1
|
Effiong UM, Khairandish H, Ramirez-Velez I, Wang Y, Belardi B. Turn-on protein switches for controlling actin binding in cells. Nat Commun 2024; 15:5840. [PMID: 38992021 PMCID: PMC11239668 DOI: 10.1038/s41467-024-49934-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
Within a shared cytoplasm, filamentous actin (F-actin) plays numerous and critical roles across the cell body. Cells rely on actin-binding proteins (ABPs) to organize F-actin and to integrate its polymeric characteristics into diverse cellular processes. Yet, the multitude of ABPs that engage with and shape F-actin make studying a single ABP's influence on cellular activities a significant challenge. Moreover, without a means of manipulating actin-binding subcellularly, harnessing the F-actin cytoskeleton for synthetic biology purposes remains elusive. Here, we describe a suite of designed proteins, Controllable Actin-binding Switch Tools (CASTs), whose actin-binding behavior can be controlled with external stimuli. CASTs were developed that respond to different external inputs, providing options for turn-on kinetics and enabling orthogonality and multiplexing. Being genetically encoded, we show that CASTs can be inserted into native protein sequences to control F-actin association locally and engineered into structures to control cell and tissue shape and behavior.
Collapse
Affiliation(s)
- Unyime M Effiong
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hannah Khairandish
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Isabela Ramirez-Velez
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yanran Wang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Brian Belardi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
2
|
Zsolnay V, Gardel ML, Kovar DR, Voth GA. Cracked actin filaments as mechanosensitive receptors. Biophys J 2024:S0006-3495(24)00411-9. [PMID: 38894540 DOI: 10.1016/j.bpj.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/10/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024] Open
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 has 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.
Collapse
Affiliation(s)
- Vilmos Zsolnay
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois
| | - Margaret L Gardel
- Department of Physics & Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics and James Franck Institute, University of Chicago, Chicago, Illinois
| | - David R Kovar
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois.
| | - Gregory A Voth
- Institute for Biophysical Dynamics and James Franck Institute, University of Chicago, Chicago, Illinois; Department of Chemistry and Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois.
| |
Collapse
|
3
|
Kadzik RS, Kovar DR. A step-by-step guide to fragmenting bundled actin filaments. J Cell Biol 2024; 223:e202403191. [PMID: 38748453 PMCID: PMC11096848 DOI: 10.1083/jcb.202403191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
There has long been conflicting evidence as to how bundled actin filaments, found in cellular structures such as filopodia, are disassembled. In this issue, Chikireddy et al. (https://doi.org/10.1083/jcb.202312106) provide a detailed in vitro analysis of the steps involved in fragmentation of fascin-bundled actin filaments and propose a novel mechanism for severing two-filament bundles.
Collapse
Affiliation(s)
- Rachel S. Kadzik
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - David R. Kovar
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
4
|
Chikireddy J, Lengagne L, Le Borgne R, Durieu C, Wioland H, Romet-Lemonne G, Jégou A. Fascin-induced bundling protects actin filaments from disassembly by cofilin. J Cell Biol 2024; 223:e202312106. [PMID: 38497788 PMCID: PMC10949937 DOI: 10.1083/jcb.202312106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Actin filament turnover plays a central role in shaping actin networks, yet the feedback mechanism between network architecture and filament assembly dynamics remains unclear. The activity of ADF/cofilin, the main protein family responsible for filament disassembly, has been mainly studied at the single filament level. This study unveils that fascin, by crosslinking filaments into bundles, strongly slows down filament disassembly by cofilin. We show that this is due to a markedly slower initiation of the first cofilin clusters, which occurs up to 100-fold slower on large bundles compared with single filaments. In contrast, severing at cofilin cluster boundaries is unaffected by fascin bundling. After the formation of an initial cofilin cluster on a filament within a bundle, we observed the local removal of fascin. Notably, the formation of cofilin clusters on adjacent filaments is highly enhanced, locally. We propose that this interfilament cooperativity arises from the local propagation of the cofilin-induced change in helicity from one filament to the other filaments of the bundle. Overall, taking into account all the above reactions, we reveal that fascin crosslinking slows down the disassembly of actin filaments by cofilin. These findings highlight the important role played by crosslinkers in tuning actin network turnover by modulating the activity of other regulatory proteins.
Collapse
Affiliation(s)
| | - Léana Lengagne
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Rémi Le Borgne
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Catherine Durieu
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Hugo Wioland
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | | | - Antoine Jégou
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| |
Collapse
|
5
|
Reed AE, Peraza J, van den Haak F, Hernandez ER, Gibbs RA, Chinn IK, Lupski JR, Marchi E, Reshef R, Alobeid B, Mace EM, Orange JS. β-Actin G342D as a Cause of NK Cell Deficiency Impairing Lytic Synapse Termination. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:962-973. [PMID: 38315012 DOI: 10.4049/jimmunol.2300671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024]
Abstract
NK cell deficiency (NKD) occurs when an individual's major clinical immunodeficiency derives from abnormal NK cells and is associated with several genetic etiologies. Three categories of β-actin-related diseases with over 60 ACTB (β-actin) variants have previously been identified, none with a distinct NK cell phenotype. An individual with mild developmental delay, macrothrombocytopenia, and susceptibility to infections, molluscum contagiosum virus, and EBV-associated lymphoma had functional NKD for over a decade. A de novo ACTB variant encoding G342D β-actin was identified and was consistent with the individual's developmental and platelet phenotype. This novel variant also was found to have direct impact in NK cells because its expression in the human NK cell line YTS (YTS-NKD) caused increased cell spreading in lytic immune synapses created on activating surfaces. YTS-NKD cells were able to degranulate and perform cytotoxicity, but they demonstrated defective serial killing because of prolonged conjugation to the killed target cell and thus were effectively unable to terminate lytic synapses. G342D β-actin results in a novel, to our knowledge, mechanism of functional NKD via increased synaptic spreading and defective lytic synapse termination with resulting impaired serial killing, leading to overall reductions in NK cell cytotoxicity.
Collapse
Affiliation(s)
- Abigail E Reed
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY
| | - Jackeline Peraza
- Department of Biology, Barnard College of Columbia University, New York, NY
| | - Frederique van den Haak
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY
| | - Evelyn R Hernandez
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Ivan K Chinn
- Division of Immunology, Allergy and Retrovirology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Texas Children's Hospital and Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX
| | - Enrica Marchi
- Division of Hematology-Oncology, Department of Medicine, NCI Designated Cancer Center, University of Virginia, Charlottesville, VA
| | - Ran Reshef
- Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, NY
| | - Bachir Alobeid
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Emily M Mace
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Jordan S Orange
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| |
Collapse
|
6
|
Greve JN, Marquardt A, Heiringhoff R, Reindl T, Thiel C, Di Donato N, Taft MH, Manstein DJ. The non-muscle actinopathy-associated mutation E334Q in cytoskeletal γ-actin perturbs interaction of actin filaments with myosin and ADF/cofilin family proteins. eLife 2024; 12:RP93013. [PMID: 38446501 PMCID: PMC10942649 DOI: 10.7554/elife.93013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Various heterozygous cytoskeletal γ-actin mutations have been shown to cause Baraitser-Winter cerebrofrontofacial syndrome, non-syndromic hearing loss, or isolated eye coloboma. Here, we report the biochemical characterization of human cytoskeletal γ-actin carrying mutation E334Q, a mutation that leads to a hitherto unspecified non-muscle actinopathy. Following expression, purification, and removal of linker and thymosin β4 tag sequences, the p.E334Q monomers show normal integration into linear and branched actin filaments. The mutation does not affect thermal stability, actin filament nucleation, elongation, and turnover. Model building and normal mode analysis predict significant differences in the interaction of p.E334Q filaments with myosin motors and members of the ADF/cofilin family of actin-binding proteins. Assays probing the interactions of p.E334Q filaments with human class 2 and class 5 myosin motor constructs show significant reductions in sliding velocity and actin affinity. E334Q differentially affects cofilin-mediated actin dynamics by increasing the rate of cofilin-mediated de novo nucleation of actin filaments and decreasing the efficiency of cofilin-mediated filament severing. Thus, it is likely that p.E334Q-mediated changes in myosin motor activity, as well as filament turnover, contribute to the observed disease phenotype.
