site. Here, we use a novel experimental strategy based on differential scanning calorimetry to systematically study the structural properties of lipid membrane systems during PLA2 cleavage and under the influence of several AIDs. For a better understanding of the AIDs-membrane interaction, we present a comprehensive and comparative set of molecular dynamics (MD) simulations. Our thermodynamic results clearly demonstrate that PLA2 cleavage is hindered by those AIDs that significantly reduce the lipid membrane cooperativity, while the rest of the AIDs oppositely tend to catalyze PLA2 activity to different extents. On the other hand, our MD simulations support experimental results by providing atomistic details on the binding, insertion, and dynamics of each AID on a pure lipid system; the drug efficacy to impact membrane cooperativity is related to the lipid order perturbation. This work suggests a membrane-based mechanism of action for diverse AIDs against PLA2 activity and provides relevant clues that must be considered in its modulation.
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Affiliation(s)
- Angela M Jaramillo-Granada
- Centro de Investigación y de Estudios Avanzados-Monterrey, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León 66600, Mexico
| | - Jinhui Li
- Department of Chemical and Biological Engineering, State University of New York (SUNY) at Buffalo, Buffalo, New York 14260, United States
| | | | - Omar Lozano
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Monterrey, Nuevo León 64460, Mexico
- Institute for Obesity Research, Tecnologico de Monterrey, Monterrey, Nuevo León 64849, Mexico
| | - J C Ruiz-Suárez
- Centro de Investigación y de Estudios Avanzados-Monterrey, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León 66600, Mexico
| | - Viviana Monje-Galvan
- Department of Chemical and Biological Engineering, State University of New York (SUNY) at Buffalo, Buffalo, New York 14260, United States
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4
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Héja L, Simon Á, Kardos J. Simulation of gap junction formation reveals critical role of Cys disulfide redox state in connexin hemichannel docking. Cell Commun Signal 2024; 22:185. [PMID: 38500186 PMCID: PMC10949817 DOI: 10.1186/s12964-023-01439-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/12/2023] [Indexed: 03/20/2024] Open
Abstract
Video Abstract.
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Affiliation(s)
- László Héja
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117, Budapest, Hungary.
| | - Ágnes Simon
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117, Budapest, Hungary
| | - Julianna Kardos
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117, Budapest, Hungary
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5
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Sharifi Panah S, Großmann R, Lepro V, Beta C. Cargo Size Limits and Forces of Cell-Driven Microtransport. Small 2024; 20:e2304666. [PMID: 37933711 DOI: 10.1002/smll.202304666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/12/2023] [Indexed: 11/08/2023]
Abstract
The integration of motile cells into biohybrid microrobots offers unique properties such as sensitive responses to external stimuli, resilience, and intrinsic energy supply. Here, biohybrid cell-cargo systems that are driven by amoeboid Dictyostelium discoideum cells are studied and how the cargo speed and the resulting viscous drag force scales with increasing radius of the spherical cargo particle are explored. Using a simplified geometrical model of the cell-cargo interaction, the findings toward larger cargo sizes, which are not accessible with the experimental setup, are extrapolated and a maximal cargo size is predicted beyond which active cell-driven movements will stall. The active forces exerted by the cells to move a cargo show mechanoresponsive adaptation and increase dramatically when challenged by an external pulling force, a mechanism that may become relevant when navigating cargo through complex heterogeneous environments.
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Affiliation(s)
- Setareh Sharifi Panah
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Straße 24/25, 14476, Potsdam, Germany
| | - Robert Großmann
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Straße 24/25, 14476, Potsdam, Germany
| | - Valentino Lepro
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Straße 24/25, 14476, Potsdam, Germany
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Straße 24/25, 14476, Potsdam, Germany
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6
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Kuschke S, Thon S, Sattler C, Schwabe T, Benndorf K, Schmauder R. cAMP binding to closed pacemaker ion channels is cooperative. Proc Natl Acad Sci U S A 2024; 121:e2315132121. [PMID: 38377199 PMCID: PMC10907242 DOI: 10.1073/pnas.2315132121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024] Open
Abstract
The cooperative action of the subunits in oligomeric receptors enables fine-tuning of receptor activation, as demonstrated for the regulation of voltage-activated HCN pacemaker ion channels by relating cAMP binding to channel activation in ensemble signals. HCN channels generate electric rhythmicity in specialized brain neurons and cardiomyocytes. There is conflicting evidence on whether binding cooperativity does exist independent of channel activation or not, as recently reported for detergent-solubilized receptors positioned in zero-mode waveguides. Here, we show positive cooperativity in ligand binding to closed HCN2 channels in native cell membranes by following the binding of individual fluorescence-labeled cAMP molecules. Kinetic modeling reveals that the affinity of the still empty binding sites rises with increased degree of occupation and that the transition of the channel to a flip state is promoted accordingly. We conclude that ligand binding to the subunits in closed HCN2 channels not pre-activated by voltage is already cooperative. Hence, cooperativity is not causally linked to channel activation by voltage. Our analysis also shows that single-molecule binding measurements at equilibrium can quantify cooperativity in ligand binding to receptors in native membranes.
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Affiliation(s)
- Stefan Kuschke
- Institute of Physiology II, Jena University Hospital, Friedrich Schiller University, Jena07743, Germany
| | - Susanne Thon
- Institute of Physiology II, Jena University Hospital, Friedrich Schiller University, Jena07743, Germany
| | - Christian Sattler
- Institute of Physiology II, Jena University Hospital, Friedrich Schiller University, Jena07743, Germany
| | - Tina Schwabe
- Institute of Physiology II, Jena University Hospital, Friedrich Schiller University, Jena07743, Germany
| | - Klaus Benndorf
- Institute of Physiology II, Jena University Hospital, Friedrich Schiller University, Jena07743, Germany
| | - Ralf Schmauder
- Institute of Physiology II, Jena University Hospital, Friedrich Schiller University, Jena07743, Germany
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7
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Zhang Y, Lauder GV. Energy conservation by collective movement in schooling fish. eLife 2024; 12:RP90352. [PMID: 38375853 PMCID: PMC10942612 DOI: 10.7554/elife.90352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Many animals moving through fluids exhibit highly coordinated group movement that is thought to reduce the cost of locomotion. However, direct energetic measurements demonstrating the energy-saving benefits of fluid-mediated collective movements remain elusive. By characterizing both aerobic and anaerobic metabolic energy contributions in schools of giant danio (Devario aequipinnatus), we discovered that fish schools have a concave upward shaped metabolism-speed curve, with a minimum metabolic cost at ~1 body length s-1. We demonstrate that fish schools reduce total energy expenditure (TEE) per tail beat by up to 56% compared to solitary fish. When reaching their maximum sustained swimming speed, fish swimming in schools had a 44% higher maximum aerobic performance and used 65% less non-aerobic energy compared to solitary individuals, which lowered the TEE and total cost of transport by up to 53%, near the lowest recorded for any aquatic organism. Fish in schools also recovered from exercise 43% faster than solitary fish. The non-aerobic energetic savings that occur when fish in schools actively swim at high speed can considerably improve both peak and repeated performance which is likely to be beneficial for evading predators. These energetic savings may underlie the prevalence of coordinated group locomotion in fishes.
