1
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Sasmal S, Pal T, Hocky GM, McCullagh M. Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM. J Chem Theory Comput 2024; 20:3492-3502. [PMID: 38662196 PMCID: PMC11104435 DOI: 10.1021/acs.jctc.4c00223] [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: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
Quantifying the conformational ensembles of biomolecules is fundamental to describing mechanisms of processes such as protein folding, interconversion between folded states, ligand binding, and allosteric regulation. Accurate quantification of these ensembles remains a challenge for conventional molecular simulations of all but the simplest molecules due to insufficient sampling. Enhanced sampling approaches, such as metadynamics, were designed to overcome this challenge; however, the nonuniform frame weights that result from many of these approaches present an additional challenge to ensemble quantification techniques such as Markov State Modeling or structural clustering. Here, we present rigorous inclusion of nonuniform frame weights into a structural clustering method entitled shapeGMM. The result of frame-weighted shapeGMM is a high dimensional probability density and generative model for the unbiased system from which we can compute important thermodynamic properties such as relative free energies and configurational entropy. The accuracy of this approach is demonstrated by the quantitative agreement between GMMs computed by Hamiltonian reweighting and direct simulation of a coarse-grained helix model system. Furthermore, the relative free energy computed from a shapeGMM probability density of alanine dipeptide reweighted from a metadynamics simulation quantitatively reproduces the underlying free energy in the basins. Finally, the method identifies hidden structures along the actin globular to filamentous-like structural transition from a metadynamics simulation on a linear discriminant analysis coordinate trained on GMM states, illustrating how structural clustering of biased data can lead to biophysical insight. Combined, these results demonstrate that frame-weighted shapeGMM is a powerful approach to quantifying biomolecular ensembles from biased simulations.
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Affiliation(s)
- Subarna Sasmal
- Department of Chemistry, New York
University, New York, New York 10003, United
States
| | - Triasha Pal
- Department of Chemistry, New York
University, New York, New York 10003, United
States
| | - Glen M. Hocky
- Department of Chemistry, New York
University, New York, New York 10003, United
States
- Simons Center for Computational Physical Chemistry,
New York University, New York, New York 10003,
United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State
University, Stillwater, Oklahoma 74078, United
States
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2
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Watterson JG. The cluster model of energy transduction in biological systems. Biosystems 2024; 240:105213. [PMID: 38616011 DOI: 10.1016/j.biosystems.2024.105213] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units - the protein domains - rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called "Newton's cradle" provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and β secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.
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3
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Joseph J, Spantzel L, Ali M, Moonnukandathil Joseph D, Unger S, Reglinski K, Krafft C, Müller AD, Eggeling C, Heintzmann R, Börsch M, Press AT, Täuber D. Nanoscale chemical characterization of secondary protein structure of F-Actin using mid-infrared photoinduced force microscopy (PiF-IR). Spectrochim Acta A Mol Biomol Spectrosc 2024; 306:123612. [PMID: 37931494 DOI: 10.1016/j.saa.2023.123612] [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: 03/20/2023] [Revised: 08/15/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
The recently developed photoinduced force microscopy for mid-infrared (PiF-IR) offers high spectral resolution in combination with surface sensitivity and a spatial resolution in the range of a few nanometers. Although PiF-IR has primarily been applied to polymer materials, this technology presents significant potential for the chemical characterization of cellular structures approaching single-molecule sensitivity. We applied PiF-IR to differently polymerized F-Actin samples finding general agreement with FTIR spectra from the same samples. Single PiF-IR spectra of F-Actin show variations in the amide I band spectral region, which is related to secondary protein structure. Local variations are also seen in PiF-IR hyperspectra in this region. Such high sensitivity is a necessary requirement for discriminating Actin organization into bundles and other networks in cells and tissue. We applied PiF-IR to mouse liver tissue ex vivo. Single-frequency PiF-IR scans at three different IR frequencies show significant variations in local contrast. However, the presence of other proteins and the unique spatial resolution of PiF-IR pose a challenge to interpreting and validating such data. Careful design of model systems and further theoretical understanding of PiF-IR data far from bulk averages are needed to fully unfold the potential of PiF-IR for high-resolution chemical investigation in the Life Sciences.
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Affiliation(s)
- Jesvin Joseph
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Lukas Spantzel
- Jena University Hospital, Single-Molecule Microscopy Group, Jena, Germany; Friedrich Schiller University Jena, Faculty of Medicine, Jena, Germany
| | - Maryam Ali
- Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Dijo Moonnukandathil Joseph
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Sebastian Unger
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Katharina Reglinski
- Leibniz Institute of Photonic Technology, Biophysical Imaging, Jena, Germany; Friedrich Schiller University Jena, Institute for Applied Optics and Biophysics, Jena, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology, Department of Spectroscopy & Imaging, Jena, Germany
| | | | - Christian Eggeling
- Leibniz Institute of Photonic Technology, Biophysical Imaging, Jena, Germany; Friedrich Schiller University Jena, Institute for Applied Optics and Biophysics, Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany
| | - Michael Börsch
- Jena University Hospital, Single-Molecule Microscopy Group, Jena, Germany; Friedrich Schiller University Jena, Faculty of Medicine, Jena, Germany
| | - Adrian T Press
- Friedrich Schiller University Jena, Faculty of Medicine, Jena, Germany; Jena University Hospital, Department of Anesthesiology and Intensive Care Medicine, Jena, Germany
| | - Daniela Täuber
- Leibniz Institute of Photonic Technology, Department of Microscopy, Jena, Germany; Friedrich Schiller University Jena, Institute of Physical Chemistry & Abbe Center of Photonics, Jena, Germany; Friedrich Schiller University Jena, Institute of Solid State Physics, Jena, Germany.
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4
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Wu J, Xue W, Voth GA. K-Means Clustering Coarse-Graining (KMC-CG): A Next Generation Methodology for Determining Optimal Coarse-Grained Mappings of Large Biomolecules. J Chem Theory Comput 2023; 19:8987-8997. [PMID: 37957028 PMCID: PMC10720621 DOI: 10.1021/acs.jctc.3c01053] [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: 09/22/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/21/2023]
Abstract
Coarse-grained (CG) molecular dynamics (MD) has become a method of choice for simulating various large scale biomolecular processes; therefore, the systematic definition of the CG mappings for biomolecules remains an important topic. Appropriate CG mappings can significantly enhance the representability of a CG model and improve its ability to capture critical features of large biomolecules. In this work, we present a systematic and more generalized method called K-means clustering coarse-graining (KMC-CG), which builds on the earlier approach of essential dynamics coarse-graining (ED-CG). KMC-CG removes the sequence-dependent constraints of ED-CG, allowing it to explore a more extensive space and thus enabling the discovery of more physically optimal CG mappings. Furthermore, the implementation of the K-means clustering algorithm can variationally optimize the CG mapping with efficiency and stability. This new method is tested in three cases: ATP-bound G-actin, the HIV-1 CA pentamer, and the Arp2/3 complex. In these examples, the CG models generated by KMC-CG are seen to better capture the structural, dynamic, and functional domains. KMC-CG therefore provides a robust and consistent approach to generating CG models of large biomolecules that can then be more accurately parametrized by either bottom-up or top-down CG force fields.
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Affiliation(s)
| | | | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, The James Franck Institute,
and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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5
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Bai Y, Zhao F, Wu T, Chen F, Pang X. Actin polymerization and depolymerization in developing vertebrates. Front Physiol 2023; 14:1213668. [PMID: 37745245 PMCID: PMC10515290 DOI: 10.3389/fphys.2023.1213668] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Development is a complex process that occurs throughout the life cycle. F-actin, a major component of the cytoskeleton, is essential for the morphogenesis of tissues and organs during development. F-actin is formed by the polymerization of G-actin, and the dynamic balance of polymerization and depolymerization ensures proper cellular function. Disruption of this balance results in various abnormalities and defects or even embryonic lethality. Here, we reviewed recent findings on the structure of G-actin and F-actin and the polymerization of G-actin to F-actin. We also focused on the functions of actin isoforms and the underlying mechanisms of actin polymerization/depolymerization in cellular and organic morphogenesis during development. This information will extend our understanding of the role of actin polymerization in the physiologic or pathologic processes during development and may open new avenues for developing therapeutics for embryonic developmental abnormalities or tissue regeneration.
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Affiliation(s)
- Yang Bai
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Feng Zhao
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Tingting Wu
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Fangchun Chen
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Xiaoxiao Pang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
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6
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Steffensen KE, Dawson JF. Actin's C-terminus coordinates actin structural changes and functions. Cytoskeleton (Hoboken) 2023; 80:313-329. [PMID: 37036084 DOI: 10.1002/cm.21757] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023]
Abstract
Actin is essential to eukaryotic cellular processes. Actin's C-terminus appears to play a direct role in modulating actin's structure and properties, facilitating the binding and function of actin-binding proteins (ABPs). The structural and functional characterization of filamentous actin's C-terminus has been impeded by its inherent flexibility, as well as actin's resistance to crystallization for x-ray diffraction and the historical resolution constraints associated with electron microscopy. Many biochemical studies have established that actin's C-terminus must retain its flexibility and structural integrity to modulate actin's structure and functions. For example, C-terminal structural changes are known to affect nucleotide binding and exchange, as well as propagate actin structural changes throughout extensive allosteric networks, facilitating the binding and function of ABPs. Advances in electron microscopy have resulted in high-resolution structures of filamentous actin, providing insights into subtle structural changes that are mediated by actin's C-terminus. Here, we review existing knowledge establishing the importance of actin's C-terminus within actin structural changes and functions and discuss how modern structural characterization techniques provide the tools to understand the role of actin's C-terminus in cellular processes.
