1
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Lin SZ, Prost J, Rupprecht JF. Curvature-induced clustering of cell adhesion proteins. Phys Rev E 2024; 109:054406. [PMID: 38907394 DOI: 10.1103/physreve.109.054406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/02/2024] [Indexed: 06/24/2024]
Abstract
Cell adhesion proteins typically form stable clusters that anchor the cell membrane to its environment. Several works have suggested that cell membrane protein clusters can emerge from a local feedback between the membrane curvature and the density of proteins. Here, we investigate the effect of such a curvature-sensing mechanism in the context of cell adhesion proteins. We show how clustering emerges in an intermediate range of adhesion and curvature-sensing strengths. We identify key differences with the tilt-induced gradient sensing mechanism we previously proposed (Lin et al., arXiv:2307.03670).
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Affiliation(s)
- Shao-Zhen Lin
- Aix Marseille Univ, Université de Toulon, CNRS, CPT (UMR 7332), Turing Centre for Living systems, Marseille, France
| | - Jacques Prost
- Laboratoire Physico-Chimie Curie, UMR 168, Institut Curie, PSL Research University, CNRS, Sorbonne Université, 75005 Paris, France
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Jean-François Rupprecht
- Aix Marseille Univ, Université de Toulon, CNRS, CPT (UMR 7332), Turing Centre for Living systems, Marseille, France
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2
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Parihar K, Ko SH, Bradley R, Taylor P, Ramakrishnan N, Baumgart T, Guo W, Weaver VM, Janmey PA, Radhakrishnan R. Free energy calculations for membrane morphological transformations and insights to physical biology and oncology. Methods Enzymol 2024; 701:359-386. [PMID: 39025576 PMCID: PMC11258396 DOI: 10.1016/bs.mie.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
In this chapter, we aim to bridge basic molecular and cellular principles surrounding membrane curvature generation with rewiring of cellular signals in cancer through multiscale models. We describe a general framework that integrates signaling with other cellular functions like trafficking, cell-cell and cell-matrix adhesion, and motility. The guiding question in our approach is: how does a physical change in cell membrane configuration caused by external stimuli (including those by the extracellular microenvironment) alter trafficking, signaling and subsequent cell fate? We answer this question by constructing a modeling framework based on stochastic spatial continuum models of cell membrane deformations. We apply this framework to explore the link between trafficking, signaling in the tumor microenvironment, and cell fate. At each stage, we aim to connect the results of our predictions with cellular experiments.
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Affiliation(s)
- Kshitiz Parihar
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Seung-Hyun Ko
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Ryan Bradley
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Phillip Taylor
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
| | - N Ramakrishnan
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Tobias Baumgart
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | - Wei Guo
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | - Valerie M Weaver
- Department of Surgery, Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA, United States
| | - Paul A Janmey
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States; Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States.
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3
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Noguchi H. Curvature sensing of curvature-inducing proteins with internal structure. Phys Rev E 2024; 109:024403. [PMID: 38491597 DOI: 10.1103/physreve.109.024403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/15/2024] [Indexed: 03/18/2024]
Abstract
Many types of peripheral and transmembrane proteins can sense and generate membrane curvature. Laterally isotropic proteins and crescent proteins with twofold rotational symmetry, such as Bin/Amphiphysin/Rvs superfamily proteins, have been studied theoretically. However, proteins often have an asymmetric structure or a higher rotational symmetry. We studied theoretically the curvature sensing of proteins with asymmetric structures and structural deformations. First, we examined proteins consisting of two rodlike segments. When proteins have mirror symmetry, their sensing ability is similar to that of single-rod proteins; hence, with increasing protein density on a cylindrical membrane tube, a second- or first-order transition occurs at a middle or small tube radius, respectively. As asymmetry is introduced, this transition becomes a continuous change and metastable states appear at high protein densities. Protein with threefold, fivefold, or higher rotational symmetry has laterally isotropic bending energy. However, when a structural deformation is allowed, the protein can have a preferred orientation and stronger curvature sensing.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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4
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Has C, Das SL. The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation. J Membr Biol 2023; 256:343-372. [PMID: 37650909 DOI: 10.1007/s00232-023-00289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.
