1
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
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2
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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3
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Demosthene B, Lee M, Marracino RR, Heidings JB, Kang EH. Molecular Basis for Actin Polymerization Kinetics Modulated by Solution Crowding. Biomolecules 2023; 13:biom13050786. [PMID: 37238656 DOI: 10.3390/biom13050786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Actin polymerization drives cell movement and provides cells with structural integrity. Intracellular environments contain high concentrations of solutes, including organic compounds, macromolecules, and proteins. Macromolecular crowding has been shown to affect actin filament stability and bulk polymerization kinetics. However, the molecular mechanisms behind how crowding influences individual actin filament assembly are not well understood. In this study, we investigated how crowding modulates filament assembly kinetics using total internal reflection fluorescence (TIRF) microscopy imaging and pyrene fluorescence assays. The elongation rates of individual actin filaments analyzed from TIRF imaging depended on the type of crowding agent (polyethylene glycol, bovine serum albumin, and sucrose) as well as their concentrations. Further, we utilized all-atom molecular dynamics (MD) simulations to evaluate the effects of crowding molecules on the diffusion of actin monomers during filament assembly. Taken together, our data suggest that solution crowding can regulate actin assembly kinetics at the molecular level.
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Affiliation(s)
- Bryan Demosthene
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA
| | - Myeongsang Lee
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA
| | - Ryan R Marracino
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA
| | - James B Heidings
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA
| | - Ellen Hyeran Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
- Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
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4
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Park J, Kravchuk P, Krishnaprasad A, Roy T, Kang EH. Graphene Enhances Actin Filament Assembly Kinetics and Modulates NIH-3T3 Fibroblast Cell Spreading. Int J Mol Sci 2022; 23:509. [PMID: 35008935 PMCID: PMC8745492 DOI: 10.3390/ijms23010509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 01/01/2023] Open
Abstract
Actin plays critical roles in various cellular functions, including cell morphogenesis, differentiation, and movement. The assembly of actin monomers into double-helical filaments is regulated in surrounding microenvironments. Graphene is an attractive nanomaterial that has been used in various biomaterial applications, such as drug delivery cargo and scaffold for cells, due to its unique physical and chemical properties. Although several studies have shown the potential effects of graphene on actin at the cellular level, the direct influence of graphene on actin filament dynamics has not been studied. Here, we investigate the effects of graphene on actin assembly kinetics using spectroscopy and total internal reflection fluorescence microscopy. We demonstrate that graphene enhances the rates of actin filament growth in a concentration-dependent manner. Furthermore, cell morphology and spreading are modulated in mouse embryo fibroblast NIH-3T3 cultured on a graphene surface without significantly affecting cell viability. Taken together, these results suggest that graphene may have a direct impact on actin cytoskeleton remodeling.
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Affiliation(s)
- Jinho Park
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA; (J.P.); (P.K.); (A.K.); (T.R.)
- Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Pavlo Kravchuk
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA; (J.P.); (P.K.); (A.K.); (T.R.)
| | - Adithi Krishnaprasad
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA; (J.P.); (P.K.); (A.K.); (T.R.)
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Tania Roy
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA; (J.P.); (P.K.); (A.K.); (T.R.)
- Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Ellen Hyeran Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL 32826, USA; (J.P.); (P.K.); (A.K.); (T.R.)
- Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
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5
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Castaneda N, Feuillie C, Molinari M, Kang EH. Actin Bundle Nanomechanics and Organization Are Modulated by Macromolecular Crowding and Electrostatic Interactions. Front Mol Biosci 2021; 8:760950. [PMID: 34901154 PMCID: PMC8662701 DOI: 10.3389/fmolb.2021.760950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
The structural and mechanical properties of actin bundles are essential to eukaryotic cells, aiding in cell motility and mechanical support of the plasma membrane. Bundle formation occurs in crowded intracellular environments composed of various ions and macromolecules. Although the roles of cations and macromolecular crowding in the mechanics and organization of actin bundles have been independently established, how changing both intracellular environmental conditions influence bundle mechanics at the nanoscale has yet to be established. Here we investigate how electrostatics and depletion interactions modulate the relative Young’s modulus and height of actin bundles using atomic force microscopy. Our results demonstrate that cation- and depletion-induced bundles display an overall reduction of relative Young’s modulus depending on either cation or crowding concentrations. Furthermore, we directly measure changes to cation- and depletion-induced bundle height, indicating that bundles experience alterations to filament packing supporting the reduction to relative Young’s modulus. Taken together, our work suggests that electrostatic and depletion interactions may act counteractively, impacting actin bundle nanomechanics and organization.
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Affiliation(s)
- Nicholas Castaneda
- NanoScience Technology Center, University of Central Florida, Orlando, FL, United States.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Cecile Feuillie
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Michael Molinari
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN CNRS UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Ellen Hyeran Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL, United States.,Department of Physics, University of Central Florida, Orlando, FL, United States.,Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, United States
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6
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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7
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Castaneda N, Park J, Kang EH. Regulation of Actin Bundle Mechanics and Structure by Intracellular Environmental Factors. FRONTIERS IN PHYSICS 2021; 9:675885. [PMID: 34422787 PMCID: PMC8376200 DOI: 10.3389/fphy.2021.675885] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The mechanical and structural properties of actin cytoskeleton drive various cellular processes, including structural support of the plasma membrane and cellular motility. Actin monomers assemble into double-stranded helical filaments as well as higher-ordered structures such as bundles and networks. Cells incorporate macromolecular crowding, cation interactions, and actin-crosslinking proteins to regulate the organization of actin bundles. Although the roles of each of these factors in actin bundling have been well-known individually, how combined factors contribute to actin bundle assembly, organization, and mechanics is not fully understood. Here, we describe recent studies that have investigated the mechanisms of how intracellular environmental factors influence actin bundling. This review highlights the effects of macromolecular crowding, cation interactions, and actin-crosslinking proteins on actin bundle organization, structure, and mechanics. Understanding these mechanisms is important in determining in vivo actin biophysics and providing insights into cell physiology.
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Affiliation(s)
- Nicholas Castaneda
- NanoScience Technology Center, University of Central Florida, Orlando, FL, United States
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Jinho Park
- NanoScience Technology Center, University of Central Florida, Orlando, FL, United States
- Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, United States
| | - Ellen Hyeran Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL, United States
- Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, United States
- Department of Physics, University of Central Florida, Orlando, FL, United States
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8
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Heidings JB, Demosthene B, Merlino TR, Castaneda N, Kang EH. Gelsolin-mediated actin filament severing in crowded environments. Biochem Biophys Res Commun 2020; 532:548-554. [PMID: 32900483 DOI: 10.1016/j.bbrc.2020.08.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/15/2020] [Indexed: 10/24/2022]
Abstract
Gelsolin is a calcium-regulated actin binding protein that severs and caps actin filaments. Gelsolin's severing activity is important for regulating actin filament assembly dynamics that are required for cell motility as well as survival. The majority of in vitro studies of gelsolin have been performed in dilute buffer conditions which do not simulate the molecular interactions occurring in the crowded intracellular environment. We hypothesize that crowding results in greater gelsolin severing activity due to induced conformational changes in actin filaments and/or gelsolin. In this study, we evaluated the effects of crowding on gelsolin-mediated actin filament severing and gelsolin binding to actin filaments in crowded solutions, utilizing total internal reflection fluorescence (TIRF) microscopy and co-sedimentation assays. Our data indicates that the presence of crowders causes a decrease in the rate of gelsolin severing as well as a decrease in the amount of gelsolin bound to actin filaments, with greater effects caused by the polymeric crowder. Despite the severing rate decrease, gelsolin-mediated filament severing is increased in the presence of crowders. Understanding the crowding effect on gelsolin-mediated actin filament severing offers insight into the interactions between gelsolin and actin that occur inside the crowded cytoplasm.