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Affiliation(s)
- Karl E Steffensen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - John F Dawson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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7
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Zsolnay V, Gardel ML, Kovar DR, Voth GA. Cracked actin filaments as mechanosensitive receptors. bioRxiv 2023:2023.06.26.546553. [PMID: 37425801 PMCID: PMC10327158 DOI: 10.1101/2023.06.26.546553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Actin filament networks are exposed to mechanical stimuli, but the effect of strain on actin filament structure has not been well-established in molecular detail. This is a critical gap in understanding because the activity of a variety of actin-binding proteins have recently been determined to be altered by actin filament strain. We therefore used all-atom molecular dynamics simulations to apply tensile strains to actin filaments and find that changes in actin subunit organization are minimal in mechanically strained, but intact, actin filaments. However, a conformational change disrupts the critical D-loop to W-loop connection between longitudinal neighboring subunits, which leads to a metastable cracked conformation of the actin filament, whereby one protofilament is broken prior to filament severing. We propose that the metastable crack presents a force-activated binding site for actin regulatory factors that specifically associate with strained actin filaments. Through protein-protein docking simulations, we find that 43 evolutionarily-diverse members of the dual zinc finger containing LIM domain family, which localize to mechanically strained actin filaments, recognize two binding sites exposed at the cracked interface. Furthermore, through its interactions with the crack, LIM domains increase the length of time damaged filaments remain stable. Our findings propose a new molecular model for mechanosensitive binding to actin filaments.
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Affiliation(s)
- Vilmos Zsolnay
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL
| | - Margaret L. Gardel
- Department of Physics & Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL
- Institute for Biophysical Dynamics and James Franck Institute, University of Chicago, Chicago, IL
| | - David R. Kovar
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Gregory A. Voth
- Institute for Biophysical Dynamics and James Franck Institute, University of Chicago, Chicago, IL
- Department of Chemistry and Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, IL
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8
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Abstract
The barbed and pointed ends of the actin filament (F-actin) are the sites of growth and shrinkage and the targets of capping proteins that block subunit exchange, including CapZ at the barbed end and tropomodulin at the pointed end. We describe cryo-electron microscopy structures of the free and capped ends of F-actin. Terminal subunits at the free barbed end adopt a "flat" F-actin conformation. CapZ binds with minor changes to the barbed end but with major changes to itself. By contrast, subunits at the free pointed end adopt a "twisted" monomeric actin (G-actin) conformation. Tropomodulin binding forces the second subunit into an F-actin conformation. The structures reveal how the ends differ from the middle in F-actin and how these differences control subunit addition, dissociation, capping, and interactions with end-binding proteins.
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Affiliation(s)
- Peter J. Carman
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
| | - Kyle R. Barrie
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
| | - Grzegorz Rebowski
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
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9
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Liu Y, Wang X, Wan Z, Ngai T, Tse YLS. Capturing coacervate formation and protein partition by molecular dynamics simulation. Chem Sci 2023; 14:1168-1175. [PMID: 36756326 PMCID: PMC9891350 DOI: 10.1039/d2sc01164f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
Biomolecules localize and function in microenvironments where their local concentration, spatial organization, and biochemical reactivity are regulated. To compartmentalize and control the local properties of the native microenvironment, cellular mimics and artificial bioreactors have been developed to study the properties of membraneless organelles or mimic the bio-environment for life origin. Here, we carried out molecular dynamics simulation with the Martini 3.0 model to reproduce the experimental salt concentration and pH dependency of different complex coacervates. We showed that coacervates inside vesicles are able to change their shape. In addition, we used these coacervate systems to explore the partitioning of the ubiquitous cytoskeletal protein actin and found that actin spontaneously partitions to all the coacervate peripheries. Therefore, we believe that our study can provide a better understanding of the versatile coacervate platform, where biomolecules partition and gather to fulfill their biological duties.
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Affiliation(s)
- Yang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China.,Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Xinyan Wang
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Zhili Wan
- School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
| | - To Ngai
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Ying-Lung Steve Tse
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
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10
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Li T, Du J, Ren M. Structural Significance of His73 in F-Actin Dynamics: Insights from Ab Initio Study. Int J Mol Sci 2022; 23:ijms231810447. [PMID: 36142357 PMCID: PMC9499316 DOI: 10.3390/ijms231810447] [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: 07/14/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
F-actin dynamics (polymerization and depolymerization) are associated with nucleotide exchange, providing the driving forces for dynamic cellular activities. As an important residue in the nucleotide state-sensing region in actin, His73 is often found to be methylated in natural actin and directly participates in F-actin dynamics by regulating nucleotide exchange. The interaction between His73 and its neighboring residue, Gly158, has significance for F-actin dynamics. However, this weak chemical interaction is difficult to characterize using classic molecular modeling methods. In this study, ab initio modeling was employed to explore the binding energy between His73 and Gly158. The results confirm that the methyl group on the His73 side chain contributes to the structural stability of atomistic networks in the nucleotide state-sensing region of actin monomers and confines the material exchange (Pi release) pathway within F-actin dynamics. Further binding energy analyses of actin structures under different nucleotide states showed that the potential model of His73/Gly158 hydrogen bond breaking in the material exchange mechanism is not obligatory within F-actin dynamics.
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Affiliation(s)
- Tong Li
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
| | - Juan Du
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
| | - Mingfa Ren
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian 116024, China
- Correspondence: ; Tel.: +86-411-8479161
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11
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Gong R, Jiang F, Moreland ZG, Reynolds MJ, de los Reyes SE, Gurel P, Shams A, Heidings JB, Bowl MR, Bird JE, Alushin GM. Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia. Sci Adv 2022; 8:eabl4733. [PMID: 35857845 PMCID: PMC9299544 DOI: 10.1126/sciadv.abl4733] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 06/03/2022] [Indexed: 05/12/2023]
Abstract
The motor protein myosin-15 is necessary for the development and maintenance of mechanosensory stereocilia, and mutations in myosin-15 cause hereditary deafness. In addition to transporting actin regulatory machinery to stereocilia tips, myosin-15 directly nucleates actin filament ("F-actin") assembly, which is disrupted by a progressive hearing loss mutation (p.D1647G, "jordan"). Here, we present cryo-electron microscopy structures of myosin-15 bound to F-actin, providing a framework for interpreting the impacts of deafness mutations on motor activity and actin nucleation. Rigor myosin-15 evokes conformational changes in F-actin yet maintains flexibility in actin's D-loop, which mediates inter-subunit contacts, while the jordan mutant locks the D-loop in a single conformation. Adenosine diphosphate-bound myosin-15 also locks the D-loop, which correspondingly blunts actin-polymerization stimulation. We propose myosin-15 enhances polymerization by bridging actin protomers, regulating nucleation efficiency by modulating actin's structural plasticity in a myosin nucleotide state-dependent manner. This tunable regulation of actin polymerization could be harnessed to precisely control stereocilium height.
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Affiliation(s)
- Rui Gong
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Fangfang Jiang
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Zane G. Moreland
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Matthew J. Reynolds
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | | | - Pinar Gurel
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Arik Shams
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - James B. Heidings
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Michael R. Bowl
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire, UK
- UCL Ear Institute, University College London, London, UK
| | - Jonathan E. Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Gregory M. Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
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12
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Abstract
Polymerization of actin into cytoskeletal filaments is coupled to its bound adenine nucleotides. The mechanism by which nucleotide modulates actin functions has not been evident from analyses of ATP- and ADP-bound crystal structures of the actin monomer. We report that NMR chemical shift differences between the two forms are globally distributed. Furthermore, microsecond–millisecond motions are spread throughout the molecule in the ATP form, but largely confined to subdomains 1 and 2, and the nucleotide binding site in the ADP form. Through these motions, the ATP- and ADP-bound forms sample different high-energy conformations. A deafness-causing, fast-nucleating actin mutant populates the high-energy conformer of ATP-actin more than the wild-type protein, suggesting that this conformer may be on the pathway to nucleation. Together, the data suggest a model in which differential sampling of a nucleation-compatible form of the actin monomer may contribute to control of actin filament dynamics by nucleotide. NMR shows that ATP- and ADP-actin differ globally, including ground and excited state structures and dynamic architecture. Analyses of an actin mutant suggest the high-energy conformer of ATP-actin may be on the pathway to filament nucleation.
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Affiliation(s)
- Rustam Ali
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Jacob A Zahm
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.
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13
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Li X, Yao Y, Liu T, Gu K, Han Q, Zhang W, Ayala GJ, Liu Y, Na H, Yu J, Zhang F, Mayo KH, Su J. Actin binding to galectin-13/placental protein-13 occurs independently of the galectin canonical ligand binding site. Glycobiology 2021; 31:1219-1229. [PMID: 34080003 DOI: 10.1093/glycob/cwab047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/08/2021] [Accepted: 05/19/2021] [Indexed: 01/09/2023] Open
Abstract
The gene for galectin-13 (Gal-13, placental protein 13) is only present in primates, and its low expression level in maternal serum may promote pre-eclampsia. In the present study, we used pull-down experiments and biolayer interferometry to assess the interaction between Gal-13 and actin. These studies uncovered that human Gal-13 (hGal-13) and Saimiri boliviensis boliviensis (sGal-13) strongly bind to α- and β/γ-actin, with Ca2+ and ATP significantly enhancing interactions. This in turn suggests that h/sGal-13 may inhibit myosin-induced contraction when vascular smooth muscle cells undergo polarization. Here, we solved the crystal structure of sGal-13 bound to lactose and found that it exists as a monomer in contrast to hGal-13 that is a dimer. The distribution of sGal-13 in HeLa cells is similar to that of hGal-13, indicating that monomeric Gal-13 is the primary form in cells. Even though sGal-13 also binds to actin, hGal-13 ligand binding site mutants do not influence hGal-13/actin binding, whereas the monomeric mutant C136S/C138S binds to actin more strongly than wild type hGal-13. Overall, our study demonstrates that monomeric Gal-13 binds to actin, an interaction that is independent of the galectin canonical ligand binding site.