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Affiliation(s)
- Yangfan Zhang
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - George V Lauder
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
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8
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Zhao Y, Zhang X, Liu L, Hu F, Chang F, Han Z, Li C. Insights into Activation Dynamics and Functional Sites of Inwardly Rectifying Potassium Channel Kir3.2 by an Elastic Network Model Combined with Perturbation Methods. J Phys Chem B 2024; 128:1360-1370. [PMID: 38308647 DOI: 10.1021/acs.jpcb.3c06739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
The inwardly rectifying potassium channel Kir3.2, a member of the inward rectifier potassium (Kir) channel family, exerts important biological functions through transporting potassium ions outside of the cell, during which a large-scale synergistic movement occurs among its different domains. Currently, it is not fully understood how the binding of the ligand to the Kir3.2 channel leads to the structural changes and which key residues are responsible for the channel gating and allosteric dynamics. Here, we construct the Gaussian network model (GNM) of the Kir3.2 channel with the secondary structure and covalent interaction information considered (sscGNM), which shows a better performance in reproducing the channel's flexibility compared with the traditional GNM. In addition, the sscANM-based perturbation method is used to simulate the channel's conformational transition caused by the activator PIP2's binding. By applying certain forces to the PIP2 binding pocket, the coarse-grained calculations generate the similar conformational changes to the experimental observation, suggesting that the topology structure as well as PIP2 binding are crucial to the allosteric activation of the Kir3.2 channel. We also utilize the sscGNM-based thermodynamic cycle method developed by us to identify the key residues whose mutations significantly alter the channel's binding free energy with PIP2. We identify not only the residues important for the specific binding but also the ones critical for the allosteric transition coupled with PIP2 binding. This study is helpful for understanding the working mechanism of Kir3.2 channels and can provide important information for related drug design.
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Affiliation(s)
- Yingchun Zhao
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Xinyu Zhang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Lamei Liu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fangrui Hu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fubin Chang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
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9
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Pajic-Lijakovic I, Eftimie R, Milivojevic M, Bordas SPA. Segregation of co-cultured multicellular systems: review and modeling consideration. Q Rev Biophys 2024; 57:e5. [PMID: 38351868 DOI: 10.1017/s0033583524000015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cell segregation caused by collective cell migration (CCM) is crucial for morphogenesis, functional development of tissue parts, and is an important aspect in other diseases such as cancer and its metastasis process. Efficiency of the cell segregation depends on the interplay between: (1) biochemical processes such as cell signaling and gene expression and (2) physical interactions between cells. Despite extensive research devoted to study the segregation of various co-cultured systems, we still do not understand the role of physical interactions in cell segregation. Cumulative effects of these physical interactions appear in the form of physical parameters such as: (1) tissue surface tension, (2) viscoelasticity caused by CCM, and (3) solid stress accumulated in multicellular systems. These parameters primarily depend on the interplay between the state of cell-cell adhesion contacts and cell contractility. The role of these physical parameters on the segregation efficiency is discussed on model systems such as co-cultured breast cell spheroids consisting of two subpopulations that are in contact. This review study aims to: (1) summarize biological aspects related to cell segregation, mechanical properties of cell collectives, effects along the biointerface between cell subpopulations and (2) describe from a biophysical/mathematical perspective the same biological aspects summarized before. So that overall it can illustrate the complexity of the biological systems that translate into very complex biophysical/mathematical equations. Moreover, by presenting in parallel these two seemingly different parts (biology vs. equations), this review aims to emphasize the need for experiments to estimate the variety of parameters entering the resulting complex biophysical/mathematical models.
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Affiliation(s)
- Ivana Pajic-Lijakovic
- Faculty of Technology and Metallurgy, Department of Chemical Engineering, University of Belgrade, Beograd, Serbia
| | - Raluca Eftimie
- Laboratoire Mathematiques de Besançon, UMR-CNRS 6623, Université de Bourgogne Franche-Comte, Besançon, France
| | - Milan Milivojevic
- Faculty of Technology and Metallurgy, Department of Chemical Engineering, University of Belgrade, Beograd, Serbia
| | - Stéphane P A Bordas
- Faculty of Science, Technology and Communication, University of Luxembourg, Institute for Computational Engineering, Esch-sur-Alzette, Luxembourg
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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10
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Xu M, Neelands T, Powers AS, Liu Y, Miller SD, Pintilie GD, Bois JD, Dror RO, Chiu W, Maduke M. CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism. eLife 2024; 12:RP90648. [PMID: 38345841 PMCID: PMC10942593 DOI: 10.7554/elife.90648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.
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Affiliation(s)
- Mengyuan Xu
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Torben Neelands
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Alexander S Powers
- Department of Chemistry, Stanford UniversityStanfordUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
- Department of Structural Biology, Stanford UniversityStanfordUnited States
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Yan Liu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford UniversityStanfordUnited States
| | - Steven D Miller
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Grigore D Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - J Du Bois
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
- Department of Structural Biology, Stanford UniversityStanfordUnited States
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford UniversityStanfordUnited States
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
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11
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Leschiera E, Al-Hity G, Flint MS, Venkataraman C, Lorenzi T, Almeida L, Audebert C. An individual-based model to explore the impact of psychological stress on immune infiltration into tumour spheroids. Phys Biol 2024; 21:026003. [PMID: 38266283 DOI: 10.1088/1478-3975/ad221a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
In recentin vitroexperiments on co-culture between breast tumour spheroids and activated immune cells, it was observed that the introduction of the stress hormone cortisol resulted in a decreased immune cell infiltration into the spheroids. Moreover, the presence of cortisol deregulated the normal levels of the pro- and anti-inflammatory cytokines IFN-γand IL-10. We present an individual-based model to explore the interaction dynamics between tumour and immune cells under psychological stress conditions. With our model, we explore the processes underlying the emergence of different levels of immune infiltration, with particular focus on the biological mechanisms regulated by IFN-γand IL-10. The set-up of numerical simulations is defined to mimic the scenarios considered in the experimental study. Similarly to the experimental quantitative analysis, we compute a score that quantifies the level of immune cell infiltration into the tumour. The results of numerical simulations indicate that the motility of immune cells, their capability to infiltrate through tumour cells, their growth rate and the interplay between these cell parameters can affect the level of immune cell infiltration in different ways. Ultimately, numerical simulations of this model support a deeper understanding of the impact of biological stress-induced mechanisms on immune infiltration.
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Affiliation(s)
- Emma Leschiera
- Léonard de Vinci Pôle Universitaire, Research Center, 92 916 Paris, La Défense, France
- Univ. Bordeaux, CNRS, INRIA, Bordeaux INP, IMB, UMR 5251, F-33400 Talence, France
| | - Gheed Al-Hity
- School of Applied Sciences, University of Brighton, Centre for Stress and Age-related Diseases, Moulsecoomb, Brighton BN2 4GJ, United Kingdom
| | - Melanie S Flint
- School of Applied Sciences, University of Brighton, Centre for Stress and Age-related Diseases, Moulsecoomb, Brighton BN2 4GJ, United Kingdom
| | - Chandrasekhar Venkataraman
- School of Mathematical and Physical Sciences, University of Sussex, Department of Mathematics, Falmer, Brighton BN1 9QH, United Kingdom
| | - Tommaso Lorenzi
- Department of Mathematical Sciences 'G. L. Lagrange', Politecnico di Torino, 10129 Torino, Italy
| | - Luis Almeida
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions UMR 7598, 75005 Paris, France
| | - Chloe Audebert
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions UMR 7598, 75005 Paris, France
- Sorbonne Université, CNRS, Institut de biologie Paris-Seine (IBPS), Laboratoire de Biologie Computationnelle et Quantitative UMR 7238, 75005 Paris, France
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12
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Galano‐Frutos JJ, Sancho J. Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable. Protein Sci 2024; 33:e4905. [PMID: 38284492 PMCID: PMC10804899 DOI: 10.1002/pro.4905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/30/2024]
Abstract
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
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Affiliation(s)
- Juan José Galano‐Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
- Aragon Health Research Institute (IIS Aragón)ZaragozaSpain
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13
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Dolgin E. Fresh tools for watching the 'lava lamps' of living cells. Nature 2024; 626:1152-1154. [PMID: 38413751 DOI: 10.1038/d41586-024-00547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
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14
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Paul B, Furst EM, Lenhoff AM, Wagner NJ, Teixeira SCM. Combined Effects of Pressure and Ionic Strength on Protein-Protein Interactions: An Empirical Approach. Biomacromolecules 2024; 25:338-348. [PMID: 38117685 DOI: 10.1021/acs.biomac.3c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Proteins are exposed to hydrostatic pressure (HP) in a variety of ecosystems as well as in processing steps such as freeze-thaw, cell disruption, sterilization, and homogenization, yet pressure effects on protein-protein interactions (PPIs) remain underexplored. With the goal of contributing toward the expanded use of HP as a fundamental control parameter in protein research, processing, and engineering, small-angle X-ray scattering was used to examine the effects of HP and ionic strength on ovalbumin, a model protein. Based on an extensive data set, we develop an empirical method for scaling PPIs to a master curve by combining HP and osmotic effects. We define an effective pressure parameter that has been shown to successfully apply to other model protein data available in the literature, with deviations evident for proteins that do not follow the apparent Hofmeister series. The limitations of the empirical scaling are discussed in the context of the hypothesized underlying mechanisms.