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Affiliation(s)
- Chandra Has
- Department of Chemical Engineering, GSFC University, Vadodara, 391750, Gujarat, India.
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology, Palakkad, 678623, Kerala, India
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5
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Khaddaj R, Kukulski W. Piecing together the structural organisation of lipid exchange at membrane contact sites. Curr Opin Cell Biol 2023; 83:102212. [PMID: 37515839 DOI: 10.1016/j.ceb.2023.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023]
Abstract
Membrane contact sites (MCSs) are areas of close proximity between organelles, implicated in transport of small molecules and in organelle biogenesis. Lipid transfer proteins at MCSs facilitate the distribution of lipid species between organelle membranes. Such exchange processes rely on the apposition of two different membranes delimiting distinct compartments and a cytosolic intermembrane space. Maintaining organelle identity while transferring molecules therefore implies control over MCS architecture both on the ultrastructural and molecular levels. Factors including intermembrane distance, density of resident proteins, and contact surface area fine-tune MCS function. Furthermore, the structural arrangement of lipid transfer proteins and associated proteins underpins the molecular mechanisms of lipid fluxes at MCSs. Thus, the architecture of MCSs emerges as an essential aspect of their function.
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Affiliation(s)
- Rasha Khaddaj
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
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6
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Vinutha AS, Rajasekaran R. Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment. J Comput Aided Mol Des 2023:10.1007/s10822-023-00516-2. [PMID: 37368161 DOI: 10.1007/s10822-023-00516-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023]
Abstract
As an alternative to antibiotics, Antimicrobial Peptides (AMPs) possess unique properties including cationic, amphipathic and their abundance in nature, but the exact characteristics of AMPs against bacterial membranes are still undetermined. To estimate the structural stability and functional activity of AMPs, the Pseudin AMPs (Pse-1, Pse-2, Pse-3, and Pse-4) from Hylid frog species, Pseudis paradoxa, an abundantly discovered source for AMPs were examined. We studied the intra-peptide interactions and thermal denaturation stability of peptides, as well as the geometrical parameters and secondary structure profiles of their conformational trajectories. On this basis, the peptides were screened out and the highly stable peptide, Pse-4 was subjected to membrane simulation in order to observe the changes in membrane curvature formed by Pse-4 insertion. Monomeric Pse-4 was found to initiate the membrane disruption; however, a stable multimeric form of Pse-4 might be competent to counterbalance the helix-coil transition and to resist the hydrophobic membrane environment. Eventually, hexameric Pse-4 on membrane simulation exhibited the hydrogen bond formation with E. coli bacterial membrane and thereby, leading to the formation of membrane spanning pore that allowed the entry of excess water molecules into the membrane shell, thus causing membrane deformation. Our report points out the mechanism of Pse-4 peptide against the bacterial membrane for the first time. Relatively, Pse-4 works on the barrel stave model against E. coli bacterial membrane; hence it might act as a good therapeutic scaffold in the treatment of multi-drug resistant bacterial strains.
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Affiliation(s)
- A S Vinutha
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
| | - R Rajasekaran
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India.
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7
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Vaisey G, Banerjee P, North AJ, Haselwandter CA, MacKinnon R. Piezo1 as a force-through-membrane sensor in red blood cells. eLife 2022; 11:e82621. [PMID: 36515266 PMCID: PMC9750178 DOI: 10.7554/elife.82621] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Piezo1 is the stretch activated Ca2+ channel in red blood cells that mediates homeostatic volume control. Here, we study the organization of Piezo1 in red blood cells using a combination of super-resolution microscopy techniques and electron microscopy. Piezo1 adopts a non-uniform distribution on the red blood cell surface, with a bias toward the biconcave 'dimple'. Trajectories of diffusing Piezo1 molecules, which exhibit confined Brownian diffusion on short timescales and hopping on long timescales, also reflect a bias toward the dimple. This bias can be explained by 'curvature coupling' between the intrinsic curvature of the Piezo dome and the curvature of the red blood cell membrane. Piezo1 does not form clusters with itself, nor does it colocalize with F-actin, Spectrin, or the Gardos channel. Thus, Piezo1 exhibits the properties of a force-through-membrane sensor of curvature and lateral tension in the red blood cell.