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Affiliation(s)
- Xumin Li
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yuan Yao
- Media Academy, Jilin Engineering Normal University, Changchun, China
| | - Tianhao Liu
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Keqi Gu
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Qiuyu Han
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Wenlu Zhang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Gabriela Jaramillo Ayala
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yuhan Liu
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Heya Na
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Jinyi Yu
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Fan Zhang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, 6-155 Jackson Hall, University of Minnesota, 321 Church Street, Minneapolis, MN 55455, U.S.A
| | - Jiyong Su
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
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14
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Das S, Stortz JF, Meissner M, Periz J. The multiple functions of actin in apicomplexan parasites. Cell Microbiol 2021; 23:e13345. [PMID: 33885206 DOI: 10.1111/cmi.13345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/29/2022]
Abstract
The cytoskeletal protein actin is highly abundant and conserved in eukaryotic cells. It occurs in two different states- the globular (G-actin) form, which can polymerise into the filamentous (F-actin) form, fulfilling various critical functions including cytokinesis, cargo trafficking and cellular motility. In higher eukaryotes, there are several actin isoforms with nearly identical amino acid sequences. Despite the high level of amino acid identity, they display regulated expression patterns and unique non-redundant roles. The number of actin isoforms together with conserved sequences may reflect the selective pressure exerted by scores of actin binding proteins (ABPs) in higher eukaryotes. In contrast, in many protozoans such as apicomplexan parasites which possess only a few ABPs, the regulatory control of actin and its multiple functions are still obscure. Here, we provide a summary of the regulation and biological functions of actin in higher eukaryotes and compare it with the current knowledge in apicomplexans. We discuss future experiments that will help us understand the multiple, critical roles of this fascinating system in apicomplexans.
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Affiliation(s)
- Sujaan Das
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig Maximilian University, Munich, Germany
| | - Johannes Felix Stortz
- Department Metabolism of Infection, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Markus Meissner
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig Maximilian University, Munich, Germany
| | - Javier Periz
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig Maximilian University, Munich, Germany
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15
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Lauer JC, Selig M, Hart ML, Kurz B, Rolauffs B. Articular Chondrocyte Phenotype Regulation through the Cytoskeleton and the Signaling Processes That Originate from or Converge on the Cytoskeleton: Towards a Novel Understanding of the Intersection between Actin Dynamics and Chondrogenic Function. Int J Mol Sci 2021; 22:3279. [PMID: 33807043 DOI: 10.3390/ijms22063279] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 02/08/2023] Open
Abstract
Numerous studies have assembled a complex picture, in which extracellular stimuli and intracellular signaling pathways modulate the chondrocyte phenotype. Because many diseases are mechanobiology-related, this review asked to what extent phenotype regulators control chondrocyte function through the cytoskeleton and cytoskeleton-regulating signaling processes. Such information would generate leverage for advanced articular cartilage repair. Serial passaging, pro-inflammatory cytokine signaling (TNF-α, IL-1α, IL-1β, IL-6, and IL-8), growth factors (TGF-α), and osteoarthritis not only induce dedifferentiation but also converge on RhoA/ROCK/Rac1/mDia1/mDia2/Cdc42 to promote actin polymerization/crosslinking for stress fiber (SF) formation. SF formation takes center stage in phenotype control, as both SF formation and SOX9 phosphorylation for COL2 expression are ROCK activity-dependent. Explaining how it is molecularly possible that dedifferentiation induces low COL2 expression but high SF formation, this review theorized that, in chondrocyte SOX9, phosphorylation by ROCK might effectively be sidelined in favor of other SF-promoting ROCK substrates, based on a differential ROCK affinity. In turn, actin depolymerization for redifferentiation would “free-up” ROCK to increase COL2 expression. Moreover, the actin cytoskeleton regulates COL1 expression, modulates COL2/aggrecan fragment generation, and mediates a fibrogenic/catabolic expression profile, highlighting that actin dynamics-regulating processes decisively control the chondrocyte phenotype. This suggests modulating the balance between actin polymerization/depolymerization for therapeutically controlling the chondrocyte phenotype.
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16
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Zsolnay V, Katkar HH, Chou SZ, Pollard TD, Voth GA. Structural basis for polarized elongation of actin filaments. Proc Natl Acad Sci U S A 2020; 117:30458-64. [PMID: 33199648 DOI: 10.1073/pnas.2011128117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Actin filaments elongate and shorten much faster at their barbed end than their pointed end, but the molecular basis of this difference has not been understood. We use all-atom molecular dynamics simulations to investigate the properties of subunits at both ends of the filament. The terminal subunits tend toward conformations that resemble actin monomers in solution, while contacts with neighboring subunits progressively flatten the conformation of internal subunits. At the barbed end the terminal subunit is loosely tethered by its DNase-1 loop to the third subunit, because its monomer-like conformation precludes stabilizing contacts with the penultimate subunit. The motions of the terminal subunit make the partially flattened penultimate subunit accessible for binding monomers. At the pointed end, unique contacts between the penultimate and terminal subunits are consistent with existing cryogenic electron microscopic (cryo-EM) maps, limit binding to incoming monomers, and flatten the terminal subunit, which likely promotes ATP hydrolysis and rapid phosphate release. These structures explain the distinct polymerization kinetics of the two ends.
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17
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A M, Latario CJ, Pickrell LE, Higgs HN. Lysine acetylation of cytoskeletal proteins: Emergence of an actin code. J Biophys Biochem Cytol 2020; 219:211455. [PMID: 33044556 PMCID: PMC7555357 DOI: 10.1083/jcb.202006151] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Reversible lysine acetylation of nuclear proteins such as histones is a long-established important regulatory mechanism for chromatin remodeling and transcription. In the cytoplasm, acetylation of a number of cytoskeletal proteins, including tubulin, cortactin, and the formin mDia2, regulates both cytoskeletal assembly and stability. More recently, acetylation of actin itself was revealed to regulate cytoplasmic actin polymerization through the formin INF2, with downstream effects on ER-to-mitochondrial calcium transfer, mitochondrial fission, and vesicle transport. This finding raises the possibility that actin acetylation, along with other post-translational modifications to actin, might constitute an "actin code," similar to the "histone code" or "tubulin code," controlling functional shifts to these central cellular proteins. Given the multiple roles of actin in nuclear functions, its modifications might also have important roles in gene expression.
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18
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Jepsen L, Sept D. Effects of Nucleotide and End-Dependent Actin Conformations on Polymerization. Biophys J 2020; 119:1800-1810. [PMID: 33080221 DOI: 10.1016/j.bpj.2020.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
The regulation of actin is key for controlled cellular function. Filaments are regulated by actin-binding proteins, but the nucleotide state of actin is also an important factor. From extended molecular dynamics simulations, we find that both nucleotide states of the actin monomer have significantly less twist than their crystal structures and that the ATP monomer is flatter than the ADP form. We also find that the filament's pointed end is flatter than the remainder of the filament and has a conformation distinct from G-actin, meaning that incoming monomers would need to undergo isomerization that would weaken the affinity and slow polymerization. Conversely, the barbed end of the filament takes on a conformation nearly identical to the ATP monomer, enhancing ATP G-actin's ability to polymerize as compared with ADP G-actin. The thermodynamic penalty imposed by differences in isomerization for the ATP and ADP growth at the barbed end exactly matches experimental results.
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Affiliation(s)
- Lauren Jepsen
- Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - David Sept
- Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.
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19
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Shaaban M, Chowdhury S, Nolen BJ. Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state. Nat Struct Mol Biol 2020; 27:1009-1016. [PMID: 32839613 DOI: 10.1038/s41594-020-0481-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/10/2020] [Indexed: 12/29/2022]
Abstract
Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the nucleation-competent state is unclear due to lack of high-resolution structures of the activated state. Here we report a ~3.9 Å resolution cryo-EM structure of activated Schizosaccharomyces pombe Arp2/3 complex bound to the S. pombe NPF Dip1 and attached to the end of the nucleated actin filament. The structure reveals global and local conformational changes that allow the two actin-related proteins in Arp2/3 complex to mimic a filamentous actin dimer and template nucleation. Activation occurs through a clamp-twisting mechanism, in which Dip1 forces two core subunits in Arp2/3 complex to pivot around one another, shifting half of the complex into a new activated position. By showing how Dip1 stimulates activation, the structure reveals how NPFs can activate Arp2/3 complex in diverse cellular processes.
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Affiliation(s)
- Mohammed Shaaban
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Saikat Chowdhury
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.
| | - Brad J Nolen
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.
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20
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Horan BG, Hall AR, Vavylonis D. Insights into Actin Polymerization and Nucleation Using a Coarse-Grained Model. Biophys J 2020; 119:553-566. [PMID: 32668234 DOI: 10.1016/j.bpj.2020.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the Cα atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, x-ray diffraction, and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at an angle with respect to the polymerizable bound structure, and the angle range depended on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G-actin form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to the antiparallel (lower) dimer. Individual monomers bound each other in a short-pitch helix complex in addition to other configurations, with several of them apparently nonproductive for polymerization. Simulations with multiple monomers in the F-actin form show assembly into filaments as well as transient aggregates at the barbed end. We discuss the implications of these observations on the kinetic pathway of actin filament nucleation and polymerization and possibilities for future improvements of the coarse-grained model.