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Affiliation(s)
- Brian Paul
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Eric M Furst
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Abraham M Lenhoff
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Norman J Wagner
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Susana C M Teixeira
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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15
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Majellaro M, Bondar A. Editorial: Advanced biophysical and biochemical technologies to study GPCR signal transduction. Front Endocrinol (Lausanne) 2024; 14:1354689. [PMID: 38239976 PMCID: PMC10795064 DOI: 10.3389/fendo.2023.1354689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/22/2024] Open
Affiliation(s)
| | - Alexey Bondar
- Faculty of Science, University of South Bohemia in Ceské Budejovice, Ceské Budejovice, Czechia
- Laboratory of Microscopy and Histology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceské Budejovice, Czechia
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16
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Abstract
Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of interest (POIs) in a single object can be probed, overcoming a major limitation of conventional single-molecule FRET. In FRET X, short fluorescently labeled DNA imager strands specifically and transiently bind their complementary docking strands on a target molecule, such that at most a single FRET pair is formed at each point in time and multiple POIs on a single molecule can be readily probed. Here, we describe the sample preparation, image acquisition, and data analysis for structural analysis of DNA nanostructures with FRET X.
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Affiliation(s)
- Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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17
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Fiori MC, Altenberg GA. Purification, Reconstitution, and Functional Analysis of Connexin Hemichannels. Methods Mol Biol 2024; 2801:1-16. [PMID: 38578409 DOI: 10.1007/978-1-0716-3842-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Connexins are the proteins that form the gap junction channels that are essential for cell-to-cell communication. These channels are formed by head-to-head docking of hemichannels (each from one of two adjacent cells). Free "undocked" hemichannels at the plasma membrane are mostly closed, although they are still important under physiological conditions. However, abnormal and sustained increase in hemichannel activity due to connexin mutations or acquired conditions can produce or contribute to cell damage. For example, mutations of Cx26, a connexin isoform, can increase hemichannel activity and cause deafness. Studies using purified isolated systems under well-controlled conditions are essential for a full understanding of molecular mechanisms of hemichannel function under normal conditions and in disease, and here, we present methodology for the expression, purification, and functional analysis of hemichannels formed by Cx26.
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Affiliation(s)
- Mariana C Fiori
- Clinical Research Institute, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Guillermo A Altenberg
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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18
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Samanta R, Gray JJ. Implicit model to capture electrostatic features of membrane environment. PLoS Comput Biol 2024; 20:e1011296. [PMID: 38252688 PMCID: PMC10833867 DOI: 10.1371/journal.pcbi.1011296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 02/01/2024] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Membrane protein structure prediction and design are challenging due to the complexity of capturing the interactions in the lipid layer, such as those arising from electrostatics. Accurately capturing electrostatic energies in the low-dielectric membrane often requires expensive Poisson-Boltzmann calculations that are not scalable for membrane protein structure prediction and design. In this work, we have developed a fast-to-compute implicit energy function that considers the realistic characteristics of different lipid bilayers, making design calculations tractable. This method captures the impact of the lipid head group using a mean-field-based approach and uses a depth-dependent dielectric constant to characterize the membrane environment. This energy function Franklin2023 (F23) is built upon Franklin2019 (F19), which is based on experimentally derived hydrophobicity scales in the membrane bilayer. We evaluated the performance of F23 on five different tests probing (1) protein orientation in the bilayer, (2) stability, and (3) sequence recovery. Relative to F19, F23 has improved the calculation of the tilt angle of membrane proteins for 90% of WALP peptides, 15% of TM-peptides, and 25% of the adsorbed peptides. The performances for stability and design tests were equivalent for F19 and F23. The speed and calibration of the implicit model will help F23 access biophysical phenomena at long time and length scales and accelerate the membrane protein design pipeline.
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Affiliation(s)
- Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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19
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Anderluh G. A label-free approach for measuring interactions of proteins with lipid membranes. Cell Rep Methods 2023; 3:100649. [PMID: 37989086 PMCID: PMC10694574 DOI: 10.1016/j.crmeth.2023.100649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023]
Abstract
In this issue of Cell Reports Methods, Sadi et al. present a nuclear magnetic resonance approach for quantitative assessment of protein interactions with lipid membranes. It is sensitive, applicable to diverse membrane systems, covers a broad range of KDs, and does not require large amounts of material.
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Affiliation(s)
- Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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20
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Yang Y, Yamauchi A, Tsuda S, Kuramochi M, Mio K, Sasaki YC, Arai T. The ice-binding site of antifreeze protein irreversibly binds to cell surface for its hypothermic protective function. Biochem Biophys Res Commun 2023; 682:343-348. [PMID: 37837755 DOI: 10.1016/j.bbrc.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Antifreeze proteins (AFPs) are multifunctional polypeptides that adsorb onto ice crystals to inhibit their growth and onto cells to protect them from nonfreezing hypothermic damage. However, the mechanism by which AFP exerts its hypothermic cell protective (HCP) function remains uncertain. Here, we assessed the HCP function of three types of fish-derived AFPs (type I, II, and III AFPs) against human T-lymphoblastic lymphoma by measuring the survival rate (%) of the cells after preservation at 4 °C for 24 h. All AFPs improved the survival rate in a concentration-dependent manner, although the HCP efficiency was inferior for type III AFP compared to other AFPs. In addition, after point mutations were introduced into the ice-binding site (IBS) of a type III AFP, HCP activity was dramatically increased, suggesting that the IBS of AFP is involved in cell adsorption. Significantly, high HCP activity was observed for a mutant that exhibited poorer antifreeze activity, indicating that AFP exerts HCP- and ice-binding functions through a different mechanism. We next incubated the cells in an AFP-containing solution, replaced it with pure EC solution, and then preserved the cells, showing that no significant reduction in the cell survival rate occurred for type I and II AFPs even after replacement. Thus, these AFPs irreversibly bind to the cells at 4 °C, and only tightly adsorbed AFP molecules contribute towards the cell-protection function.
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Affiliation(s)
- Yue Yang
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Akari Yamauchi
- Hibernation Metabolism, Physiology and Development Group, Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan
| | - Sakae Tsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan; AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan
| | - Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan
| | - Yuji C Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan; AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan
| | - Tatsuya Arai
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan; AIST-UTokyo Advanced Operando Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, 277-0882, Japan.