Collapse
Affiliation(s)
- Johannes N Greve
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Anja Marquardt
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Robin Heiringhoff
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Theresia Reindl
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Claudia Thiel
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | | | - Manuel H Taft
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Dietmar J Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
- Division for Structural Biochemistry, Hannover Medical SchoolHannoverGermany
- RESiST, Cluster of Excellence 2155, Hannover Medical SchoolHannoverGermany
| |
Collapse
|
7
|
Chavali SS, Chou SZ, Cao W, Pollard TD, De La Cruz EM, Sindelar CV. Cryo-EM structures reveal how phosphate release from Arp3 weakens actin filament branches formed by Arp2/3 complex. Nat Commun 2024; 15:2059. [PMID: 38448439 PMCID: PMC10918085 DOI: 10.1038/s41467-024-46179-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Arp2/3 complex nucleates branched actin filaments for cell and organelle movements. Here we report a 2.7 Å resolution cryo-EM structure of the mature branch junction formed by S. pombe Arp2/3 complex that provides details about interactions with both mother and daughter filaments. We determine a second structure at 3.2 Å resolution with the phosphate analog BeFx bound with ADP to Arp3 and ATP bound to Arp2. In this ADP-BeFx transition state the outer domain of Arp3 is rotated 2° toward the mother filament compared with the ADP state and makes slightly broader contacts with actin in both the mother and daughter filaments. Thus, dissociation of Pi from the ADP-Pi transition state reduces the interactions of Arp2/3 complex with the actin filaments and may contribute to the lower mechanical stability of mature branch junctions with ADP bound to the Arps. Our structures also reveal that the mother filament in contact with Arp2/3 complex is slightly bent and twisted, consistent with the preference of Arp2/3 complex binding curved actin filaments. The small degree of twisting constrains models of actin filament mechanics.
Collapse
Affiliation(s)
- Sai Shashank Chavali
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA
| | - Steven Z Chou
- Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA
| | - Thomas D Pollard
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA.
- Department of Molecular Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA.
- Department of Cell Biology, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA.
- Department of Molecular and Cell Biology, University of California, 638 Barker Hall, Berkeley, CA, 94720-3200, USA.
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA.
| | - Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA.
| |
Collapse
|
8
|
Sun ZG, Yadav V, Amiri S, Cao W, De La Cruz EM, Murrell M. Cofilin-mediated actin filament network flexibility facilitates 2D to 3D actomyosin shape change. Eur J Cell Biol 2024; 103:151379. [PMID: 38168598 DOI: 10.1016/j.ejcb.2023.151379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024] Open
Abstract
The organization of actin filaments (F-actin) into crosslinked networks determines the transmission of mechanical stresses within the cytoskeleton and subsequent changes in cell and tissue shape. Principally mediated by proteins such as α-actinin, F-actin crosslinking increases both network connectivity and rigidity, thereby facilitating stress transmission at low crosslinking yet attenuating transmission at high crosslinker concentration. Here, we engineer a two-dimensional model of the actomyosin cytoskeleton, in which myosin-induced mechanical stresses are controlled by light. We alter the extent of F-actin crosslinking by the introduction of oligomerized cofilin. At pH 6.5, F-actin severing by cofilin is weak, but cofilin bundles and crosslinks filaments. Given its effect of lowering the F-actin bending stiffness, cofilin- crosslinked networks are significantly more flexible and softer in bending than networks crosslinked by α-actinin. Thus, upon local activation of myosin-induced contractile stress, the network bends out-of-plane in contrast to the in-plane compression as observed with networks crosslinked by α-actinin. Here, we demonstrate that local effects on filament mechanics by cofilin introduces novel large-scale network material properties that enable the sculpting of complex shapes in the cell cytoskeleton.
Collapse
Affiliation(s)
- Zachary Gao Sun
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | - Vikrant Yadav
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Sorosh Amiri
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Mechanical Engineering and Material Science, Yale University, New Haven, CT 06511, USA
| | - Wenxiang Cao
- Department of Molecular Biology & Biophysics, Yale University, New Haven, CT 06511, USA
| | - Enrique M De La Cruz
- Department of Molecular Biology & Biophysics, Yale University, New Haven, CT 06511, USA
| | - Michael Murrell
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
9
|
Sexton JA, Potchernikov T, Bibeau JP, Casanova-Sepúlveda G, Cao W, Lou HJ, Boggon TJ, De La Cruz EM, Turk BE. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. Nat Commun 2024; 15:1426. [PMID: 38365893 PMCID: PMC10873347 DOI: 10.1038/s41467-024-45878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short, unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but specific aspects driving this conservation are unclear. Here, we screen a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and biochemical analysis of individual variants reveal distinct sequence requirements for actin binding and regulation by LIM kinase. LIM kinase recognition only partly explains sequence constraints on phosphoregulation, which are instead driven to a large extent by the capacity for phosphorylation to inactivate cofilin. We find loose sequence requirements for actin binding and phosphoinhibition, but collectively they restrict the N-terminus to sequences found in natural cofilins. Our results illustrate how a phosphorylation site can balance potentially competing sequence requirements for function and regulation.
Collapse
Affiliation(s)
- Joel A Sexton
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Tony Potchernikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jeffrey P Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA.
| |
Collapse
|
10
|
Mukadum F, Peña Ccoa WJ, Hocky GM. Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton. Cytoskeleton (Hoboken) 2024. [PMID: 38334204 DOI: 10.1002/cm.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Affiliation(s)
- Fatemah Mukadum
- Department of Chemistry, New York University, New York, NY, USA
| | | | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY, USA
- Simons Center for Computational Physical Chemistry, New York, New York, USA
| |
Collapse
|
11
|
Shehjar F, Almarghalani DA, Mahajan R, Hasan SAM, Shah ZA. The Multifaceted Role of Cofilin in Neurodegeneration and Stroke: Insights into Pathogenesis and Targeting as a Therapy. Cells 2024; 13:188. [PMID: 38247879 PMCID: PMC10814918 DOI: 10.3390/cells13020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
This comprehensive review explores the complex role of cofilin, an actin-binding protein, across various neurodegenerative diseases (Alzheimer's, Parkinson's, schizophrenia, amyotrophic lateral sclerosis (ALS), Huntington's) and stroke. Cofilin is an essential protein in cytoskeletal dynamics, and any dysregulation could lead to potentially serious complications. Cofilin's involvement is underscored by its impact on pathological hallmarks like Aβ plaques and α-synuclein aggregates, triggering synaptic dysfunction, dendritic spine loss, and impaired neuronal plasticity, leading to cognitive decline. In Parkinson's disease, cofilin collaborates with α-synuclein, exacerbating neurotoxicity and impairing mitochondrial and axonal function. ALS and frontotemporal dementia showcase cofilin's association with genetic factors like C9ORF72, affecting actin dynamics and contributing to neurotoxicity. Huntington's disease brings cofilin into focus by impairing microglial migration and influencing synaptic plasticity through AMPA receptor regulation. Alzheimer's, Parkinson's, and schizophrenia exhibit 14-3-3 proteins in cofilin dysregulation as a shared pathological mechanism. In the case of stroke, cofilin takes center stage, mediating neurotoxicity and neuronal cell death. Notably, there is a potential overlap in the pathologies and involvement of cofilin in various diseases. In this context, referencing cofilin dysfunction could provide valuable insights into the common pathologies associated with the aforementioned conditions. Moreover, this review explores promising therapeutic interventions, including cofilin inhibitors and gene therapy, demonstrating efficacy in preclinical models. Challenges in inhibitor development, brain delivery, tissue/cell specificity, and long-term safety are acknowledged, emphasizing the need for precision drug therapy. The call to action involves collaborative research, biomarker identification, and advancing translational efforts. Cofilin emerges as a pivotal player, offering potential as a therapeutic target. However, unraveling its complexities requires concerted multidisciplinary efforts for nuanced and effective interventions across the intricate landscape of neurodegenerative diseases and stroke, presenting a hopeful avenue for improved patient care.
Collapse
Affiliation(s)
- Faheem Shehjar
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, Toledo, OH 43614, USA; (F.S.); (R.M.)
| | - Daniyah A. Almarghalani
- Stroke Research Unit, Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Reetika Mahajan
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, Toledo, OH 43614, USA; (F.S.); (R.M.)
| | - Syed A.-M. Hasan
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA;
| | - Zahoor A. Shah
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, Toledo, OH 43614, USA; (F.S.); (R.M.)
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA;
| |
Collapse
|
12
|
Yuan B, Scholz J, Wald J, Thuenauer R, Hennell James R, Ellenberg I, Windhorst S, Faix J, Marlovits TC. Structural basis for subversion of host cell actin cytoskeleton during Salmonella infection. SCIENCE ADVANCES 2023; 9:eadj5777. [PMID: 38064550 PMCID: PMC10708208 DOI: 10.1126/sciadv.adj5777] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Secreted bacterial type III secretion system (T3SS) proteins are essential for successful infection by many human pathogens. Both T3SS translocator SipC and effector SipA are critical for Salmonella infection by subversion of the host cell cytoskeleton, but the precise molecular interplay between them remains unknown. Here, using cryo-electron microscopy, we show that SipA binds along the F-actin grooves with a unique binding pattern. SipA stabilizes F-actin through charged interface residues and appears to prevent inorganic phosphate release through closure of the "back door" of adenosine 5'-triphosphate pocket. We also show that SipC enhances the binding of SipA to F-actin, thus demonstrating that a sequential presence of T3SS proteins in host cells is associated with a sequence of infection events-starting with actin nucleation, filament growth, and stabilization. Together, our data explain the coordinated interplay of a precisely tuned and highly effective mechanism during Salmonella infection and provide a blueprint for interfering with Salmonella effectors acting on actin.