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Affiliation(s)
- Brandon G Horan
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
| | - Aaron R Hall
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
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21
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Salem FB, Bunner WP, Prabhu VV, Kuyateh AB, O'Bryant CT, Murashov AK, Szatmari EM, Hughes RM. CofActor: A light- and stress-gated optogenetic clustering tool to study disease-associated cytoskeletal dynamics in living cells. J Biol Chem 2020; 295:11231-11245. [PMID: 32424038 DOI: 10.1074/jbc.ra119.012427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/12/2020] [Indexed: 11/06/2022] Open
Abstract
The hallmarks of neurodegenerative diseases, including neural fibrils, reactive oxygen species, and cofilin-actin rods, present numerous challenges in the development of in vivo diagnostic tools. Biomarkers such as β-amyloid (Aβ) fibrils and Tau tangles in Alzheimer's disease are accessible only via invasive cerebrospinal fluid assays, and reactive oxygen species can be fleeting and challenging to monitor in vivo Although remaining a challenge for in vivo detection, the protein-protein interactions underlying these disease-specific biomarkers present opportunities for the engineering of in vitro pathology-sensitive biosensors. These tools can be useful for investigating early stage events in neurodegenerative diseases in both cellular and animal models and may lead to clinically useful reagents. Here, we report a light- and cellular stress-gated protein switch based on cofilin-actin rod formation, occurring in stressed neurons in the Alzheimer's disease brain and following ischemia. By coupling the stress-sensitive cofilin-actin interaction with the light-responsive Cry2-CIB blue-light switch, referred to hereafter as the CofActor, we accomplished both light- and energetic/oxidative stress-gated control of this interaction. Site-directed mutagenesis of both cofilin and actin revealed residues critical for sustaining or abrogating the light- and stress-gated response. Of note, the switch response varied depending on whether cellular stress was generated via glycolytic inhibition or by both glycolytic inhibition and azide-induced ATP depletion. We also demonstrate light- and cellular stress-gated switch function in cultured hippocampal neurons. CofActor holds promise for the tracking of early stage events in neurodegeneration and for investigating actin's interactions with other proteins during cellular stress.
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Affiliation(s)
- Fatema B Salem
- Department of Chemistry, East Carolina University, Greenville, North Carolina, USA
| | - Wyatt P Bunner
- Department of Physical Therapy, East Carolina University, Greenville, North Carolina, USA
| | - Vishwanath V Prabhu
- Department of Physical Therapy, East Carolina University, Greenville, North Carolina, USA
| | - Abu-Bakarr Kuyateh
- Department of Chemistry, East Carolina University, Greenville, North Carolina, USA
| | - Collin T O'Bryant
- Department of Chemistry, East Carolina University, Greenville, North Carolina, USA
| | - Alexander K Murashov
- Department of Physiology, East Carolina University, Greenville, North Carolina, USA
| | - Erzsebet M Szatmari
- Department of Physical Therapy, East Carolina University, Greenville, North Carolina, USA
| | - Robert M Hughes
- Department of Chemistry, East Carolina University, Greenville, North Carolina, USA
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22
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Das S, Ge P, Oztug Durer ZA, Grintsevich EE, Zhou ZH, Reisler E. D-loop Dynamics and Near-Atomic-Resolution Cryo-EM Structure of Phalloidin-Bound F-Actin. Structure 2020; 28:586-593.e3. [PMID: 32348747 DOI: 10.1016/j.str.2020.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/28/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022]
Abstract
Detailed molecular information on G-actin assembly into filaments (F-actin), and their structure, dynamics, and interactions, is essential for understanding their cellular functions. Previous studies indicate that a flexible DNase I binding loop (D-loop, residues 40-50) plays a major role in actin's conformational dynamics. Phalloidin, a "gold standard" for actin filament staining, stabilizes them and affects the D-loop. Using disulfide crosslinking in yeast actin D-loop mutant Q41C/V45C, light-scattering measurements, and cryoelectron microscopy reconstructions, we probed the constraints of D-loop dynamics and its contribution to F-actin formation/stability. Our data support a model of residues 41-45 distances that facilitate G- to F-actin transition. We report also a 3.3-Å resolution structure of phalloidin-bound F-actin in the ADP-Pi-like (ADP-BeFx) state. This shows the phalloidin-binding site on F-actin and how the relative movement between its two protofilaments is restricted by it. Together, our results provide molecular details of F-actin structure and D-loop dynamics.
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Affiliation(s)
- Sanchaita Das
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA
| | - Peng Ge
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA 90095, USA
| | - Zeynep A Oztug Durer
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA
| | - Elena E Grintsevich
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA
| | - Z Hong Zhou
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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23
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Schroer CFE, Baldauf L, van Buren L, Wassenaar TA, Melo MN, Koenderink GH, Marrink SJ. Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. Proc Natl Acad Sci U S A 2020; 117:5861-5872. [PMID: 32123101 PMCID: PMC7084070 DOI: 10.1073/pnas.1914884117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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] [Indexed: 12/30/2022] Open
Abstract
The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed that direct interactions between actin filaments and lipid bilayers are possible and that the net charge of the bilayer as well as the presence of divalent ions in the buffer play an important role. In vivo, colocalization of actin filaments and divalent ions are suppressed, and cells rely on linker proteins to connect the plasma membrane to the actin network. Little is known, however, about why this is the case and what microscopic interactions are important. A deeper understanding is highly beneficial, first, to obtain understanding in the biological design of cells and, second, as a possible basis for the building of artificial cortices for the stabilization of synthetic cells. Here, we report the results of coarse-grained molecular dynamics simulations of monomeric and filamentous actin in the vicinity of differently charged lipid bilayers. We observe that charges on the lipid head groups strongly determine the ability of actin to adsorb to the bilayer. The inclusion of divalent ions leads to a reversal of the binding affinity. Our in silico results are validated experimentally by reconstitution assays with actin on lipid bilayer membranes and provide a molecular-level understanding of the actin-membrane interaction.
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Affiliation(s)
- Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Lucia Baldauf
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica, New University of Lisbon, 2780-157, Oeiras, Portugal
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands;
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands;
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
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24
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Pospich S, Merino F, Raunser S. Structural Effects and Functional Implications of Phalloidin and Jasplakinolide Binding to Actin Filaments. Structure 2020; 28:437-449.e5. [PMID: 32084355 DOI: 10.1016/j.str.2020.01.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/07/2020] [Accepted: 01/28/2020] [Indexed: 12/15/2022]
Abstract
Actin undergoes structural transitions during polymerization, ATP hydrolysis, and subsequent release of inorganic phosphate. Several actin-binding proteins sense specific states during this transition and can thus target different regions of the actin filament. Here, we show in atomic detail that phalloidin, a mushroom toxin that is routinely used to stabilize and label actin filaments, suspends the structural changes in actin, likely influencing its interaction with actin-binding proteins. Furthermore, high-resolution cryoelectron microscopy structures reveal structural rearrangements in F-actin upon inorganic phosphate release in phalloidin-stabilized filaments. We find that the effect of the sponge toxin jasplakinolide differs from the one of phalloidin, despite their overlapping binding site and similar interactions with the actin filament. Analysis of structural conformations of F-actin suggests that stabilizing agents trap states within the natural conformational space of actin.
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Affiliation(s)
- Sabrina Pospich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany.
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25
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Santos A, Shauchuk Y, Cichoń U, Vavra KC, Rock RS. How Actin Tracks Affect Myosin Motors. Advances in Experimental Medicine and Biology 2020. [DOI: 10.1007/978-3-030-38062-5_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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26
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Song K, Han HJ, Kim S, Kwon J. Thymosin beta 4 attenuates PrP(106-126)-induced human brain endothelial cells dysfunction. Eur J Pharmacol 2019; 869:172891. [PMID: 31877278 DOI: 10.1016/j.ejphar.2019.172891] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 03/19/2019] [Revised: 12/06/2019] [Accepted: 12/19/2019] [Indexed: 12/24/2022]
Abstract
The blood-brain barrier (BBB) is a highly selective permeability barrier that separates the circulating blood from the brain and extracellular fluid in the central nervous system (CNS). The BBB is formed by cerebral endothelial cells connected by tight junctions. Prion diseases are neurodegenerative pathologies characterized by the accumulation of altered forms of the prion protein (PrP), named PrPSc. Thymosin beta 4 (Tβ4) is an actin-sequestering peptide known to bind monomeric actin and inhibit its polymerization, and it is known to have a neuroprotective effect. However, the effect of Tβ4 on prion disease has not yet been investigated. Therefore, in this study, we investigated the effect of Tβ4 on prion-induced BBB dysfunction in hCMEC/D3 human cerebral endothelial cells. We found that Tβ4 increased the expression of tight junction protein, but reduced the ratio of F-actin to G-actin. Moreover, we showed that Tβ4 significantly improved PrP (106-126)-induced vascular permeability dysfunction in hCMEC/D3 cells. Through human BBB in vitro model, we found that PrP (106-126) could disrupt tight junctions and cytoskeleton arrangement. These results suggest that Tβ4 may play a critical role in barrier stabilization. Furthermore, Tβ4 may prevent neurodegenerative diseases caused by prion-induced BBB dysfunction.
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Affiliation(s)
- Kibbeum Song
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeonbuk Natioanl University, 79 Gobongro, Iksan, 54596, Republic of Korea
| | - Hye-Ju Han
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeonbuk Natioanl University, 79 Gobongro, Iksan, 54596, Republic of Korea
| | - Sokho Kim
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeonbuk Natioanl University, 79 Gobongro, Iksan, 54596, Republic of Korea
| | - Jungkee Kwon
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeonbuk Natioanl University, 79 Gobongro, Iksan, 54596, Republic of Korea.