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21
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Shamsudin Y, Walker AR, Jones CM, Martínez TJ, Boxer SG. Simulation-guided engineering of split GFPs with efficient β-strand photodissociation. Nat Commun 2023; 14:7401. [PMID: 37973981 PMCID: PMC10654500 DOI: 10.1038/s41467-023-42954-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Green fluorescent proteins (GFPs) are ubiquitous for protein tagging and live-cell imaging. Split-GFPs are widely used to study protein-protein interactions by fusing proteins of interest to split GFP fragments that create a fluorophore upon typically irreversible complementation. Thus, controlled dissociation of the fragments is desirable. Although we have found that split strands can be photodissociated, the quantum efficiency of light-induced photodissociation of split GFPs is low. Traditional protein engineering approaches to increase efficiency, including extensive mutagenesis and screening, have proved difficult to implement. To reduce the search space, key states in the dissociation process are modeled by combining classical and enhanced sampling molecular dynamics with QM/MM calculations, enabling the rational design and engineering of split GFPs with up to 20-fold faster photodissociation rates using non-intuitive amino acid changes. This demonstrates the feasibility of modeling complex molecular processes using state-of-the-art computational methods, and the potential of integrating computational methods to increase the success rate in protein engineering projects.
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Affiliation(s)
- Yasmin Shamsudin
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
- Department of Chemistry-BMC, Uppsala University, 752 37, Uppsala, Sweden.
| | - Alice R Walker
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Chey M Jones
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Todd J Martínez
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
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22
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de Souza JP, Stone HA. Protein condensation regulates water availability in cells. Nature 2023; 623:698-699. [PMID: 37853191 DOI: 10.1038/d41586-023-03098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
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23
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Mosby LS, Straube A, Polin M. A general model for the motion of multivalent cargo interacting with substrates. J R Soc Interface 2023; 20:20230510. [PMID: 38016636 PMCID: PMC10684343 DOI: 10.1098/rsif.2023.0510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
Multivalent interactions are common in biology at many different length scales, and can result in the directional motion of multivalent cargo along substrates. Here, a general analytical model has been developed that can describe the directional motion of multivalent cargo as a response to position dependence in the binding and unbinding rates exhibited by their interaction sites. Cargo exhibit both an effective velocity, which acts in the direction of increasing cargo-substrate binding rate and decreasing cargo-substrate unbinding rate, and an effective diffusivity. This model can reproduce previously published experimental findings using only the binding and unbinding rate distributions of cargo interaction sites, and without any further parameter fitting. Extension of the cargo binding model to two dimensions reveals an effective velocity with the same properties as that derived for the one-dimensional case.
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Affiliation(s)
- L. S. Mosby
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, Coventry CV4 7AL, UK
- Physics Department, University of Warwick, Coventry CV4 7AL, UK
- Institute of Advanced Study, University of Warwick, Coventry CV4 7AL, UK
| | - A. Straube
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, Coventry CV4 7AL, UK
| | - M. Polin
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, Coventry CV4 7AL, UK
- Physics Department, University of Warwick, Coventry CV4 7AL, UK
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, Esporles, Illes Balears 07190, Spain
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24
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Fleming KG. Membrane defects as a generalized driving force for membrane protein interactions. Proc Natl Acad Sci U S A 2023; 120:e2315655120. [PMID: 37851703 PMCID: PMC10622890 DOI: 10.1073/pnas.2315655120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Affiliation(s)
- Karen G. Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
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25
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Liu P, Beltramo PJ. Effects of crowding on the diffusivity of membrane adhered particles. Soft Matter 2023; 19:7708-7716. [PMID: 37791427 DOI: 10.1039/d3sm01269g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The lateral diffusion of cell membrane inclusions, such as integral membrane proteins and bound receptors, drives critical biological processes, including the formation of complexes, cell-cell signaling, and membrane trafficking. These diffusive processes are complicated by how concentrated, or "crowded", the inclusions are, which can occupy between 30-50% of the area fraction of the membrane. In this work, we elucidate the effects of increasing concentration of model membrane inclusions in a free-standing artificial cell membrane on inclusion diffusivity and the apparent viscosity of the membrane. By multiple particle tracking of fluorescent microparticles covalently tethered to the bilayer, we show the transition from expected Brownian dynamics, which accurately measure the membrane viscosity, to subdiffusive behavior with decreased diffusion coefficient as the particle area fraction increases from 1% to around 30%, approaching physiological levels of crowding. At high crowding, the onset of non-Gaussian behavior is observed. Using hydrodynamic models relating the 2D diffusion coefficient to the viscosity of a membrane, we determine the apparent viscosity of the bilayer from the particle diffusivity and show an increase in the apparent membrane viscosity with increasing particle area fraction. However, the scaling of this increase is in contrast with the behavior of monolayer inclusion diffusion and bulk suspension rheology. These results demonstrate that physiological levels of model membrane crowding nontrivially alter the dynamics and apparent viscosity of the system, which has implications for understanding membrane protein interactions and particle-membrane transport processes.
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Affiliation(s)
- Paige Liu
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Peter J Beltramo
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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26
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Wang S, Wang T, Zeng X, Chu X, Zhuoma D, Zhao Y, Chen YZ. Exploring outer space biophysical phenomena via SpaceLID. Sci Rep 2023; 13:17400. [PMID: 37833498 PMCID: PMC10575925 DOI: 10.1038/s41598-023-44729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/11/2023] [Indexed: 10/15/2023] Open
Abstract
Extensive investigations in outer space have revealed not only how life adapts to the space environment, but also that interesting biophysical phenomena occur. These phenomena affect human health and other life forms (animals, plants, bacteria, and fungi), and to ensure the safety of future human space exploration need to be further investigated. This calls for joint research efforts between biologists and physicists, as these phenomena present cross-disciplinary barriers. Various national organizations provide useful forums for bridging this gap. Additional discussion avenues and database resources are helpful for facilitating the interdisciplinary investigations of these phenomena. In this paper, we present the newly established Space Life Investigation Database (SpaceLID, https://bidd.group/spacelid/ ) which provides information about biophysical phenomena occurring in space. Examples obtained using the database are given while discussing the underlying causes of these phenomena and their implications for the physiology and health of life in space.
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Affiliation(s)
- Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Tao Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Xian Zeng
- Department of Biological Medicines and Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, 201203, China
| | - Xinyi Chu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | | | - Yufen Zhao
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China.
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, and The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China.
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 102206, China.
| | - Yu Zong Chen
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China.
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27
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Shamir M, Martin FJO, Woolfson DN, Friedler A. Molecular Mechanism of STIL Coiled-Coil Domain Oligomerization. Int J Mol Sci 2023; 24:14616. [PMID: 37834064 PMCID: PMC10572602 DOI: 10.3390/ijms241914616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Coiled-coil domains (CCDs) play key roles in regulating both healthy cellular processes and the pathogenesis of various diseases by controlling protein self-association and protein-protein interactions. Here, we probe the mechanism of oligomerization of a peptide representing the CCD of the STIL protein, a tetrameric multi-domain protein that is over-expressed in several cancers and associated with metastatic spread. STIL tetramerization is mediated both by an intrinsically disordered domain (STIL400-700) and a structured CCD (STIL CCD718-749). Disrupting STIL oligomerization via the CCD inhibits its activity in vivo. We describe a comprehensive biophysical and structural characterization of the concentration-dependent oligomerization of STIL CCD peptide. We combine analytical ultracentrifugation, fluorescence and circular dichroism spectroscopy to probe the STIL CCD peptide assembly in solution and determine dissociation constants of both the dimerization, (KD = 8 ± 2 µM) and tetramerization (KD = 68 ± 2 µM) of the WT STIL CCD peptide. The higher-order oligomers result in increased thermal stability and cooperativity of association. We suggest that this complex oligomerization mechanism regulates the activated levels of STIL in the cell and during centriole duplication. In addition, we present X-ray crystal structures for the CCD containing destabilising (L736E) and stabilising (Q729L) mutations, which reveal dimeric and tetrameric antiparallel coiled-coil structures, respectively. Overall, this study offers a basis for understanding the structural molecular biology of the STIL protein, and how it might be targeted to discover anti-cancer reagents.
