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Wang Y, Wu J, Zsolnay V, Pollard TD, Voth GA. Mechanism of Phosphate Release from Actin Filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.03.551904. [PMID: 37577500 PMCID: PMC10418243 DOI: 10.1101/2023.08.03.551904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
After ATP-actin monomers assemble filaments, the ATP's γ-phosphate is hydrolyzed within seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to sample the release of phosphate from filaments and study residues that gate release. Dissociation of phosphate from Mg2+ is rate limiting and associated with an energy barrier of 20 kcal/mol, consistent with experimental rates of phosphate release. Phosphate then diffuses in an internal cavity toward a gate formed by R177 suggested in prior computational studies and cryo-EM structures. The gate is closed when R177 hydrogen bonds with N111 and is open when R177 forms a salt bridge with D179. Most of the time interactions of R177 with other residues occludes the phosphate release pathway. Machine learning analysis reveals that the occluding interactions fluctuate rapidly, underscoring the secondary role of backdoor gate opening in Pi release, in contrast with the previous hypothesis that gate opening is the primary event.
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Affiliation(s)
- Yihang Wang
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL
| | - Jiangbo Wu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL
| | - Vilmos Zsolnay
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL
| | - Thomas D. Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
- Department of Cell Biology, Yale University, New Haven, CT
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL
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2
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Barth H, Worek F, Steinritz D, Papatheodorou P, Huber-Lang M. Trauma-toxicology: concepts, causes, complications. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2935-2948. [PMID: 37999755 PMCID: PMC11074020 DOI: 10.1007/s00210-023-02845-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Trauma and toxic substances are connected in several aspects. On the one hand, toxic substances can be the reason for traumatic injuries in the context of accidental or violent and criminal circumstances. Examples for the first scenario is the release of toxic gases, chemicals, and particles during house fires, and for the second scenario, the use of chemical or biological weapons in the context of terroristic activities. Toxic substances can cause or enhance severe, life-threatening trauma, as described in this review for various chemical warfare, by inducing a tissue trauma accompanied by break down of important barriers in the body, such as the blood-air or the blood-gut barriers. This in turn initiates a "vicious circle" as the contribution of inflammatory responses to the traumatic damage enhances the macro- and micro-barrier breakdown and often results in fatal outcome. The development of sophisticated methods for detection and identification of toxic substances as well as the special treatment of the intoxicated trauma patient is summarized in this review. Moreover, some highly toxic substances, such as the protein toxins from the pathogenic bacterium Clostridioides (C.) difficile, cause severe post-traumatic complications which significantly worsens the outcome of hospitalized patients, in particular in multiply injured trauma patients. Therefore, novel pharmacological options for the treatment of such patients are necessarily needed and one promising strategy might be the neutralization of the toxins that cause the disease. This review summarizes recent findings on the molecular and cellular mechanisms of toxic chemicals and bacterial toxins that contribute to barrier breakdown in the human body as wells pharmacological options for treatment, in particular in the context of intoxicated trauma patients. "trauma-toxicology" comprises concepts regrading basic research, development of novel pharmacological/therapeutic options and clinical aspects in the complex interplay and "vicious circle" of severe tissue trauma, barrier breakdown, pathogen and toxin exposure, tissue damage, and subsequent clinical complications.
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Affiliation(s)
- Holger Barth
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, University of Ulm Medical Center, Ulm, Germany.
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Panagiotis Papatheodorou
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, University of Ulm Medical Center, Ulm, Germany
| | - Markus Huber-Lang
- Institute of Clinical and Experimental Trauma Immunology, University of Ulm Medical Center, Ulm, Germany.
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3
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Papatheodorou P, Minton NP, Aktories K, Barth H. An Updated View on the Cellular Uptake and Mode-of-Action of Clostridioides difficile Toxins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:219-247. [PMID: 38175478 DOI: 10.1007/978-3-031-42108-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Research on the human gut pathogen Clostridioides (C.) difficile and its toxins continues to attract much attention as a consequence of the threat to human health posed by hypervirulent strains. Toxin A (TcdA) and Toxin B (TcdB) are the two major virulence determinants of C. difficile. Both are single-chain proteins with a similar multidomain architecture. Certain hypervirulent C. difficile strains also produce a third toxin, namely binary toxin CDT (C. difficile transferase). C. difficile toxins are the causative agents of C. difficile-associated diseases (CDADs), such as antibiotics-associated diarrhea and pseudomembranous colitis. For that reason, considerable efforts have been expended to unravel their molecular mode-of-action and the cellular mechanisms responsible for their uptake. Many of these studies have been conducted in European laboratories. Here, we provide an update on our previous review (Papatheodorou et al. Adv Exp Med Biol, 2018) on important advances in C. difficile toxins research.