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27
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Wang S, Crevenna AH, Ugur I, Marion A, Antes I, Kazmaier U, Hoyer M, Lamb DC, Gegenfurtner F, Kliesmete Z, Ziegenhain C, Enard W, Vollmar A, Zahler S. Actin stabilizing compounds show specific biological effects due to their binding mode. Sci Rep 2019; 9:9731. [PMID: 31278311 DOI: 10.1038/s41598-019-46282-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/26/2019] [Indexed: 11/08/2022] Open
Abstract
Actin binding compounds are widely used tools in cell biology. We compare the biological and biochemical effects of miuraenamide A and jasplakinolide, a structurally related prototypic actin stabilizer. Though both compounds have similar effects on cytoskeletal morphology and proliferation, they affect migration and transcription in a distinctive manner, as shown by a transcriptome approach in endothelial cells. In vitro, miuraenamide A acts as an actin nucleating, F-actin polymerizing and stabilizing compound, just like described for jasplakinolide. However, in contrast to jasplakinolide, miuraenamide A competes with cofilin, but not gelsolin or Arp2/3 for binding to F-actin. We propose a binding mode of miuraenamide A, explaining both its similarities and its differences to jasplakinolide. Molecular dynamics simulations suggest that the bromophenol group of miurenamide A interacts with residues Tyr133, Tyr143, and Phe352 of actin. This shifts the D-loop of the neighboring actin, creating tighter packing of the monomers, and occluding the binding site of cofilin. Since relatively small changes in the molecular structure give rise to this selectivity, actin binding compounds surprisingly are promising scaffolds for creating actin binders with specific functionality instead of just "stabilizers".
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28
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Kumpula EP, Lopez AJ, Tajedin L, Han H, Kursula I. Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation. PLoS Biol 2019; 17:e3000315. [PMID: 31199804 PMCID: PMC6599135 DOI: 10.1371/journal.pbio.3000315] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/28/2019] [Accepted: 05/23/2019] [Indexed: 11/18/2022] Open
Abstract
Plasmodium actins form very short filaments and have a noncanonical link between ATP hydrolysis and polymerization. Long filaments are detrimental to the parasites, but the structural factors constraining Plasmodium microfilament lengths have remained unknown. Using high-resolution crystallography, we show that magnesium binding causes a slight flattening of the Plasmodium actin I monomer, and subsequent phosphate release results in a more twisted conformation. Thus, the Mg-bound monomer is closer in conformation to filamentous (F) actin than the Ca form, and this likely facilitates polymerization. A coordinated potassium ion resides in the active site during hydrolysis and leaves together with the phosphate, a process governed by the position of the Arg178/Asp180-containing A loop. Asp180 interacts with either Lys270 or His74, depending on the protonation state of the histidine, while Arg178 links the inner and outer domains (ID and OD) of the actin protomer. Hence, the A loop acts as a switch between stable and unstable filament conformations, the latter leading to fragmentation. Our data provide a comprehensive model for polymerization, ATP hydrolysis and phosphate release, and fragmentation of parasite microfilaments. Similar mechanisms may well exist in canonical actins, although fragmentation is much less favorable due to several subtle sequence differences as well as the methylation of His73, which is absent on the corresponding His74 in Plasmodium actin I. A detailed mechanistic study of malaria parasite actins reveals at the atomic level how they polymerize, hydrolyze ATP, and are fragmented to keep actin filament lengths short enough for parasite survival.
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Affiliation(s)
- Esa-Pekka Kumpula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Andrea J. Lopez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Leila Tajedin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Huijong Han
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- European XFEL GmbH, Schenefeld, Germany
| | - Inari Kursula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
- European XFEL GmbH, Schenefeld, Germany
- * E-mail:
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29
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Umeki N, Shibata K, Noguchi TQP, Hirose K, Sako Y, Uyeda TQP. K336I mutant actin alters the structure of neighbouring protomers in filaments and reduces affinity for actin-binding proteins. Sci Rep 2019; 9:5353. [PMID: 30926871 PMCID: PMC6441083 DOI: 10.1038/s41598-019-41795-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/18/2019] [Indexed: 12/16/2022] Open
Abstract
Mutation of the Lys-336 residue of actin to Ile (K336I) or Asp (K336E) causes congenital myopathy. To understand the effect of this mutation on the function of actin filaments and gain insight into the mechanism of disease onset, we prepared and biochemically characterised K336I mutant actin from Dictyostelium discoideum. Subtilisin cleavage assays revealed that the structure of the DNase-I binding loop (D-loop) of monomeric K336I actin, which would face the adjacent actin-protomer in filaments, differed from that of wild type (WT) actin. Although K336I actin underwent normal salt-dependent reversible polymerisation and formed apparently normal filaments, interactions of K336I filaments with alpha-actinin, myosin II, and cofilin were disrupted. Furthermore, co-filaments of K336I and WT actins also exhibited abnormal interactions with cofilin, implying that K336I actin altered the structure of the neighbouring WT actin protomers such that interaction between cofilin and the WT actin protomers was prevented. We speculate that disruption of the interactions between co-filaments and actin-binding proteins is the primary reason why the K336I mutation induces muscle disease in a dominant fashion.
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Affiliation(s)
- Nobuhisa Umeki
- Cellular Informatics Lab., RIKEN, Wako, Saitama, 351-0198, Japan. .,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan.
| | - Keitaro Shibata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan.,Advanced ICT Research Institute, National Institute of Information and Communications Technology (NICT), Kobe, Hyogo, 651-2492, Japan
| | - Taro Q P Noguchi
- National Institute of Technology, Miyakonojo College, Miyakonojo, Miyazaki, 885-8567, Japan
| | - Keiko Hirose
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan
| | - Yasushi Sako
- Cellular Informatics Lab., RIKEN, Wako, Saitama, 351-0198, Japan
| | - Taro Q P Uyeda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan.,Department of Physics, Waseda University, Shinjuku, Tokyo, 169-8555, Japan
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30
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Steinz MM, Persson M, Aresh B, Olsson K, Cheng AJ, Ahlstrand E, Lilja M, Lundberg TR, Rullman E, Möller KÄ, Sandor K, Ajeganova S, Yamada T, Beard N, Karlsson BC, Tavi P, Kenne E, Svensson CI, Rassier DE, Karlsson R, Friedman R, Gustafsson T, Lanner JT. Oxidative hotspots on actin promote skeletal muscle weakness in rheumatoid arthritis. JCI Insight 2019; 5:126347. [PMID: 30920392 DOI: 10.1172/jci.insight.126347] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle weakness in patients suffering from rheumatoid arthritis (RA) adds to their impaired working abilities and reduced quality of life. However, little molecular insight is available on muscle weakness associated with RA. Oxidative stress has been implicated in the disease pathogenesis of RA. Here we show that oxidative post-translational modifications of the contractile machinery targeted to actin result in impaired actin polymerization and reduced force production. Using mass spectrometry, we identified the actin residues targeted by oxidative 3-nitrotyrosine (3-NT) or malondialdehyde adduct (MDA) modifications in weakened skeletal muscle from mice with arthritis and patients afflicted by RA. The residues were primarily located to three distinct regions positioned at matching surface areas of the skeletal muscle actin molecule from arthritis mice and RA patients. Moreover, molecular dynamic simulations revealed that these areas, here coined "hotspots", are important for the stability of the actin molecule and its capacity to generate filaments and interact with myosin. Together, these data demonstrate how oxidative modifications on actin promote muscle weakness in RA patients and provide novel leads for targeted therapeutic treatment to improve muscle function.
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Affiliation(s)
- Maarten M Steinz
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Malin Persson
- Department of Kinesiology and Physical Education, McGill University, Montreal, Canada
| | - Bejan Aresh
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Karl Olsson
- Department of Laboratory Medicine, Division of Clinical Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Arthur J Cheng
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Emma Ahlstrand
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Mats Lilja
- Department of Laboratory Medicine, Division of Clinical Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Tommy R Lundberg
- Department of Laboratory Medicine, Division of Clinical Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Eric Rullman
- Department of Laboratory Medicine, Division of Clinical Physiology, Karolinska Institutet, Stockholm, Sweden
| | | | - Katalin Sandor
- Department of Physiology and Pharmacology, Center for Molecular Medicine, and
| | - Sofia Ajeganova
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Takashi Yamada
- Department of Physical Therapy, Sapporo Medical University, Sapporo, Japan
| | - Nicole Beard
- Faculty of Science and Technology, University of Canberra, Australia
| | - Björn Cg Karlsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Pasi Tavi
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden.,A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Ellinor Kenne
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Camilla I Svensson
- Department of Physiology and Pharmacology, Center for Molecular Medicine, and
| | - Dilson E Rassier
- Department of Kinesiology and Physical Education, McGill University, Montreal, Canada
| | - Roger Karlsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Thomas Gustafsson
- Department of Laboratory Medicine, Division of Clinical Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Johanna T Lanner
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
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31
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Chou SZ, Pollard TD. Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides. Proc Natl Acad Sci U S A 2019; 116:4265-4274. [PMID: 30760599 PMCID: PMC6410863 DOI: 10.1073/pnas.1807028115] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [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: 02/04/2023] Open
Abstract
We used cryo-electron microscopy (cryo-EM) to reconstruct actin filaments with bound AMPPNP (β,γ-imidoadenosine 5'-triphosphate, an ATP analog, resolution 3.1 Å), ADP-Pi (ADP with inorganic phosphate, resolution 3.1 Å), or ADP (resolution 3.6 Å). Subunits in the three filaments have similar backbone conformations, so assembly rather than ATP hydrolysis or phosphate dissociation is responsible for their flattened conformation in filaments. Polymerization increases the rate of ATP hydrolysis by changing the positions of the side chains of Q137 and H161 in the active site. Flattening during assembly also promotes interactions along both the long-pitch and short-pitch helices. In particular, conformational changes in subdomain 3 open up multiple favorable interactions with the DNase-I binding loop in subdomain 2 of the adjacent subunit. Subunits at the barbed end of the filament are likely to be in this favorable conformation, while monomers are not. This difference explains why filaments grow faster at the barbed end than the pointed end. When phosphate dissociates from ADP-Pi-actin through a backdoor channel, the conformation of the C terminus changes so it distorts the DNase binding loop, which allows cofilin binding, and a network of interactions among S14, H73, G74, N111, R177, and G158 rearranges to open the phosphate release site.