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Affiliation(s)
- George Vaisey
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Priyam Banerjee
- Bio-Imaging Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Alison J North
- Bio-Imaging Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Christoph A Haselwandter
- Department of Physics and Astronomy and Department of Quantitative and Computational Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
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8
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Cheppali SK, Dharan R, Sorkin R. Forces of Change: Optical Tweezers in Membrane Remodeling Studies. J Membr Biol 2022; 255:677-690. [PMID: 35616705 DOI: 10.1007/s00232-022-00241-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 12/24/2022]
Abstract
Optical tweezers allow precise measurement of forces and distances with piconewton and nanometer precision, and have thus been instrumental in elucidating the mechanistic details of various biological processes. Some examples include the characterization of motor protein activity, studies of protein-DNA interactions, and characterizing protein folding trajectories. The use of optical tweezers (OT) to study membranes is, however, much less abundant. Here, we review biophysical studies of membranes that utilize optical tweezers, with emphasis on various assays that have been developed and their benefits and limitations. First, we discuss assays that employ membrane-coated beads, and overview protein-membrane interactions studies based on manipulation of such beads. We further overview a body of studies that make use of a very powerful experimental tool, the combination of OT, micropipette aspiration, and fluorescence microscopy, that allow detailed studies of membrane curvature generation and sensitivity. Finally, we describe studies focused on membrane fusion and fission. We then summarize the overall progress in the field and outline future directions.
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Affiliation(s)
- Sudheer K Cheppali
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel.,Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.,Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv, Israel
| | - Raviv Dharan
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel.,Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.,Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv, Israel
| | - Raya Sorkin
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel. .,Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel. .,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel. .,Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv, Israel.
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9
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Božič B, Svetina S. Membrane Localization of Piezo1 in the Context of Its Role in the Regulation of Red Blood Cell Volume. Front Physiol 2022; 13:879038. [PMID: 35669579 PMCID: PMC9163432 DOI: 10.3389/fphys.2022.879038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022] Open
Abstract
Piezo1 is a membrane nonspecific cation channel involved in red blood cells (RBCs) in the regulation of their volume. Recently, it was shown that it is distributed on the RBC membrane in a nonuniform manner. Here it is shown that it is possible to interpret the lateral distribution of Piezo1 molecules on RBC membrane by the curvature dependent Piezo1—bilayer interaction which is the consequence of the mismatch between the intrinsic principal curvatures of the Piezo1 trimer and the principal curvatures of the membrane at Piezo1′s location but without its presence. This result supports the previously proposed model for the role of Piezo1 in the regulation of RBC volume.
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Affiliation(s)
- Bojan Božič
- Institute of Biophysics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Saša Svetina
- Institute of Biophysics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Jožef Stefan Institute, Ljubljana, Slovenia
- *Correspondence: Saša Svetina,
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10
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Bashkirov PV, Kuzmin PI, Vera Lillo J, Frolov VA. Molecular Shape Solution for Mesoscopic Remodeling of Cellular Membranes. Annu Rev Biophys 2022; 51:473-497. [PMID: 35239417 PMCID: PMC10787580 DOI: 10.1146/annurev-biophys-011422-100054] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellular membranes self-assemble from and interact with various molecular species. Each molecule locally shapes the lipid bilayer, the soft elastic core of cellular membranes. The dynamic architecture of intracellular membrane systems is based on elastic transformations and lateral redistribution of these elementary shapes, driven by chemical and curvature stress gradients. The minimization of the total elastic stress by such redistribution composes the most basic, primordial mechanism of membrane curvature-composition coupling (CCC). Although CCC is generally considered in the context of dynamic compositional heterogeneity of cellular membrane systems, in this article we discuss a broader involvement of CCC in controlling membrane deformations. We focus specifically on the mesoscale membrane transformations in open, reservoir-governed systems, such as membrane budding, tubulation, and the emergence of highly curved sites of membrane fusion and fission. We reveal that the reshuffling of molecular shapes constitutes an independent deformation mode with complex rheological properties.This mode controls effective elasticity of local deformations as well as stationary elastic stress, thus emerging as a major regulator of intracellular membrane remodeling.