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Affiliation(s)
- Panagiotis Papatheodorou
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany.
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, University of Nottingham, Nottingham, UK
| | - Klaus Aktories
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg, Germany
| | - Holger Barth
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
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4
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Bai Y, Zhao F, Wu T, Chen F, Pang X. Actin polymerization and depolymerization in developing vertebrates. Front Physiol 2023; 14:1213668. [PMID: 37745245 PMCID: PMC10515290 DOI: 10.3389/fphys.2023.1213668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Development is a complex process that occurs throughout the life cycle. F-actin, a major component of the cytoskeleton, is essential for the morphogenesis of tissues and organs during development. F-actin is formed by the polymerization of G-actin, and the dynamic balance of polymerization and depolymerization ensures proper cellular function. Disruption of this balance results in various abnormalities and defects or even embryonic lethality. Here, we reviewed recent findings on the structure of G-actin and F-actin and the polymerization of G-actin to F-actin. We also focused on the functions of actin isoforms and the underlying mechanisms of actin polymerization/depolymerization in cellular and organic morphogenesis during development. This information will extend our understanding of the role of actin polymerization in the physiologic or pathologic processes during development and may open new avenues for developing therapeutics for embryonic developmental abnormalities or tissue regeneration.
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Affiliation(s)
- Yang Bai
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Feng Zhao
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Tingting Wu
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Fangchun Chen
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Xiaoxiao Pang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
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5
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Li T, Du J, Ren M. Structural Significance of His73 in F-Actin Dynamics: Insights from Ab Initio Study. Int J Mol Sci 2022; 23:ijms231810447. [PMID: 36142357 PMCID: PMC9499316 DOI: 10.3390/ijms231810447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
F-actin dynamics (polymerization and depolymerization) are associated with nucleotide exchange, providing the driving forces for dynamic cellular activities. As an important residue in the nucleotide state-sensing region in actin, His73 is often found to be methylated in natural actin and directly participates in F-actin dynamics by regulating nucleotide exchange. The interaction between His73 and its neighboring residue, Gly158, has significance for F-actin dynamics. However, this weak chemical interaction is difficult to characterize using classic molecular modeling methods. In this study, ab initio modeling was employed to explore the binding energy between His73 and Gly158. The results confirm that the methyl group on the His73 side chain contributes to the structural stability of atomistic networks in the nucleotide state-sensing region of actin monomers and confines the material exchange (Pi release) pathway within F-actin dynamics. Further binding energy analyses of actin structures under different nucleotide states showed that the potential model of His73/Gly158 hydrogen bond breaking in the material exchange mechanism is not obligatory within F-actin dynamics.
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Affiliation(s)
- Tong Li
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
| | - Juan Du
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
| | - Mingfa Ren
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian 116024, China
- Correspondence: ; Tel.: +86-411-8479161
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6
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Hintzen JCJ, Ma H, Deng H, Witecka A, Andersen SB, Drozak J, Guo H, Qian P, Li H, Mecinović J. Histidine methyltransferase
SETD3
methylates structurally diverse histidine mimics in actin. Protein Sci 2022; 31:e4305. [PMID: 35481649 PMCID: PMC9004244 DOI: 10.1002/pro.4305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 01/05/2023]
Abstract
Actin histidine Nτ‐methylation by histidine methyltransferase SETD3 plays an important role in human biology and diseases. Here, we report integrated synthetic, biocatalytic, biostructural, and computational analyses on human SETD3‐catalyzed methylation of actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N‐nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical molecular dynamics and free‐energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic, and functional insight into actin histidine methylation by SETD3. PDB Code(s): 7W28 and 7W29
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Affiliation(s)
- Jordi C. J. Hintzen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
| | - Huida Ma
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua‐Peking Center for Life Sciences Tsinghua University Beijing China
| | - Hao Deng
- Chemistry and Materials Science Faculty Shandong Agricultural University Tai'an Shandong China
| | - Apolonia Witecka
- Department of Metabolic Regulation, Faculty of Biology University of Warsaw Warsaw Poland
| | - Steffen B. Andersen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology University of Warsaw Warsaw Poland
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Ping Qian