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Affiliation(s)
- Steven Z Chou
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | - Thomas D Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103
- Department of Cell Biology, Yale University, New Haven, CT 06520-8103
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32
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Dominguez R. Nucleotide-dependent conformational changes in the actin filament: Subtler than expected. Proc Natl Acad Sci U S A 2019; 116:3959-61. [PMID: 30782816 DOI: 10.1073/pnas.1900799116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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33
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Kwiatkowski S, Seliga AK, Vertommen D, Terreri M, Ishikawa T, Grabowska I, Tiebe M, Teleman AA, Jagielski AK, Veiga-da-Cunha M, Drozak J. SETD3 protein is the actin-specific histidine N-methyltransferase. eLife 2018; 7:37921. [PMID: 30526847 PMCID: PMC6289574 DOI: 10.7554/elife.37921] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 11/06/2018] [Indexed: 01/02/2023] Open
Abstract
Protein histidine methylation is a rare post-translational modification of unknown biochemical importance. In vertebrates, only a few methylhistidine-containing proteins have been reported, including β-actin as an essential example. The evolutionary conserved methylation of β-actin H73 is catalyzed by an as yet unknown histidine N-methyltransferase. We report here that the protein SETD3 is the actin-specific histidine N-methyltransferase. In vitro, recombinant rat and human SETD3 methylated β-actin at H73. Knocking-out SETD3 in both human HAP1 cells and in Drosophila melanogaster resulted in the absence of methylation at β-actin H73 in vivo, whereas β-actin from wildtype cells or flies was > 90% methylated. As a consequence, we show that Setd3-deficient HAP1 cells have less cellular F-actin and an increased glycolytic phenotype. In conclusion, by identifying SETD3 as the actin-specific histidine N-methyltransferase, our work pioneers new research into the possible role of this modification in health and disease and questions the substrate specificity of SET-domain-containing enzymes.
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Affiliation(s)
- Sebastian Kwiatkowski
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka K Seliga
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Marianna Terreri
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marcel Tiebe
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Adam K Jagielski
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maria Veiga-da-Cunha
- Metabolic Research Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
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34
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Aydin F, Katkar HH, Voth GA. Multiscale simulation of actin filaments and actin-associated proteins. Biophys Rev 2018; 10:1521-1535. [PMID: 30382557 PMCID: PMC6297090 DOI: 10.1007/s12551-018-0474-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/21/2018] [Indexed: 02/04/2023] Open
Abstract
Actin is an important cytoskeletal protein that serves as a building block to form filament networks that span across the cell. These networks are orchestrated by a myriad of other cytoskeletal entities including the unbranched filament-forming protein formin and branched network-forming protein complex Arp2/3. Computational models have been able to provide insights into many important structural transitions that are involved in forming these networks, and into the nature of interactions essential for actin filament formation and for regulating the behavior of actin-associated proteins. In this review, we summarize a subset of such models that focus on the atomistic features and those that can integrate atomistic features into a larger picture in a multiscale fashion.
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Affiliation(s)
- Fikret Aydin
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Harshwardhan H Katkar
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Gregory A Voth
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA.
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35
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Fujiwara I, Takeda S, Oda T, Honda H, Narita A, Maéda Y. Polymerization and depolymerization of actin with nucleotide states at filament ends. Biophys Rev 2018; 10:1513-1519. [PMID: 30460458 PMCID: PMC6297080 DOI: 10.1007/s12551-018-0483-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/09/2018] [Indexed: 01/20/2023] Open
Abstract
Polymerization induces hydrolysis of ATP bound to actin, followed by γ-phosphate release, which helps advance the disassembly of actin filaments into ADP-G-actin. Mechanical understanding of this correlation between actin assembly and ATP hydrolysis has been an object of intensive studies in biochemistry and structural biology for many decades. Although actin polymerization and depolymerization occur only at either the barbed or pointed ends and the kinetic and equilibrium properties are substantially different from each other, characterizing their properties is difficult to do by bulk assays, as these assays report the average of all actin filaments in solution and are therefore not able to discern the properties of individual actin filaments. Biochemical studies of actin polymerization and hydrolysis were hampered by these inherent properties of actin filaments. Total internal reflection fluorescence (TIRF) microscopy overcame this problem by observing single actin filaments. With TIRF, we now know not only that each end has distinct properties, but also that the rate of γ-phosphate release is much faster from the terminals than from the interior of actin filaments. The rate of γ-phosphate release from actin filament ends is even more accelerated when latrunculin A is bound. These findings highlight the importance of resolving structural differences between actin molecules in the interior of the filament and those at either filament end. This review provides a history of observing actin filaments under light microscopy, an overview of dynamic properties of ATP hydrolysis at the end of actin filament, and structural views of γ-phosphate release.
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Affiliation(s)
- Ikuko Fujiwara
- Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan.
| | - Shuichi Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Toshiro Oda
- Faculty of Health and Welfare, Tokai Gakuin University, Nakakirino-cyo 5-68, Kakamigahara, Gifu, 504-8511, Japan
| | - Hajime Honda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yuichiro Maéda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Toyota Physical and Chemical Research Institute, 41-1, Yokomichi, Nagakute, Aichi, 480-1192, Japan
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36
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Katkar HH, Davtyan A, Durumeric AEP, Hocky GM, Schramm AC, De La Cruz EM, Voth GA. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophys J 2018; 115:1589-1602. [PMID: 30249402 PMCID: PMC6260209 DOI: 10.1016/j.bpj.2018.08.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 05/11/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
Actin filaments continually assemble and disassemble within a cell. Assembled filaments "age" as a bound nucleotide ATP within each actin subunit quickly hydrolyzes followed by a slower release of the phosphate Pi, leaving behind a bound ADP. This subtle change in nucleotide state of actin subunits affects filament rigidity as well as its interactions with binding partners. We present here a systematic multiscale ultra-coarse-graining approach that provides a computationally efficient way to simulate a long actin filament undergoing ATP hydrolysis and phosphate-release reactions while systematically taking into account available atomistic details. The slower conformational changes and their dependence on the chemical reactions are simulated with the ultra-coarse-graining model by assigning internal states to the coarse-grained sites. Each state is represented by a unique potential surface of a local heterogeneous elastic network. Internal states undergo stochastic transitions that are coupled to conformations of the underlying molecular system. The model reproduces mechanical properties of the filament and allows us to study whether conformational fluctuations in actin subunits produce cooperative filament aging. We find that the nucleotide states of neighboring subunits modulate the reaction kinetics, implying cooperativity in ATP hydrolysis and Pi release. We further systematically coarse grain the system into a Markov state model that incorporates assembly and disassembly, facilitating a direct comparison with previously published models. We find that cooperativity in ATP hydrolysis and Pi release significantly affects the filament growth dynamics only near the critical G-actin concentration, whereas far from it, both cooperative and random mechanisms show similar growth dynamics. In contrast, filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights, to our knowledge, into the cooperative nature of ATP hydrolysis and Pi release and the implications it has for actin filament properties, providing novel predictions for future experimental studies.
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Affiliation(s)
- Harshwardhan H Katkar
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Aram Davtyan
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Aleksander E P Durumeric
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Glen M Hocky
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Anthony C Schramm
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois.
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37
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Fujiwara I, Zweifel ME, Courtemanche N, Pollard TD. Latrunculin A Accelerates Actin Filament Depolymerization in Addition to Sequestering Actin Monomers. Curr Biol 2018; 28:3183-3192.e2. [PMID: 30270183 DOI: 10.1016/j.cub.2018.07.082] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 04/30/2018] [Accepted: 07/31/2018] [Indexed: 11/16/2022]
Abstract
Latrunculin A (LatA), a toxin from the red sea sponge Latrunculia magnifica, is the most widely used reagent to depolymerize actin filaments in experiments on live cells. LatA binds actin monomers and sequesters them from polymerization [1, 2]. Low concentrations of LatA result in rapid (tens of seconds) disassembly of actin filaments in animal [3] and yeast cells [2]. Depolymerization is usually assumed to result from sequestration of actin monomers. Our observations of single-muscle actin filaments by TIRF microscopy showed that LatA bound ATP-actin monomers with a higher affinity (Kd = 0.1 μM) than ADP-Pi-actin (Kd = 0.4 μM) or ADP-actin (Kd = 4.7 μM). LatA also slowly severed filaments and increased the depolymerization rate at both ends of filaments freshly assembled from ATP-actin to the rates of ADP-actin. This rate plateaued at LatA concentrations >60 μM. LatA did not change the depolymerization rates of ADP- actin filaments or ADP-Pi-actin filaments generated with 160 mM phosphate in the buffer. LatA did not increase the rate of phosphate release from bulk samples of filaments assembled from ATP-actin. Thermodynamic analysis showed that LatA binds weakly to actin filaments with a Kd >100 μM. We propose that concentrations of LatA much lower than this Kd promote phosphate dissociation only from both ends of filaments, resulting in depolymerization limited by the rate of ADP-actin dissociation. Thus, one must consider both rapid actin depolymerization and severing in addition to sequestering actin monomers when interpreting the effects of LatA on cells.