Collapse
Affiliation(s)
- Biao Yuan
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Jonas Scholz
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Jiri Wald
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Roland Thuenauer
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Technology Platform Light Microscopy (TPLM), University of Hamburg, Hamburg, Germany
- Technology Platform Microscopy and Image Analysis (TP MIA), Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Rory Hennell James
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Irina Ellenberg
- University Medical Center Hamburg-Eppendorf (UKE), Institute for Biochemistry and Signal Transduction, Hamburg, Germany
| | - Sabine Windhorst
- University Medical Center Hamburg-Eppendorf (UKE), Institute for Biochemistry and Signal Transduction, Hamburg, Germany
| | - Jan Faix
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Thomas C. Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| |
Collapse
|
13
|
Oosterheert W, Blanc FEC, Roy A, Belyy A, Sanders MB, Hofnagel O, Hummer G, Bieling P, Raunser S. Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nat Struct Mol Biol 2023; 30:1774-1785. [PMID: 37749275 PMCID: PMC10643162 DOI: 10.1038/s41594-023-01101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/18/2023] [Indexed: 09/27/2023]
Abstract
The release of inorganic phosphate (Pi) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. The mechanisms underlying Pi release from the core and barbed end of actin filaments remain unclear. Here, using human and bovine actin isoforms, we combine cryo-EM with molecular-dynamics simulations and in vitro reconstitution to demonstrate how actin releases Pi through a 'molecular backdoor'. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and opens only transiently through concerted amino acid rearrangements. This explains why Pi escapes rapidly from the filament end but slowly from internal subunits. In a nemaline-myopathy-associated actin variant, the backdoor is predominantly open in filament-core subunits, resulting in accelerated Pi release and filaments with drastically shortened ADP-Pi caps. Our results provide the molecular basis for Pi release from actin and exemplify how a disease-linked mutation distorts the nucleotide-state distribution and atomic structure of the filament.
Collapse
Affiliation(s)
- Wout Oosterheert
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Florian E C Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ankit Roy
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alexander Belyy
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Micaela Boiero Sanders
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oliver Hofnagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute for Biophysics, Goethe University, Frankfurt am Main, Germany.
| | - Peter Bieling
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| |
Collapse
|
14
|
Effiong UM, Khairandish H, Ramirez-Velez I, Wang Y, Belardi B. Turn-On Protein Switches for Controlling Actin Binding in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.561921. [PMID: 37961502 PMCID: PMC10634840 DOI: 10.1101/2023.10.26.561921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Within a shared cytoplasm, filamentous actin (F-actin) plays numerous and critical roles across the cell body. Cells rely on actin-binding proteins (ABPs) to organize F-actin and to integrate its polymeric characteristics into diverse cellular processes. Yet, the multitude of ABPs that engage with and shape F-actin make studying a single ABP's influence on cellular activities a significant challenge. Moreover, without a means of manipulating actin-binding subcellularly, harnessing the F-actin cytoskeleton for synthetic biology purposes remains elusive. Here, we describe a suite of designed proteins, Controllable Actin-binding Switch Tools (CASTs), whose actin-binding behavior can be controlled with external stimuli. CASTs were developed that respond to different external inputs, providing options for turn-on kinetics and enabling orthogonality. Being genetically encoded, we show that CASTs can be inserted into native protein sequences to control F-actin association locally and engineered into new structures to control cell and tissue shape and behavior.
Collapse
Affiliation(s)
- Unyime M. Effiong
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Hannah Khairandish
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Isabela Ramirez-Velez
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Yanran Wang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Brian Belardi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| |
Collapse
|
15
|
Cao W, Taylor EW, De La Cruz EM. Cooperative ligand binding to a double-stranded Ising lattice-Application to cofilin binding to actin filaments. PNAS NEXUS 2023; 2:pgad331. [PMID: 37885622 PMCID: PMC10599439 DOI: 10.1093/pnasnexus/pgad331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Cooperative ligand binding to linear polymers is fundamental in many scientific disciplines, particularly biological and chemical physics and engineering. Such ligand binding interactions have been widely modeled using infinite one-dimensional (1D) Ising models even in cases where the linear polymers are more complex (e.g. actin filaments and other double-stranded linear polymers). Here, we use sequence-generating and transfer matrix methods to obtain an analytical method for cooperative equilibrium ligand binding to double-stranded Ising lattices. We use this exact solution to evaluate binding properties and features and analyze experimental binding data of cooperative binding of the regulatory protein, cofilin, to actin filaments. This analysis, with additional experimental information about the observed bound cofilin cluster sizes and filament structure, reveals that a bound cofilin promotes cooperative binding to its longitudinal nearest-neighbors but has very modest effects on lateral nearest-neighbors. The bound cofilin cluster sizes calculated from the best fit parameters from the double-stranded model are considerably larger than when calculated with the 1D model, consistent with experimental observations made by electron microscopy and fluorescence imaging. The exact solution obtained and the method for using the solution developed here can be widely used for analysis of variety of multistranded lattice systems.
Collapse
Affiliation(s)
- Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Edwin W Taylor
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
16
|
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] [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.
Collapse
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
| |
Collapse
|
17
|
Sexton JA, Potchernikov T, Bibeau JP, Casanova-Sepúlveda G, Cao W, Lou HJ, Boggon TJ, De La Cruz EM, Turk BE. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547189. [PMID: 37425676 PMCID: PMC10327202 DOI: 10.1101/2023.06.30.547189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but the aspects of cofilin functionality driving this conservation are not clear. Here, we screened a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and subsequent biochemical analysis of individual variants revealed distinct sequence requirements for actin binding and regulation by LIM kinase. While the presence of a serine, rather than threonine, phosphoacceptor residue was essential for phosphorylation by LIM kinase, the native cofilin N-terminus was otherwise a suboptimal LIM kinase substrate. This circumstance was not due to sequence requirements for actin binding and severing, but rather appeared primarily to maintain the capacity for phosphorylation to inactivate cofilin. Overall, the individual sequence requirements for cofilin function and regulation were remarkably loose when examined separately, but collectively restricted the N-terminus to sequences found in natural cofilins. Our results illustrate how a regulatory phosphorylation site can balance potentially competing sequence requirements for function and regulation.
Collapse
Affiliation(s)
- Joel A. Sexton
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
| | - Tony Potchernikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jeffrey P. Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | | | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Enrique M. De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
| |
Collapse
|
18
|
Dahlstroem C, Paraschiakos T, Sun H, Windhorst S. Cryo-EM structures of actin binding proteins as tool for drug discovery. Biochem Pharmacol 2023:115680. [PMID: 37399949 DOI: 10.1016/j.bcp.2023.115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
Cellular actin dynamic is controlled by a plethora of actin binding proteins (ABPs), including actin nucleating, bundling, cross-linking, capping, and severing proteins. In this review, regulation of actin dynamics by ABPs will be introduced, and the role of the F-actin severing protein cofilin-1 and the F-actin bundling protein L-plastin in actin dynamics discussed in more detail. Since up-regulation of these proteins in different kinds of cancers is associated with malignant progression of cancer cells, we suggest the cryogenic electron microscopy (Cryo-EM) structure of F- actin with the respective ABP as template for in silico drug design to specifically disrupt the interaction of these ABPs with F-actin.