- Chemistry and Materials Science Faculty Shandong Agricultural University Tai'an Shandong China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua‐Peking Center for Life Sciences Tsinghua University Beijing China
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
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7
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Vahokoski J, Calder LJ, Lopez AJ, Molloy JE, Kursula I, Rosenthal PB. High-resolution structures of malaria parasite actomyosin and actin filaments. PLoS Pathog 2022; 18:e1010408. [PMID: 35377914 PMCID: PMC9037914 DOI: 10.1371/journal.ppat.1010408] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 04/25/2022] [Accepted: 03/01/2022] [Indexed: 12/20/2022] Open
Abstract
Malaria is responsible for half a million deaths annually and poses a huge economic burden on the developing world. The mosquito-borne parasites (Plasmodium spp.) that cause the disease depend upon an unconventional actomyosin motor for both gliding motility and host cell invasion. The motor system, often referred to as the glideosome complex, remains to be understood in molecular terms and is an attractive target for new drugs that might block the infection pathway. Here, we present the high-resolution structure of the actomyosin motor complex from Plasmodium falciparum. The complex includes the malaria parasite actin filament (PfAct1) complexed with the class XIV myosin motor (PfMyoA) and its two associated light-chains. The high-resolution core structure reveals the PfAct1:PfMyoA interface in atomic detail, while at lower-resolution, we visualize the PfMyoA light-chain binding region, including the essential light chain (PfELC) and the myosin tail interacting protein (PfMTIP). Finally, we report a bare PfAct1 filament structure at improved resolution.
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Affiliation(s)
- Juha Vahokoski
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Lesley J. Calder
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
| | - Andrea J. Lopez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Justin E. Molloy
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
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8
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Ali R, Zahm JA, Rosen MK. Bound nucleotide can control the dynamic architecture of monomeric actin. Nat Struct Mol Biol 2022; 29:320-328. [PMID: 35332323 PMCID: PMC9010300 DOI: 10.1038/s41594-022-00743-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/11/2022] [Indexed: 11/12/2022]
Abstract
Polymerization of actin into cytoskeletal filaments is coupled to its bound adenine nucleotides. The mechanism by which nucleotide modulates actin functions has not been evident from analyses of ATP- and ADP-bound crystal structures of the actin monomer. We report that NMR chemical shift differences between the two forms are globally distributed. Furthermore, microsecond–millisecond motions are spread throughout the molecule in the ATP form, but largely confined to subdomains 1 and 2, and the nucleotide binding site in the ADP form. Through these motions, the ATP- and ADP-bound forms sample different high-energy conformations. A deafness-causing, fast-nucleating actin mutant populates the high-energy conformer of ATP-actin more than the wild-type protein, suggesting that this conformer may be on the pathway to nucleation. Together, the data suggest a model in which differential sampling of a nucleation-compatible form of the actin monomer may contribute to control of actin filament dynamics by nucleotide. NMR shows that ATP- and ADP-actin differ globally, including ground and excited state structures and dynamic architecture. Analyses of an actin mutant suggest the high-energy conformer of ATP-actin may be on the pathway to filament nucleation.
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Affiliation(s)
- Rustam Ali
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Jacob A Zahm
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.
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9
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Wieczorek M, Huang TL, Urnavicius L, Hsia KC, Kapoor TM. MZT Proteins Form Multi-Faceted Structural Modules in the γ-Tubulin Ring Complex. Cell Rep 2021; 31:107791. [PMID: 32610146 PMCID: PMC7416306 DOI: 10.1016/j.celrep.2020.107791] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/16/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Microtubule organization depends on the γ-Tubulin ring complex (γ-TuRC), a ~2.3-MDa nucleation factor comprising an asymmetric assembly of γ-Tubulin and GCP2-GCP6. However, it is currently unclear how the γ-TuRC-associated microproteins MZT1 and MZT2 contribute to the structure and regulation of the holocomplex. Here, we report cryo-EM structures of MZT1 and MZT2 in the context of the native human γ-TuRC. MZT1 forms two subcomplexes with the N-terminal α-helical domains of GCP3 or GCP6 (GCP-NHDs) within the γ-TuRC “lumenal bridge.” We determine the X-ray structure of recombinant MZT1/GCP6-NHD and find it is similar to that within the native γ-TuRC. We identify two additional MZT/GCP-NHD-like subcomplexes, one of which is located on the outer face of the γ-TuRC and comprises MZT2 and GCP2-NHD in complex with a centrosomin motif 1 (CM1)-containing peptide. Our data reveal how MZT1 and MZT2 establish multi-faceted, structurally mimetic “modules” that can expand structural and regulatory interfaces in the γ-TuRC. Wieczorek et al. show how the microproteins MZT1 and MZT2 expand binding interfaces across the γ-TuRC—the cell’s microtubule nucleating machinery—by forming similarly shaped, “modular” subcomplexes with the α-helical N-terminal domains of different γ-Tubulin complex proteins (GCPs).