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Affiliation(s)
- James B Heidings
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32816, USA; NanoScience Technology Center, University of Central Florida, Orlando, FL, 32826, USA
| | - Bryan Demosthene
- NanoScience Technology Center, University of Central Florida, Orlando, FL, 32826, USA
| | - Theresa R Merlino
- NanoScience Technology Center, University of Central Florida, Orlando, FL, 32826, USA
| | - Nicholas Castaneda
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32816, USA; NanoScience Technology Center, University of Central Florida, Orlando, FL, 32826, USA
| | - Ellen H Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL, 32826, USA; Department of Physics, University of Central Florida, Orlando, FL, 32816, USA; Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, 32816, USA.
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9
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Park J, Lee M, Lee B, Castaneda N, Tetard L, Kang EH. Crowding tunes the organization and mechanics of actin bundles formed by crosslinking proteins. FEBS Lett 2020; 595:26-40. [PMID: 33020904 DOI: 10.1002/1873-3468.13949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 01/05/2023]
Abstract
Fascin and α-actinin form higher-ordered actin bundles that mediate numerous cellular processes including cell morphogenesis and movement. While it is understood crosslinked bundle formation occurs in crowded cytoplasm, how crowding affects the bundling activities of the two crosslinking proteins is not known. Here, we demonstrate how solution crowding modulates the organization and mechanical properties of fascin- and α-actinin-induced bundles, utilizing total internal reflection fluorescence and atomic force microscopy imaging. Molecular dynamics simulations support the inference that crowding reduces binding interaction between actin filaments and fascin or the calponin homology 1 domain of α-actinin evidenced by interaction energy and hydrogen bonding analysis. Based on our findings, we suggest a mechanism of crosslinked actin bundle assembly and mechanics in crowded intracellular environments.
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Affiliation(s)
- Jinho Park
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA
| | - Myeongsang Lee
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Briana Lee
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Nicholas Castaneda
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Laurene Tetard
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Ellen Hyeran Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA.,Department of Physics, University of Central Florida, Orlando, FL, USA
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10
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Lee M, Kang EH. Molecular dynamics study of interactions between polymorphic actin filaments and gelsolin segment-1. Proteins 2019; 88:385-392. [PMID: 31498927 DOI: 10.1002/prot.25813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/22/2019] [Accepted: 09/04/2019] [Indexed: 11/08/2022]
Abstract
The assembly of protein actin into double-helical filaments promotes many eukaryotic cellular processes that are regulated by actin-binding proteins (ABPs). Actin filaments can adopt multiple conformations, known as structural polymorphism, which possibly influences the interaction between filaments and ABPs. Gelsolin is a Ca2+ -regulated ABP that severs and caps actin filaments. Gelsolin binding modulates filament structure; however, it is not known how polymorphic actin filament structures influence an interaction of gelsolin S1 with the barbed-end of filament. Herein, we investigated how polymorphic structures of actin filaments affect the interactions near interfaces between the gelsolin segment 1 (S1) domain and the filament barbed-end. Using all-atom molecular dynamics simulations, we demonstrate that different tilted states of subunits modulate gelsolin S1 interactions with the barbed-end of polymorphic filaments. Hydrogen bonding and interaction energy at the filament-gelsolin S1 interface indicate distinct conformations of filament barbed ends, resulting in different interactions of gelsolin S1. This study demonstrates that filament's structural multiplicity plays important roles in the interactions of actin with ABPs.
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Affiliation(s)
- Myeongsang Lee
- NanoScience Technology Center, University of Central Florida, Orlando, Florida
| | - Ellen H Kang
- NanoScience Technology Center, University of Central Florida, Orlando, Florida.,Department of Physics, University of Central Florida, Orlando, Florida.,Department of Materials Science and Engineering, University of Central Florida, Orlando, Florida
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