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Affiliation(s)
- Mai Shamir
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904, Israel;
| | - Freddie J. O. Martin
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK;
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK;
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Bristol BioDesign Institute, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904, Israel;
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28
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Xue Z, Ren K, Wu R, Sun Z, Zheng R, Tian Q, Ali A, Mi L, You M. Targeted RNA condensation in living cells via genetically encodable triplet repeat tags. Nucleic Acids Res 2023; 51:8337-8347. [PMID: 37486784 PMCID: PMC10484661 DOI: 10.1093/nar/gkad621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
Living systems contain various membraneless organelles that segregate proteins and RNAs via liquid-liquid phase separation. Inspired by nature, many protein-based synthetic compartments have been engineered in vitro and in living cells. Here, we introduce a genetically encoded CAG-repeat RNA tag to reprogram cellular condensate formation and recruit various non-phase-transition RNAs for cellular modulation. With the help of fluorogenic RNA aptamers, we have systematically studied the formation dynamics, spatial distributions, sizes and densities of these cellular RNA condensates. The cis- and trans-regulation functions of these CAG-repeat tags in cellular RNA localization, life time, RNA-protein interactions and gene expression have also been investigated. Considering the importance of RNA condensation in health and disease, we expect that these genetically encodable modular and self-assembled tags can be widely used for chemical biology and synthetic biology studies.
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Affiliation(s)
- Zhaolin Xue
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ahsan Ausaf Ali
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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29
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Vallina Estrada E, Zhang N, Wennerström H, Danielsson J, Oliveberg M. Diffusive intracellular interactions: On the role of protein net charge and functional adaptation. Curr Opin Struct Biol 2023; 81:102625. [PMID: 37331204 DOI: 10.1016/j.sbi.2023.102625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
A striking feature of nucleic acids and lipid membranes is that they all carry net negative charge and so is true for the majority of intracellular proteins. It is suggested that the role of this negative charge is to assure a basal intermolecular repulsion that keeps the cytosolic content suitably 'fluid' for function. We focus in this review on the experimental, theoretical and genetic findings which serve to underpin this idea and the new questions they raise. Unlike the situation in test tubes, any functional protein-protein interaction in the cytosol is subject to competition from the densely crowded background, i.e. surrounding stickiness. At the nonspecific limit of this stickiness is the 'random' protein-protein association, maintaining profuse populations of transient and constantly interconverting complexes at physiological protein concentrations. The phenomenon is readily quantified in studies of the protein rotational diffusion, showing that the more net negatively charged a protein is the less it is retarded by clustering. It is further evident that this dynamic protein-protein interplay is under evolutionary control and finely tuned across organisms to maintain optimal physicochemical conditions for the cellular processes. The emerging picture is then that specific cellular function relies on close competition between numerous weak and strong interactions, and where all parts of the protein surfaces are involved. The outstanding challenge is now to decipher the very basics of this many-body system: how the detailed patterns of charged, polar and hydrophobic side chains not only control protein-protein interactions at close- and long-range but also the collective properties of the cellular interior as a whole.
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Affiliation(s)
- Eloy Vallina Estrada
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Nannan Zhang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Håkan Wennerström
- Division of Physical Chemistry, Department of Chemistry, Lund University, Box 124, 22100 Lund, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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30
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Chakraborty S, Haldar S. Single-molecule covalent magnetic tweezers. Trends Biochem Sci 2023; 48:740-741. [PMID: 37246021 DOI: 10.1016/j.tibs.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/30/2023]
Affiliation(s)
- Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India; Department of Chemistry, Ashoka University, Sonepat, Haryana 131029, India; Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India.
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31
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Lin YY, Brouns T, Kolbeck PJ, Vanderlinden W, Lipfert J. High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays. J Biol Chem 2023; 299:104874. [PMID: 37257819 PMCID: PMC10404619 DOI: 10.1016/j.jbc.2023.104874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Force and torque spectroscopy have provided unprecedented insights into the mechanical properties, conformational transitions, and dynamics of DNA and DNA-protein complexes, notably nucleosomes. Reliable single-molecule manipulation measurements require, however, specific and stable attachment chemistries to tether the molecules of interest. Here, we present a functionalization strategy for DNA that enables high-yield production of constructs for torsionally constrained and very stable attachment. The method is based on two subsequent PCRs: first ∼380 bp long DNA strands are generated that contain multiple labels, which are used as "megaprimers" in a second PCR to generate ∼kbp long double-stranded DNA constructs with multiple labels at the respective ends. To achieve high-force stability, we use dibenzocyclooctyne-based click chemistry for covalent attachment to the surface and biotin-streptavidin coupling to the bead. The resulting tethers are torsionally constrained and extremely stable under load, with an average lifetime of 70 ± 3 h at 45 pN. The high yield of the approach enables nucleosome reconstitution by salt dialysis on the functionalized DNA, and we demonstrate proof-of-concept measurements on nucleosome assembly statistics and inner turn unwrapping under force. We anticipate that our approach will facilitate a range of studies of DNA interactions and nucleoprotein complexes under forces and torques.
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Affiliation(s)
- Yi-Yun Lin
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Tine Brouns
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Division of Molecular Imaging and Photonics, KU Leuven, Leuven, Belgium
| | - Pauline J Kolbeck
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
| | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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32
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Atkinson BN, Willis NJ, Zhao Y, Patel C, Frew S, Costelloe K, Magno L, Svensson F, Jones EY, Fish PV. Designed switch from covalent to non-covalent inhibitors of carboxylesterase Notum activity. Eur J Med Chem 2023; 251:115132. [PMID: 36934521 PMCID: PMC10626578 DOI: 10.1016/j.ejmech.2023.115132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/14/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
N-Acyl indolines 4 are potent, non-covalent Notum inhibitors developed from a covalent virtual screening hit 2a. The lead compounds were simple to synthesise, achieved excellent potency in a biochemical Notum-OPTS assay and restored Wnt signalling in a cell-based TCF/LEF reporter assay. Multiple high resolution X-ray structures established a common binding mode of these inhibitors with the indoline bound centred in the palmiteolate pocket with key interactions being aromatic stacking and a water mediated hydrogen bond to the oxyanion hole. These N-acyl indolines 4 will be useful tools for use in vitro studies to investigate the role of Notum in disease models, especially when paired with a structurally related covalent inhibitor (e.g. 4w and 2a). Overall, this study highlights the designed switch from covalent to non-covalent Notum inhibitors and so illustrates a complementary approach for hit generation and target inhibition.
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Affiliation(s)
- Benjamin N Atkinson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Nicky J Willis
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Chandni Patel
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Sarah Frew
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Kathryn Costelloe
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Lorenza Magno
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK.
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Paul V Fish
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London, WC1E 6BT, UK
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33
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Robertson GA, Clemons WM, Griffith TN. Being Black in biophysics. Biophys J 2023; 122:E1-E3. [PMID: 36990087 PMCID: PMC10147933 DOI: 10.1016/j.bpj.2023.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Gail A Robertson
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
| | - Theanne N Griffith
- Department of Physiology and Membrane Biology, University of California Davis, Davis, California.