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Affiliation(s)
- Michal Wieczorek
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Tzu-Lun Huang
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica, and National Defense Medical Center, Taipei, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Linas Urnavicius
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Laboratory of Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Kuo-Chiang Hsia
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica, and National Defense Medical Center, Taipei, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan.
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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10
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New Insights into Cellular Functions of Nuclear Actin. BIOLOGY 2021; 10:biology10040304. [PMID: 33916969 PMCID: PMC8067577 DOI: 10.3390/biology10040304] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary It is well known that actin forms a cytoplasmic network of microfilaments, the part of the cytoskeleton, in the cytoplasm of eukaryotic cells. The presence of nuclear actin was elusive for a very long time. Now, there is a very strong evidence that actin plays many important roles in the nucleus. Here, we discuss the recently discovered functions of the nuclear actin pool. Actin does not have nuclear localization signal (NLS), so its import to the nucleus is facilitated by the NLS-containing proteins. Nuclear actin plays a role in the maintenance of the nuclear structure and the nuclear envelope breakdown. It is also involved in chromatin remodeling, and chromatin and nucleosome movement necessary for DNA recombination, repair, and the initiation of transcription. It also binds RNA polymerases, promoting transcription. Because of the multifaceted role of nuclear actin, the future challenge will be to further define its functions in various cellular processes and diseases. Abstract Actin is one of the most abundant proteins in eukaryotic cells. There are different pools of nuclear actin often undetectable by conventional staining and commercial antibodies used to identify cytoplasmic actin. With the development of more sophisticated imaging and analytical techniques, it became clear that nuclear actin plays a crucial role in shaping the chromatin, genomic, and epigenetic landscape, transcriptional regulation, and DNA repair. This multifaceted role of nuclear actin is not only important for the function of the individual cell but also for the establishment of cell fate, and tissue and organ differentiation during development. Moreover, the changes in the nuclear, chromatin, and genomic architecture are preamble to various diseases. Here, we discuss some of the newly described functions of nuclear actin.
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11
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Structural basis for polarized elongation of actin filaments. Proc Natl Acad Sci U S A 2020; 117:30458-30464. [PMID: 33199648 DOI: 10.1073/pnas.2011128117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Actin filaments elongate and shorten much faster at their barbed end than their pointed end, but the molecular basis of this difference has not been understood. We use all-atom molecular dynamics simulations to investigate the properties of subunits at both ends of the filament. The terminal subunits tend toward conformations that resemble actin monomers in solution, while contacts with neighboring subunits progressively flatten the conformation of internal subunits. At the barbed end the terminal subunit is loosely tethered by its DNase-1 loop to the third subunit, because its monomer-like conformation precludes stabilizing contacts with the penultimate subunit. The motions of the terminal subunit make the partially flattened penultimate subunit accessible for binding monomers. At the pointed end, unique contacts between the penultimate and terminal subunits are consistent with existing cryogenic electron microscopic (cryo-EM) maps, limit binding to incoming monomers, and flatten the terminal subunit, which likely promotes ATP hydrolysis and rapid phosphate release. These structures explain the distinct polymerization kinetics of the two ends.