Collapse
Affiliation(s)
- Christian Dahlstroem
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg
| | - Themistoklis Paraschiakos
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leipniz-Forschungsinstitut für Moekulare Pharmakologie, Robert-Rössle-Strasse 10, D-13125, Berlin; Institute of Chemistry, Technical University of Berlin, D-10623, Berlin
| | - Sabine Windhorst
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg.
| |
Collapse
|
19
|
Zsolnay V, Gardel ML, Kovar DR, Voth GA. Cracked actin filaments as mechanosensitive receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546553. [PMID: 37425801 PMCID: PMC10327158 DOI: 10.1101/2023.06.26.546553] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
20
|
Purnell C, Heebner J, Swulius MT, Hylton R, Kabonick S, Grillo M, Grigoryev S, Heberle F, Waxham MN, Swulius MT. Rapid Synthesis of Cryo-ET Data for Training Deep Learning Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538636. [PMID: 37162972 PMCID: PMC10168359 DOI: 10.1101/2023.04.28.538636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Deep learning excels at cryo-tomographic image restoration and segmentation tasks but is hindered by a lack of training data. Here we introduce cryo-TomoSim (CTS), a MATLAB-based software package that builds coarse-grained models of macromolecular complexes embedded in vitreous ice and then simulates transmitted electron tilt series for tomographic reconstruction. We then demonstrate the effectiveness of these simulated datasets in training different deep learning models for use on real cryotomographic reconstructions. Computer-generated ground truth datasets provide the means for training models with voxel-level precision, allowing for unprecedented denoising and precise molecular segmentation of datasets. By modeling phenomena such as a three-dimensional contrast transfer function, probabilistic detection events, and radiation-induced damage, the simulated cryo-electron tomograms can cover a large range of imaging content and conditions to optimize training sets. When paired with small amounts of training data from real tomograms, networks become incredibly accurate at segmenting in situ macromolecular assemblies across a wide range of biological contexts.
Collapse
|
21
|
Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochem Soc Trans 2023; 51:87-99. [PMID: 36695514 PMCID: PMC9987995 DOI: 10.1042/bst20220221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/26/2023]
Abstract
The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.
Collapse
|
22
|
Rajan S, Terman JR, Reisler E. MICAL-mediated oxidation of actin and its effects on cytoskeletal and cellular dynamics. Front Cell Dev Biol 2023; 11:1124202. [PMID: 36875759 PMCID: PMC9982024 DOI: 10.3389/fcell.2023.1124202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Actin and its dynamic structural remodelings are involved in multiple cellular functions, including maintaining cell shape and integrity, cytokinesis, motility, navigation, and muscle contraction. Many actin-binding proteins regulate the cytoskeleton to facilitate these functions. Recently, actin's post-translational modifications (PTMs) and their importance to actin functions have gained increasing recognition. The MICAL family of proteins has emerged as important actin regulatory oxidation-reduction (Redox) enzymes, influencing actin's properties both in vitro and in vivo. MICALs specifically bind to actin filaments and selectively oxidize actin's methionine residues 44 and 47, which perturbs filaments' structure and leads to their disassembly. This review provides an overview of the MICALs and the impact of MICAL-mediated oxidation on actin's properties, including its assembly and disassembly, effects on other actin-binding proteins, and on cells and tissue systems.
Collapse
Affiliation(s)
- Sudeepa Rajan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jonathan R. Terman
- Departments of Neuroscience and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
23
|
Prakash S, Krishna A, Sengupta D. Cofilin-Membrane Interactions: Electrostatic Effects in Phosphoinositide Lipid Binding. Chemphyschem 2023; 24:e202200509. [PMID: 36200760 DOI: 10.1002/cphc.202200509] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/06/2022] [Indexed: 02/04/2023]
Abstract
The actin cytoskeleton interacts with the cell membrane primarily through the indirect interactions of actin-binding proteins such as cofilin-1. The molecular mechanisms underlying the specific interactions of cofilin-1 with membrane lipids are still unclear. Here, we performed coarse-grain molecular dynamics simulations of cofilin-1 with complex lipid bilayers to analyze the specificity of protein-lipid interactions. We observed the maximal interactions with phosphoinositide (PIP) lipids, especially PIP2 and PIP3 lipids. A good match was observed between the residues predicted to interact and previous experimental studies. The clustering of PIP lipids around the membrane bound protein leads to an overall lipid demixing and gives rise to persistent membrane curvature. Further, through a series of control simulations, we observe that both electrostatics and geometry are critical for specificity of lipid binding. Our current study is a step towards understanding the physico-chemical basis of cofilin-PIP lipid interactions.
Collapse
Affiliation(s)
- Shikha Prakash
- CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Anjali Krishna
- CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Current Address: School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Durba Sengupta
- CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| |
Collapse
|
24
|
Abstract
Actin cytoskeleton force generation, sensing, and adaptation are dictated by the bending and twisting mechanics of filaments. Here, we use magnetic tweezers and microfluidics to twist and pull individual actin filaments and evaluate their response to applied loads. Twisted filaments bend and dissipate torsional strain by adopting a supercoiled plectoneme. Pulling prevents plectoneme formation, which causes twisted filaments to sever. Analysis over a range of twisting and pulling forces and direct visualization of filament and single subunit twisting fluctuations yield an actin filament torsional persistence length of ~10 µm, similar to the bending persistence length. Filament severing by cofilin is driven by local twist strain at boundaries between bare and decorated segments and is accelerated by low pN pulling forces. This work explains how contractile forces generated by myosin motors accelerate filament severing by cofilin and establishes a role for filament twisting in the regulation of actin filament stability and assembly dynamics.
Collapse
|
25
|
Lappalainen P, Kotila T, Jégou A, Romet-Lemonne G. Biochemical and mechanical regulation of actin dynamics. Nat Rev Mol Cell Biol 2022; 23:836-852. [PMID: 35918536 DOI: 10.1038/s41580-022-00508-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/30/2022]
Abstract
Polymerization of actin filaments against membranes produces force for numerous cellular processes, such as migration, morphogenesis, endocytosis, phagocytosis and organelle dynamics. Consequently, aberrant actin cytoskeleton dynamics are linked to various diseases, including cancer, as well as immunological and neurological disorders. Understanding how actin filaments generate forces in cells, how force production is regulated by the interplay between actin-binding proteins and how the actin-regulatory machinery responds to mechanical load are at the heart of many cellular, developmental and pathological processes. During the past few years, our understanding of the mechanisms controlling actin filament assembly and disassembly has evolved substantially. It has also become evident that the activities of key actin-binding proteins are not regulated solely by biochemical signalling pathways, as mechanical regulation is critical for these proteins. Indeed, the architecture and dynamics of the actin cytoskeleton are directly tuned by mechanical load. Here we discuss the general mechanisms by which key actin regulators, often in synergy with each other, control actin filament assembly, disassembly, and monomer recycling. By using an updated view of actin dynamics as a framework, we discuss how the mechanics and geometry of actin networks control actin-binding proteins, and how this translates into force production in endocytosis and mesenchymal cell migration.
Collapse
Affiliation(s)
- Pekka Lappalainen
- Institute of Biotechnology and Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
| | - Tommi Kotila
- Institute of Biotechnology and Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Antoine Jégou
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | | |
Collapse
|
26
|
Oosterheert W, Klink BU, Belyy A, Pospich S, Raunser S. Structural basis of actin filament assembly and aging. Nature 2022; 611:374-379. [DOI: 10.1038/s41586-022-05241-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/16/2022] [Indexed: 12/12/2022]
Abstract
AbstractThe dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and is coupled to changes in the F-actin nucleotide state1–3. It remains unclear how F-actin hydrolyses ATP and subsequently undergoes subtle conformational rearrangements that ultimately lead to filament depolymerization by actin-binding proteins. Here we present cryo-electron microscopy structures of F-actin in all nucleotide states, polymerized in the presence of Mg2+ or Ca2+ at approximately 2.2 Å resolution. The structures show that actin polymerization induces the relocation of water molecules in the nucleotide-binding pocket, activating one of them for the nucleophilic attack of ATP. Unexpectedly, the back door for the subsequent release of inorganic phosphate (Pi) is closed in all structures, indicating that Pi release occurs transiently. The small changes in the nucleotide-binding pocket after ATP hydrolysis and Pi release are sensed by a key amino acid, amplified and transmitted to the filament periphery. Furthermore, differences in the positions of water molecules in the nucleotide-binding pocket explain why Ca2+-actin shows slower polymerization rates than Mg2+-actin. Our work elucidates the solvent-driven rearrangements that govern actin filament assembly and aging and lays the foundation for the rational design of drugs and small molecules for imaging and therapeutic applications.
Collapse
|
27
|
King ZT, Butler MT, Hockenberry MA, Subramanian BC, Siesser PF, Graham DM, Legant WR, Bear JE. Coro1B and Coro1C regulate lamellipodia dynamics and cell motility by tuning branched actin turnover. J Cell Biol 2022; 221:e202111126. [PMID: 35657370 PMCID: PMC9170525 DOI: 10.1083/jcb.202111126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/01/2022] [Accepted: 05/18/2022] [Indexed: 02/03/2023] Open
Abstract
Actin filament dynamics must be precisely controlled in cells to execute behaviors such as vesicular trafficking, cytokinesis, and migration. Coronins are conserved actin-binding proteins that regulate several actin-dependent subcellular processes. Here, we describe a new conditional knockout cell line for two ubiquitous coronins, Coro1B and Coro1C. These coronins, which strongly co-localize with Arp2/3-branched actin, require Arp2/3 activity for proper subcellular localization. Coronin null cells have altered lamellipodial protrusion dynamics due to increased branched actin density and reduced actin turnover within lamellipodia, leading to defective haptotaxis. Surprisingly, excessive cofilin accumulates in coronin null lamellipodia, a result that is inconsistent with the current models of coronin-cofilin functional interaction. However, consistent with coronins playing a pro-cofilin role, coronin null cells have increased F-actin levels. Lastly, we demonstrate that the loss of coronins increases accompanied by an increase in cellular contractility. Together, our observations reveal that coronins are critical for proper turnover of branched actin networks and that decreased actin turnover leads to increased cellular contractility.