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34
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Du L, Li Y, Zhang X, Zhou Z, Wang Y, Jing D, Zhou J. One-Step Fabrication of Droplet Arrays Using a Biomimetic Structural Chip. ACS Appl Mater Interfaces 2023; 15:17413-17420. [PMID: 36972187 DOI: 10.1021/acsami.3c01654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In the field of one-step efficient preparation of dewetting droplet arrays, the process is hampered by the requirement for low chemical wettability of solid surfaces, which restricts the complete transition of wetting state and its broad prospects in biological applications. Inspired by the physical structure of the lotus leaf, enabling it to promote the change of the infiltration state of an aqueous solution on the surface, we developed a method of one-step fabrication of droplet arrays on the biomimetic structural chip designed in the present work. This greatly reduces the need for chemical modification techniques to achieve low wettability and reduces the reliance on complex and sophisticated surface preparation techniques, thus improving the fabrication efficiency of droplet arrays fully generated on a chip by one-step operation without the need for extra liquid phase or the control of harsh barometric pressure. We also studied the influence of dimensions of the biomimetic structure and the preparation process parameters such as number of smears and speed of smearing on the preparation rate and uniformity of the droplet arrays. The amplification of templating DNA molecules in the droplet arrays prepared in a one-step fabrication way is also performed to verify its application potential for DNA molecular diagnosis.
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Affiliation(s)
- Lin Du
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yuxin Li
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xinlian Zhang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200433, China
| | - Zijian Zhou
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yan Wang
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Dalei Jing
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jia Zhou
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China
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35
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Liekkinen J, Olżyńska A, Cwiklik L, Bernardino de la Serna J, Vattulainen I, Javanainen M. Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein-Lipid Interactions. Langmuir 2023; 39:4338-4350. [PMID: 36917773 PMCID: PMC10061932 DOI: 10.1021/acs.langmuir.2c03349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The lining of the alveoli is covered by pulmonary surfactant, a complex mixture of surface-active lipids and proteins that enables efficient gas exchange between inhaled air and the circulation. Despite decades of advancements in the study of the pulmonary surfactant, the molecular scale behavior of the surfactant and the inherent role of the number of different lipids and proteins in surfactant behavior are not fully understood. The most important proteins in this complex system are the surfactant proteins SP-B and SP-C. Given this, in this work we performed nonequilibrium all-atom molecular dynamics simulations to study the interplay of SP-B and SP-C with multicomponent lipid monolayers mimicking the pulmonary surfactant in composition. The simulations were complemented by z-scan fluorescence correlation spectroscopy and atomic force microscopy measurements. Our state-of-the-art simulation model reproduces experimental pressure-area isotherms and lateral diffusion coefficients. In agreement with previous research, the inclusion of either SP-B and SP-C increases surface pressure, and our simulations provide a molecular scale explanation for this effect: The proteins display preferential lipid interactions with phosphatidylglycerol, they reside predominantly in the lipid acyl chain region, and they partition into the liquid expanded phase or even induce it in an otherwise packed monolayer. The latter effect is also visible in our atomic force microscopy images. The research done contributes to a better understanding of the roles of specific lipids and proteins in surfactant function, thus helping to develop better synthetic products for surfactant replacement therapy used in the treatment of many fatal lung-related injuries and diseases.
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Affiliation(s)
- Juho Liekkinen
- Department
of Physics, University of Helsinki, FI-00560 Helsinki, Finland
| | - Agnieszka Olżyńska
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, CZ-18223 Prague, Czech Republic
| | - Lukasz Cwiklik
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, CZ-18223 Prague, Czech Republic
| | - Jorge Bernardino de la Serna
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
- NIHR
Imperial Biomedical Research Centre, London SW7 2AZ, U.K.
| | - Ilpo Vattulainen
- Department
of Physics, University of Helsinki, FI-00560 Helsinki, Finland
| | - Matti Javanainen
- Institute
of Biotechnology, University of Helsinki, FI-00790 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, CZ-16100 Prague 6, Czech Republic
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36
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Dai Y, Wu M. Covalent-like bondings and abnormal formation of ferroelectric structures in binary ionic salts. Sci Adv 2023; 9:eadf8706. [PMID: 36662853 PMCID: PMC9858496 DOI: 10.1126/sciadv.adf8706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
In the Mooser-Pearson diagram, binary ionic compoundss form into nonpolar symmetrical structures with high coordination numbers, while wurtzite structures should appear in the covalent region. Their tetrahedral bonding configurations break the inversion symmetry, with polarizations almost unswitchable due to the high barriers of abrupt breaking and reformation of covalent bonds. Here, through first-principles calculations, we find some exceptional cases of highly ionic ferroelectric binary salts such as lithium halides, which may form into wurtzite structures with covalent-like sp3 bondings, and the origin of these abnormal formations is clarified. Their high polarizations induced by symmetry breaking are switchable, with much smoother switching pathway refrained from abrupt bond breaking due to the long-range feature of Coulomb interactions. These covalent-like ionic bondings do reduce not only their ferroelectric switching barriers but also the phase transition barriers between polar and nonpolar phases, rendering high performance in applications such as nonvolatile memory and energy storage.
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37
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Zullo G, Cibin P, Bortolan L, Botteon M, Petrone N. An Innovative Compact System to Measure Skiing Ground Reaction Forces and Flexural Angles of Alpine and Touring Ski Boots. Sensors (Basel) 2023; 23:836. [PMID: 36679634 PMCID: PMC9867497 DOI: 10.3390/s23020836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Skiing is a popular winter activity spanning various subdisciplines. Key hardware are ski boots, bindings, and skis, which are designed to withstand loads generated during skiing. Obtaining service forces and moments has always been challenging to researchers in the past. The goal of the present study is to develop and test a lightweight and compact measurement system to obtain the Ground Reaction Forces and the kinematics for ski touring and alpine ski. To do so, we adapted two six-axis load cells to fit into ski touring and alpine skis adding 20 mm height and 500 g weight to the original ski. To measure kinematics, we created custom angular sensors from rotary potentiometers. The system was tested indoors using a force platform and motion capture system before a first set of field tests in which the sensors were used to measure ski touring and alpine skis kinetics and kinematics. Validation trials showed maximum errors of 10% for kinetics and 5% for kinematics. Field tests showed data in agreement with previous findings on the topic. The results of this study show the possibility of using our system to study biomechanics and equipment performances for ski touring, alpine skiing, and possibly other disciplines.
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Affiliation(s)
- Giuseppe Zullo
- Department of Industrial Engineering, University of Padua, Via Venezia 1, 35131 Padova, Italy
| | - Pierluigi Cibin
- Department of Industrial Engineering, University of Padua, Via Venezia 1, 35131 Padova, Italy
| | - Lorenzo Bortolan
- CeRiSM, Sport Mountain and Health Research Centre, University of Verona, 38068 Rovereto, Italy
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | | | - Nicola Petrone
- Department of Industrial Engineering, University of Padua, Via Venezia 1, 35131 Padova, Italy
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38
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Szewczyk MM, Owens DDG, Barsyte-Lovejoy D. Measuring Protein-Protein Interactions in Cells using Nanoluciferase Bioluminescence Resonance Energy Transfer (NanoBRET) Assay. Methods Mol Biol 2023; 2706:137-148. [PMID: 37558946 DOI: 10.1007/978-1-0716-3397-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly recognized for their roles in functional cellular networks and their importance in disease-targeting contexts. Assessing PPI in the native cellular environment is challenging and requires specific and quantitative methods. Bioluminescence resonance energy transfer (BRET) is a biophysical process that can be used to quantify PPI. With Nanoluciferase bioluminescent protein as a donor and a fluorescent chloroalkane ligand covalently bound to HaloTag protein as an acceptor, NanoBRET provides a versatile and robust system to quantitatively measure PPI in living cells. BRET efficiency is proportional to the distance between the donor and acceptor, allowing for the measurement of PPI in real time. In this paper, we describe the use of NanoBRET to study specific interactions between proteins of interest in living cells that can be perturbed by using small-molecule antagonists and genetic mutations. Here, we provide a detailed protocol for expressing NanoLuc and HaloTag fusion proteins in cell culture and the necessary optimization of NanoBRET assay conditions. Our example results demonstrate the reliability and sensitivity of NanoBRET for measuring interactions between proteins, protein domains, and short peptides and quantitating the PPI antagonist compound activity in living cells.