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12
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Deng H, Ma Y, Ren WS, Vuong VQ, Qian P, Guo H. Structure and Dynamics of the Reactive State for the Histidine Methylation Process and Catalytic Mechanism of SETD3: Insights from Quantum Mechanics/Molecular Mechanics Investigation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hao Deng
- Chemistry and Material Science Faculty, Shandong Agricultural University, Taian 271018, P. R. China
| | - Yue Ma
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Wan-Sheng Ren
- Chemistry and Material Science Faculty, Shandong Agricultural University, Taian 271018, P. R. China
| | - Van Quan Vuong
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ping Qian
- Chemistry and Material Science Faculty, Shandong Agricultural University, Taian 271018, P. R. China
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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13
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Horan BG, Hall AR, Vavylonis D. Insights into Actin Polymerization and Nucleation Using a Coarse-Grained Model. Biophys J 2020; 119:553-566. [PMID: 32668234 DOI: 10.1016/j.bpj.2020.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the Cα atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, x-ray diffraction, and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at an angle with respect to the polymerizable bound structure, and the angle range depended on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G-actin form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to the antiparallel (lower) dimer. Individual monomers bound each other in a short-pitch helix complex in addition to other configurations, with several of them apparently nonproductive for polymerization. Simulations with multiple monomers in the F-actin form show assembly into filaments as well as transient aggregates at the barbed end. We discuss the implications of these observations on the kinetic pathway of actin filament nucleation and polymerization and possibilities for future improvements of the coarse-grained model.
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Affiliation(s)
- Brandon G Horan
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
| | - Aaron R Hall
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania
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14
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Consolati T, Locke J, Roostalu J, Chen ZA, Gannon J, Asthana J, Lim WM, Martino F, Cvetkovic MA, Rappsilber J, Costa A, Surrey T. Microtubule Nucleation Properties of Single Human γTuRCs Explained by Their Cryo-EM Structure. Dev Cell 2020; 53:603-617.e8. [PMID: 32433913 PMCID: PMC7280788 DOI: 10.1016/j.devcel.2020.04.019] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/21/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022]
Abstract
The γ-tubulin ring complex (γTuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. We purified human γTuRC and measured its nucleation properties in a total internal reflection fluorescence (TIRF) microscopy-based real-time nucleation assay. We find that γTuRC stably caps the minus ends of microtubules that it nucleates stochastically. Nucleation is inefficient compared with microtubule elongation. The 4 Å resolution cryoelectron microscopy (cryo-EM) structure of γTuRC, combined with crosslinking mass spectrometry analysis, reveals an asymmetric conformation with only part of the complex in a "closed" conformation matching the microtubule geometry. Actin in the core of the complex, and MZT2 at the outer perimeter of the closed part of γTuRC appear to stabilize the closed conformation. The opposite side of γTuRC is in an "open," nucleation-incompetent conformation, leading to a structural asymmetry explaining the low nucleation efficiency of purified human γTuRC. Our data suggest possible regulatory mechanisms for microtubule nucleation by γTuRC closure.
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Affiliation(s)
- Tanja Consolati
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Julia Locke
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Zhuo Angel Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Julian Gannon
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jayant Asthana
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Wei Ming Lim
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Alessandro Costa
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain; ICREA, Passeig de Lluis Companys 23, 08010 Barcelona, Spain.
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15
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Das S, Ge P, Oztug Durer ZA, Grintsevich EE, Zhou ZH, Reisler E. D-loop Dynamics and Near-Atomic-Resolution Cryo-EM Structure of Phalloidin-Bound F-Actin. Structure 2020; 28:586-593.e3. [PMID: 32348747 DOI: 10.1016/j.str.2020.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/28/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022]
Abstract
Detailed molecular information on G-actin assembly into filaments (F-actin), and their structure, dynamics, and interactions, is essential for understanding their cellular functions. Previous studies indicate that a flexible DNase I binding loop (D-loop, residues 40-50) plays a major role in actin's conformational dynamics. Phalloidin, a "gold standard" for actin filament staining, stabilizes them and affects the D-loop. Using disulfide crosslinking in yeast actin D-loop mutant Q41C/V45C, light-scattering measurements, and cryoelectron microscopy reconstructions, we probed the constraints of D-loop dynamics and its contribution to F-actin formation/stability. Our data support a model of residues 41-45 distances that facilitate G- to F-actin transition. We report also a 3.3-Å resolution structure of phalloidin-bound F-actin in the ADP-Pi-like (ADP-BeFx) state. This shows the phalloidin-binding site on F-actin and how the relative movement between its two protofilaments is restricted by it. Together, our results provide molecular details of F-actin structure and D-loop dynamics.