Collapse
Affiliation(s)
- Zayna T. King
- Department of Cell Biology and Physiology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- University of North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| | - Mitchell T. Butler
- Department of Cell Biology and Physiology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- University of North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| | - Max A. Hockenberry
- Department of Cell Biology and Physiology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- University of North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| | - Bhagawat C. Subramanian
- Department of Cell Biology and Physiology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- University of North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| | - Priscila F. Siesser
- Department of Cell Biology and Physiology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- University of North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| | - David M. Graham
- Department of Cell Biology and Physiology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- University of North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| | - Wesley R. Legant
- Department of Pharmacology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| | - James E. Bear
- Department of Cell Biology and Physiology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- University of North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
- Department of Pharmacology, University of North Carolina-Chapel Hill School of Medicine, Chapel Hill, NC
| |
Collapse
|
28
|
Jaswandkar SV, Katti KS, Katti DR. Molecular and structural basis of actin filament severing by ADF/cofilin. Comput Struct Biotechnol J 2022; 20:4157-4171. [PMID: 36016710 PMCID: PMC9379983 DOI: 10.1016/j.csbj.2022.07.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 12/04/2022] Open
Abstract
ADF/cofilin’s cooperative binding to actin filament modifies the conformation and alignment of G-actin subunits locally, causing the filament to sever at “boundaries” formed among bare and ADF/cofilin-occupied regions. Analysis of the impact of the ADF/cofilin cluster boundary on the deformation behavior of actin filaments in a mechanically strained environment is critical for understanding the biophysics of their severing. The present investigation uses molecular dynamics simulations to generate atomic resolution models of bare, partially, and fully cofilin decorated actin filaments. Steered molecular dynamics simulations are utilized to determine the mechanical properties of three filament models when subjected to axial stretching, axial compression, and bending forces. We highlight differences in strain distribution, failure mechanisms in the three filament models, and biomechanical effects of cofilin cluster boundaries in overall filament rupture. Based on the influence of ADF/cofilin binding on intrastrand and interstrand G-actin interfaces, the cofilin-mediated actin filament severing model proposed here can help understand cofilin mediated actin dynamics.
Collapse
|
29
|
Sun X, Alushin GM. Cellular force-sensing through actin filaments. FEBS J 2022; 290:2576-2589. [PMID: 35778931 PMCID: PMC9945651 DOI: 10.1111/febs.16568] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 02/05/2023]
Abstract
The actin cytoskeleton orchestrates cell mechanics and facilitates the physical integration of cells into tissues, while tissue-scale forces and extracellular rigidity in turn govern cell behaviour. Here, we discuss recent evidence that actin filaments (F-actin), the core building blocks of the actin cytoskeleton, also serve as molecular force sensors. We delineate two classes of proteins, which interpret forces applied to F-actin through enhanced binding interactions: 'mechanically tuned' canonical actin-binding proteins, whose constitutive F-actin affinity is increased by force, and 'mechanically switched' proteins, which bind F-actin only in the presence of force. We speculate mechanically tuned and mechanically switched actin-binding proteins are biophysically suitable for coordinating cytoskeletal force-feedback and mechanical signalling processes, respectively. Finally, we discuss potential mechanisms mediating force-activated actin binding, which likely occurs both through the structural remodelling of F-actin itself and geometric rearrangements of higher-order actin networks. Understanding the interplay of these mechanisms will enable the dissection of force-activated actin binding's specific biological functions.
Collapse
Affiliation(s)
- Xiaoyu Sun
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University. New York, NY, USA.,Correspondence: ;
| | - Gregory M. Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University. New York, NY, USA.,Correspondence: ;
| |
Collapse
|
30
|
Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite. Nat Commun 2022; 13:3442. [PMID: 35705539 PMCID: PMC9200798 DOI: 10.1038/s41467-022-31068-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/01/2022] [Indexed: 11/08/2022] Open
Abstract
Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the ‘ancient’ actin turnover machineries is limited. We show that, despite > 1 billion years of evolution, pathogenic Leishmania major parasite and mammalian actins share the same overall fold and co-polymerize with each other. Interestingly, Leishmania harbors a simple actin-regulatory machinery that lacks cofilin ‘cofactors’, which accelerate filament disassembly in higher eukaryotes. By applying single-filament biochemistry we discovered that, compared to mammalian proteins, Leishmania actin filaments depolymerize more rapidly from both ends, and are severed > 100-fold more efficiently by cofilin. Our high-resolution cryo-EM structures of Leishmania ADP-, ADP-Pi- and cofilin-actin filaments identify specific features at actin subunit interfaces and cofilin-actin interactions that explain the unusually rapid dynamics of parasite actin filaments. Our findings reveal how divergent parasites achieve rapid actin dynamics using a remarkably simple set of actin-binding proteins, and elucidate evolution of the actin cytoskeleton. The authors report here the structure-function analysis of highly divergent actin from Leishmania parasite. The study reveals remarkably rapid dynamics of parasite actin as well as the underlying molecular basis, thus providing insight into evolution of the actin cytoskeleton.
Collapse
|
31
|
Hylton RK, Heebner JE, Grillo MA, Swulius MT. Cofilactin filaments regulate filopodial structure and dynamics in neuronal growth cones. Nat Commun 2022; 13:2439. [PMID: 35508487 PMCID: PMC9068697 DOI: 10.1038/s41467-022-30116-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Cofilin is best known for its ability to sever actin filaments and facilitate cytoskeletal recycling inside of cells, but at higher concentrations in vitro, cofilin stabilizes a more flexible, hyper-twisted state of actin known as “cofilactin”. While this filament state is well studied, a structural role for cofilactin in dynamic cellular processes has not been observed. With a combination of cryo-electron tomography and fluorescence imaging in neuronal growth cones, we observe that filopodial actin filaments switch between a fascin-linked and a cofilin-decorated state, and that cofilactin is associated with a variety of dynamic events within filopodia. The switch to cofilactin filaments occurs in a graded fashion and correlates with a decline in fascin cross-linking within the filopodia, which is associated with curvature in the bundle. Our tomographic data reveal that the hyper-twisting of actin from cofilin binding leads to a rearrangement of filament packing, which largely excludes fascin from the base of filopodia. Our results provide mechanistic insight into the fundamentals of cytoskeletal remodeling inside of confined cellular spaces, and how the interplay between fascin and cofilin regulates the dynamics of searching filopodia. In this manuscript the authors show that Filopodia switch between bundles of fascin-crosslinked actin and cofilin-decorated filaments, which exclude fascin binding due to altered structure and packing, as well as affect filopodial searching dynamics.
Collapse
Affiliation(s)
- Ryan K Hylton
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Jessica E Heebner
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Michael A Grillo
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Matthew T Swulius
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA.
| |
Collapse
|
32
|
Kraus J, Russell RW, Kudryashova E, Xu C, Katyal N, Perilla JR, Kudryashov DS, Polenova T. Magic angle spinning NMR structure of human cofilin-2 assembled on actin filaments reveals isoform-specific conformation and binding mode. Nat Commun 2022; 13:2114. [PMID: 35440100 PMCID: PMC9018683 DOI: 10.1038/s41467-022-29595-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/24/2022] [Indexed: 12/16/2022] Open
Abstract
Actin polymerization dynamics regulated by actin-binding proteins are essential for various cellular functions. The cofilin family of proteins are potent regulators of actin severing and filament disassembly. The structural basis for cofilin-isoform-specific severing activity is poorly understood as their high-resolution structures in complex with filamentous actin (F-actin) are lacking. Here, we present the atomic-resolution structure of the muscle-tissue-specific isoform, cofilin-2 (CFL2), assembled on ADP-F-actin, determined by magic-angle-spinning (MAS) NMR spectroscopy and data-guided molecular dynamics (MD) simulations. We observe an isoform-specific conformation for CFL2. This conformation is the result of a unique network of hydrogen bonding interactions within the α2 helix containing the non-conserved residue, Q26. Our results indicate F-site interactions that are specific between CFL2 and ADP-F-actin, revealing mechanistic insights into isoform-dependent F-actin disassembly.