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Affiliation(s)
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
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39
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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40
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Gnanasekaran P, Pappu HR. Forster Resonance Energy Transfer (FRET) to Visualize Protein-Protein Interactions in the Plant Cell. Methods Mol Biol 2023; 2690:133-135. [PMID: 37450144 DOI: 10.1007/978-1-0716-3327-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Forster resonance energy transfer (FRET) is an efficient method to visualize the protein-protein interaction in living cells. This technique is based on transfer of energy between two different fluorophores that are fused to two interacting proteins. In this chapter, we described the FRET assay to visualize the protein-protein interaction in plant cells.
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Affiliation(s)
- Prabu Gnanasekaran
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, USA.
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41
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Bruno JG. Successes and Failures of Static Aptamer-Target 3D Docking Models. Int J Mol Sci 2022; 23:ijms232214410. [PMID: 36430888 PMCID: PMC9695435 DOI: 10.3390/ijms232214410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
While Molecular Dynamics simulation programs are probably superior for predicting the binding and affinity of aptamers and their cognate ligands, such molecular dynamics programs require more computing power and analysis time than static docking programs that are more widely accessible to the scientific community on the internet. Static docking programs can be used to investigate the geometric fit of rigid DNA or RNA aptamer 3D structures and their ligands to aid in predicting the relative affinities and cross-reactivity of various potential ligands. Herein, the author describes when such static 3D docking analysis has worked well to produce useful predictions or confirmation of high-affinity aptamer interactions or successful aptamer beacon behavior and when it has not worked well. The analysis of why failures may occur with static 3D computer models is also discussed.
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Maya-Martinez R, Xu Y, Guthertz N, Walko M, Karamanos TK, Sobott F, Breeze AL, Radford SE. Dimers of D76N-β 2-microglobulin display potent antiamyloid aggregation activity. J Biol Chem 2022; 298:102659. [PMID: 36328246 PMCID: PMC9712992 DOI: 10.1016/j.jbc.2022.102659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022] Open
Abstract
Self-association of WT β2-microglobulin (WT-β2m) into amyloid fibrils is associated with the disorder dialysis related amyloidosis. In the familial variant D76N-β2m, the single amino acid substitution enhances the aggregation propensity of the protein dramatically and gives rise to a disorder that is independent of renal dysfunction. Numerous biophysical and structural studies on WT- and D76N-β2m have been performed in order to better understand the structure and dynamics of the native proteins and their different potentials to aggregate into amyloid. However, the structural properties of transient D76N-β2m oligomers and their role(s) in assembly remained uncharted. Here, we have utilized NMR methods, combined with photo-induced crosslinking, to detect, trap, and structurally characterize transient dimers of D76N-β2m. We show that the crosslinked D76N-β2m dimers have different structures from those previously characterized for the on-pathway dimers of ΔN6-β2m and are unable to assemble into amyloid. Instead, the crosslinked D76N-β2m dimers are potent inhibitors of amyloid formation, preventing primary nucleation and elongation/secondary nucleation when added in substoichiometric amounts with D76N-β2m monomers. The results highlight the specificity of early protein-protein interactions in amyloid formation and show how mapping these interfaces can inform new strategies to inhibit amyloid assembly.
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Affiliation(s)
- Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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43
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Reis A, Teixeira JPF, Silva AMG, Ferreira M, Gameiro P, de Freitas V. Modelling Hyperglycaemia in an Epithelial Membrane Model: Biophysical Characterisation. Biomolecules 2022; 12:biom12101534. [PMID: 36291743 PMCID: PMC9599690 DOI: 10.3390/biom12101534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Biomimetic models are valuable platforms to improve our knowledge on the molecular mechanisms governing membrane-driven processes in (patho)physiological conditions, including membrane permeability, transport, and fusion. However, current membrane models are over simplistic and do not include the membrane’s lipid remodelling in response to extracellular stimuli. Our study describes the synthesis of glycated dimyristoyl-phosphatidylethanolamine (DMPE-glyc), which was structurally characterised by mass spectrometry (ESI-MS) and quantified by NMR spectroscopy to be further incorporated in a complex phospholipid (PL) membrane model enriched in cholesterol (Chol) and (glyco)sphingolipids (GSL) designed to mimic epithelial membranes (PL/Chol/GSL) under hyperglycaemia conditions. Characterisation of synthesised DMPE-glyc adducts by tandem mass spectrometry (ESI-MS/MS) show that synthetic DMPE-glyc adducts correspond to Amadori products and quantification by 1H NMR spectroscopy show that the yield of glycation reaction was 8%. The biophysical characterisation of the epithelial membrane model shows that excess glucose alters the thermotropic behaviour and fluidity of epithelial membrane models likely to impact permeability of solutes. The epithelial membrane models developed to mimic normo- and hyperglycaemic scenarios are the basis to investigate (poly)phenol-lipid and drug–membrane interactions crucial in nutrition, pharmaceutics, structural biochemistry, and medicinal chemistry.
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44
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Gorfe AA. Biophysics of cancer. Biophys J 2022; 121:E1-E2. [PMID: 36152633 PMCID: PMC9617146 DOI: 10.1016/j.bpj.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas; Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas.
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45
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Spatola Rossi T, Pain C, Botchway SW, Kriechbaumer V. FRET-FLIM to Determine Protein Interactions and Membrane Topology of Enzyme Complexes. Curr Protoc 2022; 2:e598. [PMID: 36300920 DOI: 10.1002/cpz1.598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Determining protein-protein interactions is vital for gaining knowledge on cellular and metabolic processes including enzyme complexes and metabolons. Förster resonance energy transfer with fluorescence lifetime imaging microscopy (FRET-FLIM) is an advanced imaging methodology that allows for the quantitative detection of protein-protein interactions. In this method, proteins of interest for interaction studies are fused to different fluorophores such as enhanced green fluorescent protein (eGFP; donor molecule) and monomeric red fluorescent protein (mRFP; acceptor molecule). Energy transfer between the two fluorophore groups can only occur efficiently when the proteins of interest are in close physical proximity, around ≤10 nm, and therefore are most likely interacting. FRET-FLIM measures the decrease in excited-state lifetime of the donor fluorophore (eGFP) with and without the presence of the acceptor (mRFP) and can therefore give information on protein-protein interactions and the membrane topology of the tested protein. Here we describe the production of fluorescent protein fusions for FRET-FLIM analysis in tobacco leaf epidermal cells using Agrobacterium-mediated plant transformation and a FRET-FLIM data acquisition and analysis protocol in plant cells. These protocols are applicable and can be adapted for both membrane and soluble proteins in different cellular localizations. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Protein expression in tobacco leaf cells via transient Agrobacterium-mediated plant transformation Basic Protocol 2: FRET-FLIM data acquisition and analysis.