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Affiliation(s)
- Sanchaita Das
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA
| | - Peng Ge
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA 90095, USA
| | - Zeynep A Oztug Durer
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA
| | - Elena E Grintsevich
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA
| | - Z Hong Zhou
- California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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16
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Zheng Y, Zhang X, Li H. Molecular basis for histidine N3-specific methylation of actin H73 by SETD3. Cell Discov 2020; 6:3. [PMID: 31993215 PMCID: PMC6971037 DOI: 10.1038/s41421-019-0135-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/14/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Yihui Zheng
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Xingrun Zhang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084 China
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17
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Wieczorek M, Urnavicius L, Ti SC, Molloy KR, Chait BT, Kapoor TM. Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex. Cell 2020; 180:165-175.e16. [PMID: 31862189 PMCID: PMC7027161 DOI: 10.1016/j.cell.2019.12.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/21/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022]
Abstract
The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the native human γ-TuRC at ∼3.8 Å resolution, revealing an asymmetric, cone-shaped structure. Pseudo-atomic models indicate that GCP4, GCP5, and GCP6 form distinct Y-shaped assemblies that structurally mimic GCP2/GCP3 subcomplexes distal to the γ-TuRC "seam." We also identify an unanticipated structural bridge that includes an actin-like protein and spans the γ-TuRC lumen. Despite its asymmetric architecture, the γ-TuRC arranges γ-tubulins into a helical geometry poised to nucleate microtubules. Diversity in the γ-TuRC subunits introduces large (>100,000 Å2) surfaces in the complex that allow for interactions with different regulatory factors. The observed compositional complexity of the γ-TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g., within biological condensates or alongside existing filaments.
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Affiliation(s)
- Michal Wieczorek
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Linas Urnavicius
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Laboratory of Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shih-Chieh Ti
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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18
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Merino F, Pospich S, Raunser S. Towards a structural understanding of the remodeling of the actin cytoskeleton. Semin Cell Dev Biol 2019; 102:51-64. [PMID: 31836290 PMCID: PMC7221352 DOI: 10.1016/j.semcdb.2019.11.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/03/2022]
Abstract
Actin filaments (F-actin) are a key component of eukaryotic cells. Whether serving as a scaffold for myosin or using their polymerization to push onto cellular components, their function is always related to force generation. To control and fine-tune force production, cells have a large array of actin-binding proteins (ABPs) dedicated to control every aspect of actin polymerization, filament localization, and their overall mechanical properties. Although great advances have been made in our biochemical understanding of the remodeling of the actin cytoskeleton, the structural basis of this process is still being deciphered. In this review, we summarize our current understanding of this process. We outline how ABPs control the nucleation and disassembly, and how these processes are affected by the nucleotide state of the filaments. In addition, we highlight recent advances in the understanding of actomyosin force generation, and describe recent advances brought forward by the developments of electron cryomicroscopy.
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Affiliation(s)
- Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sabrina Pospich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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19
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Kumpula EP, Lopez AJ, Tajedin L, Han H, Kursula I. Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation. PLoS Biol 2019; 17:e3000315. [PMID: 31199804 PMCID: PMC6599135 DOI: 10.1371/journal.pbio.3000315] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/28/2019] [Accepted: 05/23/2019] [Indexed: 11/18/2022] Open
Abstract
Plasmodium actins form very short filaments and have a noncanonical link between ATP hydrolysis and polymerization. Long filaments are detrimental to the parasites, but the structural factors constraining Plasmodium microfilament lengths have remained unknown. Using high-resolution crystallography, we show that magnesium binding causes a slight flattening of the Plasmodium actin I monomer, and subsequent phosphate release results in a more twisted conformation. Thus, the Mg-bound monomer is closer in conformation to filamentous (F) actin than the Ca form, and this likely facilitates polymerization. A coordinated potassium ion resides in the active site during hydrolysis and leaves together with the phosphate, a process governed by the position of the Arg178/Asp180-containing A loop. Asp180 interacts with either Lys270 or His74, depending on the protonation state of the histidine, while Arg178 links the inner and outer domains (ID and OD) of the actin protomer. Hence, the A loop acts as a switch between stable and unstable filament conformations, the latter leading to fragmentation. Our data provide a comprehensive model for polymerization, ATP hydrolysis and phosphate release, and fragmentation of parasite microfilaments. Similar mechanisms may well exist in canonical actins, although fragmentation is much less favorable due to several subtle sequence differences as well as the methylation of His73, which is absent on the corresponding His74 in Plasmodium actin I. A detailed mechanistic study of malaria parasite actins reveals at the atomic level how they polymerize, hydrolyze ATP, and are fragmented to keep actin filament lengths short enough for parasite survival.