Collapse
Affiliation(s)
- Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544-1014, United States
| | - Ryan W Russell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, United States
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Nidhi Katyal
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States.
| |
Collapse
|
33
|
Atherton J, Stouffer M, Francis F, Moores CA. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. J Cell Sci 2022; 135:274968. [PMID: 35383828 PMCID: PMC9016625 DOI: 10.1242/jcs.259234] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/02/2022] [Indexed: 12/12/2022] Open
Abstract
Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration. Summary: Cryo-electron tomographic reconstruction of neuronal growth cone subdomains reveals distinctive F-actin and microtubule cytoskeleton architectures and modulation at molecular detail.
Collapse
Affiliation(s)
- Joseph Atherton
- Randall Centre for Cell and Molecular Biophysics, King's College, London SE1 1YR, UK.,Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
| | - Melissa Stouffer
- INSERM UMR-S 1270, 17 Rue du Fer à Moulin, 75005 Paris, France.,Sorbonne University UMR-S 1270, 4 Place Jussieu, 75005 Paris, France.,Institut du Fer à Moulin, 17 Rue du Fer à Moulin, 75005 Paris, France.,Institute of Science and Technology Austria, Am campus 1, 3400 Klosterneuberg, Austria
| | - Fiona Francis
- INSERM UMR-S 1270, 17 Rue du Fer à Moulin, 75005 Paris, France.,Sorbonne University UMR-S 1270, 4 Place Jussieu, 75005 Paris, France.,Institut du Fer à Moulin, 17 Rue du Fer à Moulin, 75005 Paris, France
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
| |
Collapse
|
34
|
Luo M, Wang Z, Wu J, Xie X, You W, Yu Z, Shen H, Li X, Li H, Liu Y, Wang Z, Chen G. Effects of PAK1/LIMK1/Cofilin-mediated Actin Homeostasis on Axonal Injury after Experimental Intracerebral Hemorrhage. Neuroscience 2022; 490:155-170. [DOI: 10.1016/j.neuroscience.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
|
35
|
Neijenhuis T, van Keulen SC, Bonvin AMJJ. Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4. Structure 2022; 30:476-484.e3. [PMID: 35216656 DOI: 10.1016/j.str.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
Abstract
A wide range of cellular processes requires the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The density maps produced can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low- to medium-resolution maps. Unfortunately, the models produced frequently contain atomic clashes at the protein-protein interfaces (PPIs), as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best-performing protocol, consisting of a semi-flexible simulated annealing refinement with centroid restraints on the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.
Collapse
Affiliation(s)
- Tim Neijenhuis
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Siri C van Keulen
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
| |
Collapse
|
36
|
Chatterjee D, Preuss F, Dederer V, Knapp S, Mathea S. Structural Aspects of LIMK Regulation and Pharmacology. Cells 2022; 11:cells11010142. [PMID: 35011704 PMCID: PMC8750758 DOI: 10.3390/cells11010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Malfunction of the actin cytoskeleton is linked to numerous human diseases including neurological disorders and cancer. LIMK1 (LIM domain kinase 1) and its paralogue LIMK2 are two closely related kinases that control actin cytoskeleton dynamics. Consequently, they are potential therapeutic targets for the treatment of such diseases. In the present review, we describe the LIMK conformational space and its dependence on ligand binding. Furthermore, we explain the unique catalytic mechanism of the kinase, shedding light on substrate recognition and how LIMK activity is regulated. The structural features are evaluated for implications on the drug discovery process. Finally, potential future directions for targeting LIMKs pharmacologically, also beyond just inhibiting the kinase domain, are discussed.
Collapse
Affiliation(s)
- Deep Chatterjee
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Franziska Preuss
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Verena Dederer
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str 15, 60438 Frankfurt am Main, Germany; (D.C.); (F.P.); (V.D.); (S.K.)
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str 9, 60438 Frankfurt am Main, Germany
- Correspondence:
| |
Collapse
|
37
|
Shen LW, Jiang XX, Li ZQ, Li J, Wang M, Jia GF, Ding X, Lei L, Gong QH, Gao N. Cepharanthine sensitizes human triple negative breast cancer cells to chemotherapeutic agent epirubicin via inducing cofilin oxidation-mediated mitochondrial fission and apoptosis. Acta Pharmacol Sin 2022; 43:177-193. [PMID: 34294886 PMCID: PMC8724299 DOI: 10.1038/s41401-021-00715-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
Inhibition of autophagy has been accepted as a promising therapeutic strategy in cancer, but its clinical application is hindered by lack of effective and specific autophagy inhibitors. We previously identified cepharanthine (CEP) as a novel autophagy inhibitor, which inhibited autophagy/mitophagy through blockage of autophagosome-lysosome fusion in human breast cancer cells. In this study we investigated whether and how inhibition of autophagy/mitophagy by cepharanthine affected the efficacy of chemotherapeutic agent epirubicin in triple negative breast cancer (TNBC) cells in vitro and in vivo. In human breast cancer MDA-MB-231 and BT549 cells, application of CEP (2 μM) greatly enhanced cepharanthine-induced inhibition on cell viability and colony formation. CEP interacted with epirubicin synergistically to induce apoptosis in TNBC cells via the mitochondrial pathway. We demonstrated that co-administration of CEP and epirubicin induced mitochondrial fission in MDA-MB-231 cells, and the production of mitochondrial superoxide was correlated with mitochondrial fission and apoptosis induced by the combination. Moreover, we revealed that co-administration of CEP and epirubicin markedly increased the generation of mitochondrial superoxide, resulting in oxidation of the actin-remodeling protein cofilin, which promoted formation of an intramolecular disulfide bridge between Cys39 and Cys80 as well as Ser3 dephosphorylation, leading to mitochondria translocation of cofilin, thus causing mitochondrial fission and apoptosis. Finally, in mice bearing MDA-MB-231 cell xenografts, co-administration of CEP (12 mg/kg, ip, once every other day for 36 days) greatly enhanced the therapeutic efficacy of epirubicin (2 mg/kg) as compared with administration of either drug alone. Taken together, our results implicate that a combination of cepharanthine with chemotherapeutic agents could represent a novel therapeutic strategy for the treatment of breast cancer.
Collapse
Affiliation(s)
- Li-wen Shen
- grid.417409.f0000 0001 0240 6969Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006 China
| | - Xiu-xing Jiang
- grid.410570.70000 0004 1760 6682College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Zhi-qiang Li
- grid.410570.70000 0004 1760 6682College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Jie Li
- grid.410570.70000 0004 1760 6682College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Mei Wang
- grid.417409.f0000 0001 0240 6969Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006 China
| | - Guan-fei Jia
- grid.410570.70000 0004 1760 6682College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Xin Ding
- grid.410570.70000 0004 1760 6682College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Ling Lei
- grid.410570.70000 0004 1760 6682College of Pharmacy, Army Medical University, Chongqing, 400038 China
| | - Qi-hai Gong
- grid.417409.f0000 0001 0240 6969Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006 China
| | - Ning Gao
- grid.417409.f0000 0001 0240 6969Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006 China ,grid.410570.70000 0004 1760 6682College of Pharmacy, Army Medical University, Chongqing, 400038 China
| |
Collapse
|
38
|
Duong HTT, Suzuki H, Katagiri S, Shibata M, Arai M, Yura K. Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin. Biophys Physicobiol 2022; 19:e190025. [PMID: 36160324 PMCID: PMC9465404 DOI: 10.2142/biophysico.bppb-v19.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
Sequencing of individual human genomes enables studying relationship among nucleotide variations, amino acid substitutions, effect on protein structures and diseases. Many studies have found general tendencies, for instance, that pathogenic variations tend to be found in the buried regions of the protein structures, that benign variations tend to be found on the surface of the proteins, and that variations on evolutionary conserved residues tend to be pathogenic. These tendencies were deduced from globular proteins with standard evolutionary changes in amino acid sequences. In this study, we investigated the variation distribution on actin, one of the highly conserved proteins. Many nucleotide variations and three-dimensional structures of actin have been registered in databases. By combining those data, we found that variations buried inside the protein were rather benign and variations on the surface of the protein were pathogenic. This idiosyncratic distribution of the variation impact is likely ascribed to the extensive use of the surface of the protein for protein-protein interactions in actin.