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Affiliation(s)
- Pavel V Bashkirov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Peter I Kuzmin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Javier Vera Lillo
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain;
| | - Vadim A Frolov
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain;
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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11
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Noguchi H, Tozzi C, Arroyo M. Binding of anisotropic curvature-inducing proteins onto membrane tubes. SOFT MATTER 2022; 18:3384-3394. [PMID: 35416229 DOI: 10.1039/d2sm00274d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bin/Amphiphysin/Rvs superfamily proteins and other curvature-inducing proteins have anisotropic shapes and anisotropically bend biomembranes. Here, we report how the anisotropic proteins bind the membrane tube and are orientationally ordered using mean-field theory including an orientation-dependent excluded volume. The proteins exhibit a second-order or first-order nematic transition with increasing protein density depending on the radius of the membrane tube. The tube curvatures for the maximum protein binding and orientational order are different and varied by the protein density and rigidity. As the external force along the tube axis increases, a first-order transition from a large tube radius with low protein density to a small radius with high density occurs once, and subsequently, the protein orientation tilts to the tube-axis direction. When an isotropic bending energy is used for the proteins with an elliptic shape, the force-dependence curves become symmetric and the first-order transition occurs twice. This theory quantitatively reproduces the results of meshless membrane simulation for short proteins, whereas deviations are seen for long proteins owing to the formation of protein clusters.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
| | - Caterina Tozzi
- Universitat Politèdcnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
| | - Marino Arroyo
- Universitat Politèdcnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), 08028 Barcelona, Spain
- Centre Internacional de Mètodes Numèrics en Enginyeria (CIMNE), 08034 Barcelona, Spain
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12
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Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions. J Membr Biol 2022; 255:237-259. [PMID: 35451616 PMCID: PMC9028910 DOI: 10.1007/s00232-022-00237-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022]
Abstract
Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein’s ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure–function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins.
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13
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Tourdot RW, Ramakrishnan N, Parihar K, Radhakrishnan R. Quantification of Curvature Sensing Behavior of Curvature-Inducing Proteins on Model Wavy Substrates. J Membr Biol 2022; 255:175-184. [PMID: 35333976 DOI: 10.1007/s00232-022-00228-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/02/2022] [Indexed: 12/29/2022]
Abstract
Curvature-inducing proteins are involved in a variety of membrane remodeling processes in the cell. Several in vitro experiments have quantified the curvature sensing behavior of these proteins in model lipid systems. One such system consists of a membrane bilayer laid atop a wavy substrate (Hsieh in Langmuir 28:12838-12843, 2012). In these experiments, the bilayer conforms to the wavy substrate, and curvature-inducing proteins show preferential segregation on the wavy membrane. Using a mesoscale computational membrane model based on the Helfrich Hamiltonian, here we present a study which analyzes the curvature sensing characteristics of this membrane-protein system, and elucidates key physical principles governing protein segregation on the wavy substrate and other in vitro systems. In this article we compute the local protein densities from the free energy landscape associated with membrane remodeling by curvature-inducing proteins. In specific, we use the Widom insertion technique to compute the free energy landscape for an inhomogeneous system with spatially varying density and the results obtained with this minimal model show excellent agreement with experimental studies that demonstrate the association between membrane curvature and local protein density. The free energy-based framework employed in this study can be used for different membrane morphologies and varied protein characteristics to gain mechanistic insights into protein sorting on membranes.
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Affiliation(s)
- Richard W Tourdot
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kshitiz Parihar
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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14
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Recent developments in membrane curvature sensing and induction by proteins. Biochim Biophys Acta Gen Subj 2021; 1865:129971. [PMID: 34333084 DOI: 10.1016/j.bbagen.2021.129971] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding. SCOPE OF REVIEW We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins. MAJOR CONCLUSIONS Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood. GENERAL SIGNIFICANCE The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.
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