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Affiliation(s)
- Esa-Pekka Kumpula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Andrea J. Lopez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Leila Tajedin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Huijong Han
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- European XFEL GmbH, Schenefeld, Germany
| | - Inari Kursula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
- European XFEL GmbH, Schenefeld, Germany
- * E-mail:
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20
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Chou SZ, Pollard TD. Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides. Proc Natl Acad Sci U S A 2019; 116:4265-4274. [PMID: 30760599 PMCID: PMC6410863 DOI: 10.1073/pnas.1807028115] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We used cryo-electron microscopy (cryo-EM) to reconstruct actin filaments with bound AMPPNP (β,γ-imidoadenosine 5'-triphosphate, an ATP analog, resolution 3.1 Å), ADP-Pi (ADP with inorganic phosphate, resolution 3.1 Å), or ADP (resolution 3.6 Å). Subunits in the three filaments have similar backbone conformations, so assembly rather than ATP hydrolysis or phosphate dissociation is responsible for their flattened conformation in filaments. Polymerization increases the rate of ATP hydrolysis by changing the positions of the side chains of Q137 and H161 in the active site. Flattening during assembly also promotes interactions along both the long-pitch and short-pitch helices. In particular, conformational changes in subdomain 3 open up multiple favorable interactions with the DNase-I binding loop in subdomain 2 of the adjacent subunit. Subunits at the barbed end of the filament are likely to be in this favorable conformation, while monomers are not. This difference explains why filaments grow faster at the barbed end than the pointed end. When phosphate dissociates from ADP-Pi-actin through a backdoor channel, the conformation of the C terminus changes so it distorts the DNase binding loop, which allows cofilin binding, and a network of interactions among S14, H73, G74, N111, R177, and G158 rearranges to open the phosphate release site.
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Affiliation(s)
- Steven Z Chou
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | - Thomas D Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103
- Department of Cell Biology, Yale University, New Haven, CT 06520-8103
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21
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Nucleotide-dependent conformational changes in the actin filament: Subtler than expected. Proc Natl Acad Sci U S A 2019; 116:3959-3961. [PMID: 30782816 DOI: 10.1073/pnas.1900799116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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Aydin F, Katkar HH, Voth GA. Multiscale simulation of actin filaments and actin-associated proteins. Biophys Rev 2018; 10:1521-1535. [PMID: 30382557 PMCID: PMC6297090 DOI: 10.1007/s12551-018-0474-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/21/2018] [Indexed: 02/04/2023] Open
Abstract
Actin is an important cytoskeletal protein that serves as a building block to form filament networks that span across the cell. These networks are orchestrated by a myriad of other cytoskeletal entities including the unbranched filament-forming protein formin and branched network-forming protein complex Arp2/3. Computational models have been able to provide insights into many important structural transitions that are involved in forming these networks, and into the nature of interactions essential for actin filament formation and for regulating the behavior of actin-associated proteins. In this review, we summarize a subset of such models that focus on the atomistic features and those that can integrate atomistic features into a larger picture in a multiscale fashion.
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Affiliation(s)
- Fikret Aydin
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Harshwardhan H Katkar
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Gregory A Voth
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA.
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23
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Fujiwara I, Takeda S, Oda T, Honda H, Narita A, Maéda Y. Polymerization and depolymerization of actin with nucleotide states at filament ends. Biophys Rev 2018; 10:1513-1519. [PMID: 30460458 PMCID: PMC6297080 DOI: 10.1007/s12551-018-0483-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/09/2018] [Indexed: 01/20/2023] Open
Abstract
Polymerization induces hydrolysis of ATP bound to actin, followed by γ-phosphate release, which helps advance the disassembly of actin filaments into ADP-G-actin. Mechanical understanding of this correlation between actin assembly and ATP hydrolysis has been an object of intensive studies in biochemistry and structural biology for many decades. Although actin polymerization and depolymerization occur only at either the barbed or pointed ends and the kinetic and equilibrium properties are substantially different from each other, characterizing their properties is difficult to do by bulk assays, as these assays report the average of all actin filaments in solution and are therefore not able to discern the properties of individual actin filaments. Biochemical studies of actin polymerization and hydrolysis were hampered by these inherent properties of actin filaments. Total internal reflection fluorescence (TIRF) microscopy overcame this problem by observing single actin filaments. With TIRF, we now know not only that each end has distinct properties, but also that the rate of γ-phosphate release is much faster from the terminals than from the interior of actin filaments. The rate of γ-phosphate release from actin filament ends is even more accelerated when latrunculin A is bound. These findings highlight the importance of resolving structural differences between actin molecules in the interior of the filament and those at either filament end. This review provides a history of observing actin filaments under light microscopy, an overview of dynamic properties of ATP hydrolysis at the end of actin filament, and structural views of γ-phosphate release.