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Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Charlotte Pain
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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46
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Tam JZ, Palumbo T, Miwa JM, Chen BY. Analysis of Protein-Protein Interactions for Intermolecular Bond Prediction. Molecules 2022; 27:molecules27196178. [PMID: 36234723 PMCID: PMC9572624 DOI: 10.3390/molecules27196178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/03/2022] [Accepted: 09/10/2022] [Indexed: 11/24/2022] Open
Abstract
Protein-protein interactions often involve a complex system of intermolecular interactions between residues and atoms at the binding site. A comprehensive exploration of these interactions can help reveal key residues involved in protein-protein recognition that are not obvious using other protein analysis techniques. This paper presents and extends DiffBond, a novel method for identifying and classifying intermolecular bonds while applying standard definitions of bonds in chemical literature to explain protein interactions. DiffBond predicted intermolecular bonds from four protein complexes: Barnase-Barstar, Rap1a-raf, SMAD2-SMAD4, and a subset of complexes formed from three-finger toxins and nAChRs. Based on validation through manual literature search and through comparison of two protein complexes from the SKEMPI dataset, DiffBond was able to identify intermolecular ionic bonds and hydrogen bonds with high precision and recall, and identify salt bridges with high precision. DiffBond predictions on bond existence were also strongly correlated with observations of Gibbs free energy change and electrostatic complementarity in mutational experiments. DiffBond can be a powerful tool for predicting and characterizing influential residues in protein-protein interactions, and its predictions can support research in mutational experiments and drug design.
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Affiliation(s)
- Justin Z. Tam
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Talulla Palumbo
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Julie M. Miwa
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Brian Y. Chen
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
- Correspondence:
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47
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Juste-Dolz A, Delgado-Pinar M, Avella-Oliver M, Fernández E, Cruz JL, Andrés MV, Maquieira Á. Denaturing for Nanoarchitectonics: Local and Periodic UV-Laser Photodeactivation of Protein Biolayers to Create Functional Patterns for Biosensing. ACS Appl Mater Interfaces 2022; 14:41640-41648. [PMID: 36047566 PMCID: PMC9940103 DOI: 10.1021/acsami.2c12808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The nanostructuration of biolayers has become a paradigm for exploiting nanoscopic light-matter phenomena for biosensing, among other biomedical purposes. In this work, we present a photopatterning method to create periodic structures of biomacromolecules based on a local and periodic mild denaturation of protein biolayers mediated by UV-laser irradiation. These nanostructures are constituted by a periodic modulation of the protein activity, so they are free of topographic and compositional changes along the pattern. Herein, we introduce the approach, explore the patterning parameters, characterize the resulting structures, and assess their overall homogeneity. This UV-based patterning principle has proven to be an easy, cost-effective, and fast way to fabricate large areas of homogeneous one-dimensional protein patterns (2 min, 15 × 1.2 mm, relative standard deviation ≃ 16%). This work also investigates the implementation of these protein patterns as transducers for diffractive biosensing. Using a model immunoassay, these patterns have demonstrated negligible signal contributions from non-specific bindings and comparable experimental limits of detection in buffer media and in human serum (53 and 36 ng·mL-1 of unlabeled IgG, respectively).
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Affiliation(s)
- Augusto Juste-Dolz
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, 46022 Valencia, Spain
| | - Martina Delgado-Pinar
- Department
of Applied Physics and Electromagnetism-ICMUV, Universitat de València, 46100 Burjassot, Spain
| | - Miquel Avella-Oliver
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, 46022 Valencia, Spain
- Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain
| | - Estrella Fernández
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, 46022 Valencia, Spain
| | - Jose Luís Cruz
- Department
of Applied Physics and Electromagnetism-ICMUV, Universitat de València, 46100 Burjassot, Spain
| | - Miguel V. Andrés
- Department
of Applied Physics and Electromagnetism-ICMUV, Universitat de València, 46100 Burjassot, Spain
| | - Ángel Maquieira
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, 46022 Valencia, Spain
- Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain
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48
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Gabriel DA. Teaching Essential EMG Theory to Kinesiologists and Physical Therapists Using Analogies Visual Descriptions, and Qualitative Analysis of Biophysical Concepts. Sensors (Basel) 2022; 22:6555. [PMID: 36081014 PMCID: PMC9460425 DOI: 10.3390/s22176555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Electromyography (EMG) is a multidisciplinary field that brings together allied health (kinesiology and physical therapy) and the engineering sciences (biomedical and electrical). Since the physical sciences are used in the measurement of a biological process, the presentation of the theoretical foundations of EMG is most conveniently conducted using math and physics. However, given the multidisciplinary nature of EMG, a course will most likely include students from diverse backgrounds, with varying levels of math and physics. This is a pedagogical paper that outlines an approach for teaching foundational concepts in EMG to kinesiologists and physical therapists that uses a combination of analogies, visual descriptions, and qualitative analysis of biophysical concepts to develop an intuitive understanding for those who are new to surface EMG. The approach focuses on muscle fiber action potentials (MFAPs), motor unit action potentials (MUAPs), and compound muscle action potentials (CMAPs) because changes in these waveforms are much easier to identify and describe in comparison to the surface EMG interference pattern (IP).
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Affiliation(s)
- David A Gabriel
- Electromyographic Kinesiology Laboratory, Faculty of Applied Health Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
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49
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Kusova AM, Sitnitsky AE, Uversky VN, Zuev YF. Effect of Protein–Protein Interactions on Translational Diffusion of Spheroidal Proteins. Int J Mol Sci 2022; 23:ijms23169240. [PMID: 36012504 PMCID: PMC9409276 DOI: 10.3390/ijms23169240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 11/21/2022] Open
Abstract
One of the commonly accepted approaches to estimate protein–protein interactions (PPI) in aqueous solutions is the analysis of their translational diffusion. The present review article observes a phenomenological approach to analyze PPI effects via concentration dependencies of self- and collective translational diffusion coefficient for several spheroidal proteins derived from the pulsed field gradient NMR (PFG NMR) and dynamic light scattering (DLS), respectively. These proteins are rigid globular α-chymotrypsin (ChTr) and human serum albumin (HSA), and partly disordered α-casein (α-CN) and β-lactoglobulin (β-Lg). The PPI analysis enabled us to reveal the dominance of intermolecular repulsion at low ionic strength of solution (0.003–0.01 M) for all studied proteins. The increase in the ionic strength to 0.1–1.0 M leads to the screening of protein charges, resulting in the decrease of the protein electrostatic potential. The increase of the van der Waals potential for ChTr and α-CN characterizes their propensity towards unstable weak attractive interactions. The decrease of van der Waals interactions for β-Lg is probably associated with the formation of stable oligomers by this protein. The PPI, estimated with the help of interaction potential and idealized spherical molecular geometry, are in good agreement with experimental data.
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Affiliation(s)
- Aleksandra M. Kusova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, 420111 Kazan, Russia
| | - Aleksandr E. Sitnitsky
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, 420111 Kazan, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA
| | - Yuriy F. Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str., 2/31, 420111 Kazan, Russia
- Correspondence: ; Tel.: +7-(843)-2319036
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50
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Noble D. Review of historic article: Huxley 1957 Muscle Structure and theories of contraction. Progress in Biophysics and biophysical chemistry, 7, 255-318. Prog Biophys Mol Biol 2022; 171:19-21. [PMID: 35381233 DOI: 10.1016/j.pbiomolbio.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The article by Andrew Huxley in this journal in 1957, "Muscle Structure and theories of Contraction" is much more than a standard review of a field. It is itself a major theoretical modelling achievement: the first mathematical model of the contractile process in skeletal muscle. That model was based on careful microscopic analysis of the striation patterns in skeletal muscles. Cited 4456 times, it holds the record for this journal.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, UK.
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