Collapse
Affiliation(s)
- Ha T. T. Duong
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Hirofumi Suzuki
- Graduate School of Advanced Science and Engineering, Waseda University
| | - Saki Katagiri
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Mayu Shibata
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Misae Arai
- Graduate School of Humanities and Sciences, Ochanomizu University
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
| |
Collapse
|
39
|
Gautreau AM, Fregoso FE, Simanov G, Dominguez R. Nucleation, stabilization, and disassembly of branched actin networks. Trends Cell Biol 2021; 32:421-432. [PMID: 34836783 PMCID: PMC9018471 DOI: 10.1016/j.tcb.2021.10.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
Arp2/3 complex is an actin filament nucleation and branching machinery conserved in all eukaryotes from yeast to human. Arp2/3 complex branched networks generate pushing forces that drive cellular processes ranging from membrane remodeling to cell and organelle motility. Several molecules regulate these processes by directly inhibiting or activating Arp2/3 complex and by stabilizing or disassembling branched networks. Here, we review recent advances in our understanding of Arp2/3 complex regulation, including high-resolution cryoelectron microscopy (cryo-EM) structures that illuminate the mechanisms of Arp2/3 complex activation and branch formation, and novel cellular pathways of branch formation, stabilization, and debranching. We also identify major gaps in our understanding of Arp2/3 complex inhibition and branch stabilization and disassembly.
Collapse
Affiliation(s)
- Alexis M Gautreau
- Laboratoire de Biologie Structurale de la Cellule, CNRS, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.
| | - Fred E Fregoso
- Department of Physiology and Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gleb Simanov
- Laboratoire de Biologie Structurale de la Cellule, CNRS, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Roberto Dominguez
- Department of Physiology and Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
40
|
Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress. Redox Biol 2021; 46:102111. [PMID: 34425387 PMCID: PMC8379693 DOI: 10.1016/j.redox.2021.102111] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
Thiol-based post-translational modifications (PTMs) play a key role in redox-dependent regulation and signaling. Functional cysteine (Cys) sites serve as redox switches, regulated through multiple types of PTMs. Herein, we aim to characterize the complexity of thiol PTMs at the proteome level through the establishment of a direct detection workflow. The LC-MS/MS based workflow allows for simultaneous quantification of protein abundances and multiple types of thiol PTMs. To demonstrate its utility, the workflow was applied to mouse pancreatic β-cells (β-TC-6) treated with thapsigargin to induce endoplasmic reticulum (ER) stress. This resulted in the quantification of >9000 proteins and multiple types of thiol PTMs, including intra-peptide disulfide (S–S), S-glutathionylation (SSG), S-sulfinylation (SO2H), S-sulfonylation (SO3H), S-persulfidation (SSH), and S-trisulfidation (SSSH). Proteins with significant changes in abundance were observed to be involved in canonical pathways such as autophagy, unfolded protein response, protein ubiquitination pathway, and EIF2 signaling. Moreover, ~500 Cys sites were observed with one or multiple types of PTMs with SSH and S–S as the predominant types of modifications. In many cases, significant changes in the levels of different PTMs were observed on various enzymes and their active sites, while their protein abundance exhibited little change. These results provide evidence of independent translational and post-translational regulation of enzyme activity. The observed complexity of thiol modifications on the same Cys residues illustrates the challenge in the characterization and interpretation of protein thiol modifications and their functional regulation. Simultaneous quantification of protein abundances and multiple types of thiol PTMs. Multiple types PTMs observed on the same Cys sites for redox-regulated proteins. Data revealed complexity of thiol PTMs and their regulation. Distinctive translational and post-translational regulation under ER stress in β-cells.
Collapse
|
41
|
Cancer type-specific alterations in actin genes: Worth a closer look? INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 360:133-184. [PMID: 33962749 DOI: 10.1016/bs.ircmb.2021.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Actins form a strongly conserved family of proteins that are central to the functioning of the actin cytoskeleton partaking in natural processes such as cell division, adhesion, contraction and migration. These processes, however, also occur during the various phases of cancer progression. Yet, surprisingly, alterations in the six human actin genes in cancer studies have received little attention and the focus was mostly on deregulated expression levels of actins and even more so of actin-binding or regulatory proteins. Starting from the early mutation work in the 1980s, we propose based on reviewing literature and data from patient cancer genomes that alterations in actin genes are different in distinct cancer subtypes, suggesting some specificity. These actin gene alterations include (missense) mutations, gene fusions and copy number alterations (deletions and amplifications) and we illustrate their occurrence for a limited number of examples including actin mutations in lymphoid cancers and nonmelanoma skin cancer and actin gene copy number alterations for breast, prostate and liver cancers. A challenge in the future will be to further sort out the specificity per actin gene, alteration type and cancer subtype. Even more challenging is (experimentally) distinguishing between cause and consequence: which alterations are passengers and which are involved in tumor progression of particular cancer subtypes?
Collapse
|
42
|
Bibeau JP, Gray S, De La Cruz EM. Clusters of a Few Bound Cofilins Sever Actin Filaments. J Mol Biol 2021; 433:166833. [PMID: 33524412 DOI: 10.1016/j.jmb.2021.166833] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023]
Abstract
Cofilin is an essential actin filament severing protein that accelerates the assembly dynamics and turnover of actin networks by increasing the number of filament ends where subunits add and dissociate. It binds filament subunits stoichiometrically and cooperatively, forming clusters of contiguously-bound cofilin at sub-saturating occupancies. Filaments partially occupied with cofilin sever at boundaries between bare and cofilin-decorated segments. Imaging studies concluded that bound clusters must reach a critical size (Cc) of 13-100 cofilins to sever filaments. In contrast, structural and modeling studies suggest that a few or even a single cofilin can sever filaments, possibly with different severing rate constants. How clusters grow through the cooperative incorporation of additional cofilin molecules, specifically if they elongate asymmetrically or uniformly from both ends and if they are modulated by filament shape and external force, also lacks consensus. Here, using hydrodynamic flow to visualize individual actin filaments with TIRF microscopy, we found that neither flow-induced filament bending, tension, nor surface attachment conditions substantially affected the kinetics of cofilin binding to actin filaments. Clusters of bound cofilin preferentially extended toward filament pointed ends and displayed severing competency at small sizes (Cc < 3), with no detectable severing dependence on cluster size. These data support models in which small clusters of cofilin introduce local, but asymmetric, structural changes in actin filaments that promote filament severing with a rate constant that depends weakly on the size of the cluster.
Collapse
Affiliation(s)
- Jeffrey P Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States
| | - Shawn Gray
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States.
| |
Collapse
|
43
|
Smith H, Pinkerton N, Heisler DB, Kudryashova E, Hall AR, Karch KR, Norris A, Wysocki V, Sotomayor M, Reisler E, Vavylonis D, Kudryashov DS. Rounding Out the Understanding of ACD Toxicity with the Discovery of Cyclic Forms of Actin Oligomers. Int J Mol Sci 2021; 22:E718. [PMID: 33450834 PMCID: PMC7828245 DOI: 10.3390/ijms22020718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/09/2021] [Indexed: 11/17/2022] Open
Abstract
Actin is an essential element of both innate and adaptive immune systems and can aid in motility and translocation of bacterial pathogens, making it an attractive target for bacterial toxins. Pathogenic Vibrio and Aeromonas genera deliver actin cross-linking domain (ACD) toxin into the cytoplasm of the host cell to poison actin regulation and promptly induce cell rounding. At early stages of toxicity, ACD covalently cross-links actin monomers into oligomers (AOs) that bind through multivalent interactions and potently inhibit several families of actin assembly proteins. At advanced toxicity stages, we found that the terminal protomers of linear AOs can get linked together by ACD to produce cyclic AOs. When tested against formins and Ena/VASP, linear and cyclic AOs exhibit similar inhibitory potential, which for the cyclic AOs is reduced in the presence of profilin. In coarse-grained molecular dynamics simulations, profilin and WH2-motif binding sites on actin subunits remain exposed in modeled AOs of both geometries. We speculate, therefore, that the reduced toxicity of cyclic AOs is due to their reduced configurational entropy. A characteristic feature of cyclic AOs is that, in contrast to the linear forms, they cannot be straightened to form filaments (e.g., through stabilization by cofilin), which makes them less susceptible to neutralization by the host cell.
Collapse
Affiliation(s)
- Harper Smith
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Nick Pinkerton
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - David B. Heisler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Aaron R. Hall
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA; (A.R.H.); (D.V.)
| | - Kelly R. Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - Andrew Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA;
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA; (A.R.H.); (D.V.)
| | - Dmitri S. Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (H.S.); (N.P.); (D.B.H.); (E.K.); (K.R.K.); (A.N.); (V.W.); (M.S.)