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Affiliation(s)
- Ikuko Fujiwara
- Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan; Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520, USA.
| | - Mark E Zweifel
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Naomi Courtemanche
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Thomas D Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520, USA; Departments of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA
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38
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Sandestig A, Green A, Jonasson J, Vogt H, Wahlström J, Pepler A, Ellnebo K, Biskup S, Stefanova M. Could Dissimilar Phenotypic Effects of ACTB Missense Mutations Reflect the Actin Conformational Change? Two Novel Mutations and Literature Review. Mol Syndromol 2018; 9:259-265. [PMID: 30733661 DOI: 10.1159/000492267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2018] [Indexed: 02/03/2023] Open
Abstract
The beta-actin gene encodes 1 of 6 different actin proteins. De novo heterozygous missense mutations in ACTB have been identified in patients with Baraitser-Winter syndrome (BRWS) and also in patients with developmental disorders other than BRWS, such as deafness, dystonia, and neutrophil dysfunction. We describe 2 different novel de novo missense ACTB mutations, c.208C>G (p.Pro70Ala) and c.511C>T (p.Leu171Phe), found by trio exome sequencing analysis of 2 unrelated patients: an 8-year-old boy with a suspected BRWS and a 4-year-old girl with unclear developmental disorder. The mutated residue in the first case is situated in the actin H-loop, which is involved in actin polymerization. The mutated residue in the second case (p.Leu171Phe) is found at the actin barbed end in the W-loop, important for binding to profilin and other actin-binding molecules. While the boy presented with a typical BRWS facial appearance, the girl showed facial features not recognizable as a BRWS gestalt as well as ventricular arrhythmia, cleft palate, thrombocytopenia, and gray matter heterotopia. We reviewed previously published ACTB missense mutations and ascertained that a number of them do not cause typical BRWS. By comparing clinical and molecular data, we speculate that the phenotypic differences found in ACTB missense mutation carriers might supposedly be dependent on the conformational change of ACTB.
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Affiliation(s)
- Anna Sandestig
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Anna Green
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Jon Jonasson
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Hartmut Vogt
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | - Johan Wahlström
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | | | - Katarina Ellnebo
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | | | - Margarita Stefanova
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
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39
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Merino F, Pospich S, Funk J, Wagner T, Küllmer F, Arndt HD, Bieling P, Raunser S. Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM. Nat Struct Mol Biol 2018; 25:528-37. [PMID: 29867215 DOI: 10.1038/s41594-018-0074-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/02/2018] [Indexed: 11/08/2022]
Abstract
The function of actin is coupled to the nucleotide bound to its active site. ATP hydrolysis is activated during polymerization; a delay between hydrolysis and inorganic phosphate (Pi) release results in a gradient of ATP, ADP-Pi and ADP along actin filaments (F-actin). Actin-binding proteins can recognize F-actin's nucleotide state, using it as a local 'age' tag. The underlying mechanism is complex and poorly understood. Here we report six high-resolution cryo-EM structures of F-actin from rabbit skeletal muscle in different nucleotide states. The structures reveal that actin polymerization repositions the proposed catalytic base, His161, closer to the γ-phosphate. Nucleotide hydrolysis and Pi release modulate the conformational ensemble at the periphery of the filament, thus resulting in open and closed states, which can be sensed by coronin-1B. The drug-like toxin jasplakinolide locks F-actin in an open state. Our results demonstrate in detail how ATP hydrolysis links to F-actin's conformational dynamics and protein interaction.
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40
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Miao Y, Tipakornsaowapak T, Zheng L, Mu Y, Lewellyn E. Phospho-regulation of intrinsically disordered proteins for actin assembly and endocytosis. FEBS J 2018; 285:2762-2784. [PMID: 29722136 DOI: 10.1111/febs.14493] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/04/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Abstract
Actin filament assembly contributes to the endocytic pathway pleiotropically, with active roles in clathrin-dependent and clathrin-independent endocytosis as well as subsequent endosomal trafficking. Endocytosis comprises a series of dynamic events, including the initiation of membrane curvature, bud invagination, vesicle abscission and subsequent vesicular transport. The ultimate success of endocytosis requires the coordinated activities of proteins that trigger actin polymerization, recruit actin-binding proteins (ABPs) and organize endocytic proteins (EPs) that promote membrane curvature through molecular crowding or scaffolding mechanisms. A particularly interesting phenomenon is that multiple EPs and ABPs contain a substantial percentage of intrinsically disordered regions (IDRs), which can contribute to protein coacervation and phase separation. In addition, intrinsically disordered proteins (IDPs) frequently contain sites for post-translational modifications (PTMs) such as phosphorylation, and these modifications exhibit a high preference for IDR residues [Groban ES et al. (2006) PLoS Comput Biol 2, e32]. PTMs are implicated in regulating protein function by modulating the protein conformation, protein-protein interactions and the transition between order and disorder states of IDPs. The molecular mechanisms by which IDRs of ABPs and EPs fine-tune actin assembly and endocytosis remain mostly unexplored and elusive. In this review, we analyze protein sequences of budding yeast EPs and ABPs, and discuss the potential underlying mechanisms for regulating endocytosis and actin assembly through the emerging concept of IDR-mediated protein multivalency, coacervation, and phase transition, with an emphasis on the phospho-regulation of IDRs. Finally, we summarize the current understanding of how these mechanisms coordinate actin cytoskeleton assembly and membrane curvature formation during endocytosis in budding yeast.
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Affiliation(s)
- Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Liangzhen Zheng
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Eric Lewellyn
- Department of Biology, Division of Natural Sciences, St Norbert College, De Pere, WI, USA
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41
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Kotila T, Kogan K, Enkavi G, Guo S, Vattulainen I, Goode BL, Lappalainen P. Structural basis of actin monomer re-charging by cyclase-associated protein. Nat Commun 2018; 9:1892. [PMID: 29760438 PMCID: PMC5951797 DOI: 10.1038/s41467-018-04231-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/13/2018] [Indexed: 11/10/2022] Open
Abstract
Actin polymerization powers key cellular processes, including motility, morphogenesis, and endocytosis. The actin turnover cycle depends critically on "re-charging" of ADP-actin monomers with ATP, but whether this reaction requires dedicated proteins in cells, and the underlying mechanism, have remained elusive. Here we report that nucleotide exchange catalyzed by the ubiquitous cytoskeletal regulator cyclase-associated protein (CAP) is critical for actin-based processes in vivo. We determine the structure of the CAP-actin complex, which reveals that nucleotide exchange occurs in a compact, sandwich-like complex formed between the dimeric actin-binding domain of CAP and two ADP-actin monomers. In the crystal structure, the C-terminal tail of CAP associates with the nucleotide-sensing region of actin, and this interaction is required for rapid re-charging of actin by both yeast and mammalian CAPs. These data uncover the conserved structural basis and biological role of protein-catalyzed re-charging of actin monomers.
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Affiliation(s)
- Tommi Kotila
- Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland
| | - Konstantin Kogan
- Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, 00014, Helsinki, Finland
| | - Siyang Guo
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, 00014, Helsinki, Finland.,Laboratory of Physics, Tampere University of Technology, 33101, Tampere, Finland
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Pekka Lappalainen
- Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland.
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42
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Schummel PH, Jaworek MW, Rosin C, Högg J, Winter R. Exploring the influence of natural cosolvents on the free energy and conformational landscape of filamentous actin and microtubules. Phys Chem Chem Phys 2018; 20:28400-28411. [DOI: 10.1039/c8cp03041c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural osmolytes have a significant influence on the temperature- and pressure-dependent stability of filamentous actin and microtubules.
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Affiliation(s)
- Paul Hendrik Schummel
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Michel W. Jaworek
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Christopher Rosin
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Jessica Högg
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
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43
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Abstract
Many free-energy sampling and quantum mechanics/molecular mechanics (QM/MM) computations on protein complexes have been performed where, by necessity, a single component is studied isolated in solution while its overall configuration is kept in the complex-like state by either rigid restraints or harmonic constraints. A drawback in these studies is that the system's native fluctuations are lost, both due to the change of environment and the imposition of the extra potential. Yet, we know that having both accurate structure and fluctuations is likely crucial to achieving correct simulation estimates for the subsystem within its native larger protein complex context. In this work, we provide a new approach to this problem by drawing on ideas developed to incorporate experimental information into a molecular simulation by relative entropy minimization to a target system. We show that by using linear biases on coarse-grained (CG) observables (such as distances or angles between large subdomains within a protein), we can maintain the protein in a particular target conformation while also preserving the correct equilibrium fluctuations of the subsystem within its larger biomolecular complex. As an application, we demonstrate this algorithm by training a bias that causes an actin monomer (and trimer) in solution to sample the same average structure and fluctuations as if it were embedded within a much larger actin filament. Additionally, we have developed a number of algorithmic improvements that accelerate convergence of the on-the-fly relative entropy minimization algorithms for this type of application. Finally, we have contributed these methods to the PLUMED open source free energy sampling software library.