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
44
|
Wioland H, Frémont S, Guichard B, Echard A, Jégou A, Romet-Lemonne G. Actin filament oxidation by MICAL1 suppresses protections from cofilin-induced disassembly. EMBO Rep 2021; 22:e50965. [PMID: 33393173 DOI: 10.15252/embr.202050965] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 02/01/2023] Open
Abstract
Proteins of the ADF/cofilin family play a central role in the disassembly of actin filaments, and their activity must be tightly regulated in cells. Recently, the oxidation of actin filaments by the enzyme MICAL1 was found to amplify the severing action of cofilin through unclear mechanisms. Using single filament experiments in vitro, we found that actin filament oxidation by MICAL1 increases, by several orders of magnitude, both cofilin binding and severing rates, explaining the dramatic synergy between oxidation and cofilin for filament disassembly. Remarkably, we found that actin oxidation bypasses the need for cofilin activation by dephosphorylation. Indeed, non-activated, phosphomimetic S3D-cofilin binds and severs oxidized actin filaments rapidly, in conditions where non-oxidized filaments are unaffected. Finally, tropomyosin Tpm1.8 loses its ability to protect filaments from cofilin severing activity when actin is oxidized by MICAL1. Together, our results show that MICAL1-induced oxidation of actin filaments suppresses their physiological protection from the action of cofilin. We propose that, in cells, direct post-translational modification of actin filaments by oxidation is a way to trigger their disassembly.
Collapse
Affiliation(s)
- Hugo Wioland
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Stéphane Frémont
- Membrane Traffic and Cell Division Lab, Institut Pasteur, UMR3691, CNRS, Paris, France
| | | | - Arnaud Echard
- Membrane Traffic and Cell Division Lab, Institut Pasteur, UMR3691, CNRS, Paris, France
| | - Antoine Jégou
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | | |
Collapse
|
45
|
Hocky GM, Sindelar CV, Cao W, Voth GA, De La Cruz EM. Structural basis of fast- and slow-severing actin-cofilactin boundaries. J Biol Chem 2021; 296:100337. [PMID: 33508320 PMCID: PMC7961102 DOI: 10.1016/j.jbc.2021.100337] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/24/2023] Open
Abstract
Members of the ADF/cofilin family of regulatory proteins bind actin filaments cooperatively, locally change actin subunit conformation and orientation, and sever filaments at "boundaries" between bare and cofilin-occupied segments. A cluster of bound cofilin introduces two distinct classes of boundaries due to the intrinsic polarity of actin filaments, one at the "pointed" end side and the other at the "barbed" end-side of the cluster; severing occurs more readily at the pointed end side of the cluster ("fast-severing" boundary) than the barbed end side ("slow-severing" boundary). A recent electron-cryomicroscopy (cryo-EM) model of the slow-severing boundary revealed structural "defects" at the interface that potentially contribute to severing. However, the structure of the fast-severing boundary remains uncertain. Here, we use extensive molecular dynamics simulations to produce atomic resolution models of both severing boundaries. Our equilibrated simulation model of the slow-severing boundary is consistent with the cryo-EM structural model. Simulations indicate that actin subunits at both boundaries adopt structures intermediate between those of bare and cofilin-bound actin subunits. These "intermediate" states have compromised intersubunit contacts, but those at the slow-severing boundary are stabilized by cofilin bridging interactions, accounting for its lower fragmentation probability. Simulations where cofilin proteins are removed from cofilactin filaments favor a mechanism in which a cluster of two contiguously bound cofilins is needed to fully stabilize the cofilactin conformation, promote cooperative binding interactions, and accelerate filament severing. Together, these studies provide a molecular-scale foundation for developing coarse-grained and theoretical descriptions of cofilin-mediated actin filament severing.
Collapse
Affiliation(s)
- Glen M Hocky
- Department of Chemistry, New York University, New York, New York, USA.
| | - Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois, USA
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
| |
Collapse
|
46
|
Harris AR, Jreij P, Belardi B, Joffe AM, Bausch AR, Fletcher DA. Biased localization of actin binding proteins by actin filament conformation. Nat Commun 2020; 11:5973. [PMID: 33239610 PMCID: PMC7688639 DOI: 10.1038/s41467-020-19768-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/30/2020] [Indexed: 11/09/2022] Open
Abstract
The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1-CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells. We demonstrate that the binding kinetics of CH1-CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs and other binding proteins. These findings suggest that conformational changes of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.
Collapse
Affiliation(s)
- Andrew R Harris
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Pamela Jreij
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Brian Belardi
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Aaron M Joffe
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA
| | - Andreas R Bausch
- Lehrstuhl für Biophysik (E27), Technische Universität München, Garching, 85748, Germany
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 648 Stanley Hall MC 1762, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| |
Collapse
|
47
|
Mechanically tuning actin filaments to modulate the action of actin-binding proteins. Curr Opin Cell Biol 2020; 68:72-80. [PMID: 33160108 DOI: 10.1016/j.ceb.2020.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022]
Abstract
In cells, the actin cytoskeleton is regulated by an interplay between mechanics and biochemistry. A key mechanism, which has emerged based on converging indications from structural, cellular, and biophysical data, depicts the actin filament as a mechanically tunable substrate: mechanical stress applied to an actin filament induces conformational changes, which modify the binding and the regulatory action of actin-binding proteins. For a long time, however, direct evidence of this mechanotransductive mechanism was very scarce. This situation is changing rapidly, and recent in vitro single-filament studies using different techniques have revealed that several actin-binding proteins are able to sense tension, curvature, and/or torsion, applied to actin filaments. Here, we discuss these recent advances and their possible implications.
Collapse
|
48
|
Tang VW, Nadkarni AV, Brieher WM. Catastrophic actin filament bursting by cofilin, Aip1, and coronin. J Biol Chem 2020; 295:13299-13313. [PMID: 32723865 DOI: 10.1074/jbc.ra120.015018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/24/2020] [Indexed: 11/06/2022] Open
Abstract
Cofilin is an actin filament severing protein necessary for fast actin turnover dynamics. Coronin and Aip1 promote cofilin-mediated actin filament disassembly, but the mechanism is somewhat controversial. An early model proposed that the combination of cofilin, coronin, and Aip1 disassembled filaments in bursts. A subsequent study only reported severing. Here, we used EM to show that actin filaments convert directly into globular material. A monomer trap assay also shows that the combination of all three factors produces actin monomers faster than any two factors alone. We show that coronin accelerates the release of Pi from actin filaments and promotes highly cooperative cofilin binding to actin to create long stretches of polymer with a hypertwisted morphology. Aip1 attacks these hypertwisted regions along their sides, disintegrating them into monomers or short oligomers. The results are consistent with a catastrophic mode of disassembly, not enhanced severing alone.
Collapse
Affiliation(s)
- Vivian W Tang
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Ambika V Nadkarni
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - William M Brieher
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA.
| |
Collapse
|
49
|
Regulation of Actin Filament Length by Muscle Isoforms of Tropomyosin and Cofilin. Int J Mol Sci 2020; 21:ijms21124285. [PMID: 32560136 PMCID: PMC7352323 DOI: 10.3390/ijms21124285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022] Open
Abstract
In striated muscle the extent of the overlap between actin and myosin filaments contributes to the development of force. In slow twitch muscle fibers actin filaments are longer than in fast twitch fibers, but the mechanism which determines this difference is not well understood. We hypothesized that tropomyosin isoforms Tpm1.1 and Tpm3.12, the actin regulatory proteins, which are specific respectively for fast and slow muscle fibers, differently stabilize actin filaments and regulate severing of the filaments by cofilin-2. Using in vitro assays, we showed that Tpm3.12 bound to F-actin with almost 2-fold higher apparent binding constant (Kapp) than Tpm1.1. Cofilin2 reduced Kapp of both tropomyosin isoforms. In the presence of Tpm1.1 and Tpm3.12 the filaments were longer than unregulated F-actin by 25% and 40%, respectively. None of the tropomyosins affected the affinity of cofilin-2 for F-actin, but according to the linear lattice model both isoforms increased cofilin-2 binding to an isolated site and reduced binding cooperativity. The filaments decorated with Tpm1.1 and Tpm3.12 were severed by cofilin-2 more often than unregulated filaments, but depolymerization of the severed filaments was inhibited. The stabilization of the filaments by Tpm3.12 was more efficient, which can be attributed to lower dynamics of Tpm3.12 binding to actin.
Collapse
|
50
|
Parker F, Baboolal TG, Peckham M. Actin Mutations and Their Role in Disease. Int J Mol Sci 2020; 21:ijms21093371. [PMID: 32397632 PMCID: PMC7247010 DOI: 10.3390/ijms21093371] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
Actin is a widely expressed protein found in almost all eukaryotic cells. In humans, there are six different genes, which encode specific actin isoforms. Disease-causing mutations have been described for each of these, most of which are missense. Analysis of the position of the resulting mutated residues in the protein reveals mutational hotspots. Many of these occur in regions important for actin polymerization. We briefly discuss the challenges in characterizing the effects of these actin mutations, with a focus on cardiac actin mutations.
Collapse
|