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Affiliation(s)
- Glen M Hocky
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Thomas Dannenhoffer-Lafage
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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44
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Ohnuki J, Yodogawa A, Takano M. Electrostatic balance between global repulsion and local attraction in reentrant polymerization of actin. Cytoskeleton (Hoboken) 2017; 74:504-511. [DOI: 10.1002/cm.21391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/11/2017] [Accepted: 07/21/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Jun Ohnuki
- Department of Pure and Applied Physics; Waseda University; Tokyo 169-8555 Japan
| | - Akira Yodogawa
- Department of Advanced Science and Engineering; Waseda University; Tokyo 169-8555 Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics; Waseda University; Tokyo 169-8555 Japan
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45
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Fedorov EG, Shemesh T. Physical Model for Stabilization and Repair of Trans-endothelial Apertures. Biophys J 2017; 112:388-397. [PMID: 28122224 DOI: 10.1016/j.bpj.2016.11.3207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 01/13/2023] Open
Abstract
Bacterial toxins that disrupt the stability of contractile structures in endothelial cells promote the opening of large-scale apertures, thereby breaching the endothelium barrier. These apertures are formed by fusion of the basal and apical membranes into a tunnel that spans the height of the cell. Subsequent to the aperture formation, an active repair process, driven by a stimulated polymerization of actin, results in asymmetrical membrane protrusions and, ultimately, the closure of the aperture. Here, we propose a physics-based model for the generation, stabilization and repair of trans-endothelial apertures. Our model is based on the mechanical interplay between tension in the plasma membrane and stresses that develop within different actin structures at the aperture's periphery. We suggest that accumulation of cytoskeletal fragments around the aperture's rim during the expansion phase results in parallel bundles of actin filaments and myosin motors, generating progressively greater contraction forces that resist further expansion of the aperture. Our results indicate that closure of the tunnel is driven by mechanical stresses that develop within a cross-linked actin gel that forms at localized regions of the aperture periphery. We show that stresses within the gel are due to continuous polymerization of actin filaments against the membrane surfaces of the aperture's edges. Based on our mechanical model, we construct a dynamic simulation of the aperture repair process. Our model fully accounts for the phenomenology of the trans-endothelial aperture formation and stabilization, and recaptures the experimentally observed asymmetry of the intermediate aperture shapes during closure. We make experimentally testable predictions for localization of myosin motors to the tunnel periphery and of adhesion complexes to the edges of apertures undergoing closure, and we estimate the minimal nucleation size of cross-linked actin gel that can lead to a successful repair of the aperture.
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Affiliation(s)
- Eduard G Fedorov
- Department of Biology, Israel Institute of Technology, Haifa, Israel
| | - Tom Shemesh
- Department of Biology, Israel Institute of Technology, Haifa, Israel.
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46
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Zhang Y, Cao Z, Zhang JZ, Xia F. Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules. J Chem Inf Model 2017; 57:214-222. [PMID: 28128949 DOI: 10.1021/acs.jcim.6b00683] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Construction of coarse-grained (CG) models for large biomolecules used for multiscale simulations demands a rigorous definition of CG sites for them. Several coarse-graining methods such as the simulated annealing and steepest descent (SASD) based on the essential dynamics coarse-graining (ED-CG) or the stepwise local iterative optimization (SLIO) based on the fluctuation maximization coarse-graining (FM-CG), were developed to do it. However, the practical applications of these methods such as SASD based on ED-CG are subject to limitations because they are too expensive. In this work, we extend the applicability of ED-CG by combining it with the SLIO algorithm. A comprehensive comparison of optimized results and accuracy of various algorithms based on ED-CG show that SLIO is the fastest as well as the most accurate algorithm among them. ED-CG combined with SLIO could give converged results as the number of CG sites increases, which demonstrates that it is another efficient method for coarse-graining large biomolecules. The construction of CG sites for Ras protein by using MD fluctuations demonstrates that the CG sites derived from FM-CG can reflect the fluctuation properties of secondary structures in Ras accurately.
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Affiliation(s)
- Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University , Xiamen 361005, China.,School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemistry Engineering, Xiamen University , Xiamen 361005, China
| | - John Zenghui Zhang
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry, NYU Shanghai , Shanghai 200062, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry, NYU Shanghai , Shanghai 200062, China
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47
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Colonne PM, Winchell CG, Voth DE. Hijacking Host Cell Highways: Manipulation of the Host Actin Cytoskeleton by Obligate Intracellular Bacterial Pathogens. Front Cell Infect Microbiol 2016; 6:107. [PMID: 27713866 PMCID: PMC5031698 DOI: 10.3389/fcimb.2016.00107] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/05/2016] [Indexed: 12/31/2022] Open
Abstract
Intracellular bacterial pathogens replicate within eukaryotic cells and display unique adaptations that support key infection events including invasion, replication, immune evasion, and dissemination. From invasion to dissemination, all stages of the intracellular bacterial life cycle share the same three-dimensional cytosolic space containing the host cytoskeleton. For successful infection and replication, many pathogens hijack the cytoskeleton using effector proteins introduced into the host cytosol by specialized secretion systems. A subset of effectors contains eukaryotic-like motifs that mimic host proteins to exploit signaling and modify specific cytoskeletal components such as actin and microtubules. Cytoskeletal rearrangement promotes numerous events that are beneficial to the pathogen, including internalization of bacteria, structural support for bacteria-containing vacuoles, altered vesicular trafficking, actin-dependent bacterial movement, and pathogen dissemination. This review highlights a diverse group of obligate intracellular bacterial pathogens that manipulate the host cytoskeleton to thrive within eukaryotic cells and discusses underlying molecular mechanisms that promote these dynamic host-pathogen interactions.
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Affiliation(s)
- Punsiri M Colonne
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Caylin G Winchell
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Daniel E Voth
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences Little Rock, AR, USA
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48
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Barkó S, Szatmári D, Bódis E, Türmer K, Ujfalusi Z, Popp D, Robinson RC, Nyitrai M. Large-scale purification and in vitro characterization of the assembly of MreB from Leptospira interrogans. Biochim Biophys Acta Gen Subj 2016; 1860:1942-52. [PMID: 27297907 DOI: 10.1016/j.bbagen.2016.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/23/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Weil's syndrome is caused by Leptospira interrogans infections, a Gram negative bacterium with a distinct thin corkscrew cell shape. The molecular basis for this unusual morphology is unknown. In many bacteria, cell wall synthesis is orchestrated by the actin homolog, MreB. METHODS Here we have identified the MreB within the L. interrogans genome and expressed the His-tagged protein product of the synthesized gene (Li-MreB) in Escherichia coli. Li-MreB did not purify under standard nucleotide-free conditions used for MreBs from other species, requiring the continual presence of ATP to remain soluble. Covalent modification of Li-MreB free thiols with Alexa488 produced a fluorescent version of Li-MreB. RESULTS We developed native and denaturing/refolding purification schemes for Li-MreB. The purified product was shown to assemble and disassemble in MgCl2 and KCl dependent manners, as monitored by light scattering and sedimentation studies. The fluorescence spectrum of labeled Li-MreB-Alexa488 showed cation-induced changes in line with an activation process followed by a polymerization phase. The resulting filaments appeared as bundles and sheets under the fluorescence microscope. Finally, since the Li-MreB polymerization was cation dependent, we developed a simple method to measure monovalent cation concentrations within a test case prokaryote, E. coli. CONCLUSIONS We have identified and initially characterized the cation-dependent polymerization properties of a novel MreB from a non-rod shaped bacterium and developed a method to measure cation concentrations within prokaryotes. GENERAL SIGNIFICANCE This initial characterization of Li-MreB will enable future structural determination of the MreB filament from this corkscrew-shaped bacterium.
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Affiliation(s)
- Szilvia Barkó
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Dávid Szatmári
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Emőke Bódis
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Katalin Türmer
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Zoltán Ujfalusi
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - David Popp
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Miklós Nyitrai
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary; MTA-PTE Nuclear-Mitochondrial Interactions Research Group, Szigeti str. 12, Pécs H-7624, Hungary
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49
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Rosin C, Erlkamp M, Ecken JV, Raunser S, Winter R. Exploring the stability limits of actin and its suprastructures. Biophys J 2014; 107:2982-92. [PMID: 25517163 DOI: 10.1016/j.bpj.2014.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/28/2014] [Accepted: 11/05/2014] [Indexed: 12/30/2022] Open
Abstract
Actin is the main component of the microfilament system in eukaryotic cells and can be found in distinct morphological states. Global (G)-actin is able to assemble into highly organized, supramolecular cellular structures known as filamentous (F)-actin and bundled (B)-actin. To evaluate the structure and stability of G-, F-, and B-actin over a wide range of temperatures and pressures, we used Fourier transform infrared spectroscopy in combination with differential scanning and pressure perturbation calorimetry, small-angle x-ray scattering, laser confocal scanning microscopy, and transmission electron microscopy. Our analysis was designed to provide new (to our knowledge) insights into the stabilizing forces of actin self-assembly and to reveal the stability of the actin polymorphs, including in conditions encountered in extreme environments. In addition, we sought to explain the limited pressure stability of actin self-assembly observed in vivo. G-actin is not only the least temperature-stable but also the least pressure-stable actin species. Under abyssal conditions, where temperatures as low as 1-4°C and pressures up to 1 kbar are reached, G-actin is hardly stable. However, the supramolecular assemblies of actin are stable enough to withstand the extreme conditions usually encountered on Earth. Beyond ∼3-4 kbar, filamentous structures disassemble, and beyond ∼4 kbar, complete dissociation of F-actin structures is observed. Between ∼1 and 2 kbar, some disordering of actin assemblies commences, in agreement with in vivo observations. The limited pressure stability of the monomeric building block seems to be responsible for the suppression of actin assembly in the kbar pressure range.
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50
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Abstract
This minireview is dedicated to the memory of Henryk Eisenberg and honors his major contributions to many areas of biophysics and to the analysis of macromolecular states and interactions in particular. This work reviews the ATP and ADP states of a ubiquitous protein, actins, and considers the present evidence for and against unique, nucleotide-dependent conformations of this protein. The effects of ATP and ADP on specific structural elements of actins, its loops and clefts, as revealed by mutational, crosslinking, spectroscopic, and EPR methods are discussed. It is concluded that the existing evidence points to dynamic equilibria of these structural elements among various conformational states in both ATP- and ADP-actins, with the nucleotides impacting the equilibria distributions.
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Affiliation(s)
- Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, the Ohio State University, Columbus, OH 43210.
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