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Affiliation(s)
- Ikuko Fujiwara
- Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan.
| | - Shuichi Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Toshiro Oda
- Faculty of Health and Welfare, Tokai Gakuin University, Nakakirino-cyo 5-68, Kakamigahara, Gifu, 504-8511, Japan
| | - Hajime Honda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yuichiro Maéda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Toyota Physical and Chemical Research Institute, 41-1, Yokomichi, Nagakute, Aichi, 480-1192, Japan
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24
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Katkar HH, Davtyan A, Durumeric AEP, Hocky GM, Schramm AC, De La Cruz EM, Voth GA. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophys J 2018; 115:1589-1602. [PMID: 30249402 PMCID: PMC6260209 DOI: 10.1016/j.bpj.2018.08.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
Actin filaments continually assemble and disassemble within a cell. Assembled filaments "age" as a bound nucleotide ATP within each actin subunit quickly hydrolyzes followed by a slower release of the phosphate Pi, leaving behind a bound ADP. This subtle change in nucleotide state of actin subunits affects filament rigidity as well as its interactions with binding partners. We present here a systematic multiscale ultra-coarse-graining approach that provides a computationally efficient way to simulate a long actin filament undergoing ATP hydrolysis and phosphate-release reactions while systematically taking into account available atomistic details. The slower conformational changes and their dependence on the chemical reactions are simulated with the ultra-coarse-graining model by assigning internal states to the coarse-grained sites. Each state is represented by a unique potential surface of a local heterogeneous elastic network. Internal states undergo stochastic transitions that are coupled to conformations of the underlying molecular system. The model reproduces mechanical properties of the filament and allows us to study whether conformational fluctuations in actin subunits produce cooperative filament aging. We find that the nucleotide states of neighboring subunits modulate the reaction kinetics, implying cooperativity in ATP hydrolysis and Pi release. We further systematically coarse grain the system into a Markov state model that incorporates assembly and disassembly, facilitating a direct comparison with previously published models. We find that cooperativity in ATP hydrolysis and Pi release significantly affects the filament growth dynamics only near the critical G-actin concentration, whereas far from it, both cooperative and random mechanisms show similar growth dynamics. In contrast, filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights, to our knowledge, into the cooperative nature of ATP hydrolysis and Pi release and the implications it has for actin filament properties, providing novel predictions for future experimental studies.
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Affiliation(s)
- Harshwardhan H Katkar
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Aram Davtyan
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Aleksander E P Durumeric
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Glen M Hocky
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois
| | - Anthony C Schramm
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, Illinois.
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25
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Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM. Nat Struct Mol Biol 2018; 25:528-537. [PMID: 29867215 DOI: 10.1038/s41594-018-0074-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/02/2018] [Indexed: 11/08/2022]
Abstract
The function of actin is coupled to the nucleotide bound to its active site. ATP hydrolysis is activated during polymerization; a delay between hydrolysis and inorganic phosphate (Pi) release results in a gradient of ATP, ADP-Pi and ADP along actin filaments (F-actin). Actin-binding proteins can recognize F-actin's nucleotide state, using it as a local 'age' tag. The underlying mechanism is complex and poorly understood. Here we report six high-resolution cryo-EM structures of F-actin from rabbit skeletal muscle in different nucleotide states. The structures reveal that actin polymerization repositions the proposed catalytic base, His161, closer to the γ-phosphate. Nucleotide hydrolysis and Pi release modulate the conformational ensemble at the periphery of the filament, thus resulting in open and closed states, which can be sensed by coronin-1B. The drug-like toxin jasplakinolide locks F-actin in an open state. Our results demonstrate in detail how ATP hydrolysis links to F-actin's conformational dynamics and protein interaction.
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26
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Conti J, Viola MG, Camberg JL. FtsA reshapes membrane architecture and remodels the Z-ring in Escherichia coli. Mol Microbiol 2018; 107:558-576. [PMID: 29280220 DOI: 10.1111/mmi.13902] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 12/14/2017] [Accepted: 12/17/2017] [Indexed: 12/20/2022]
Abstract
Cell division in prokaryotes initiates with assembly of the Z-ring at midcell, which, in Escherichia coli, is tethered to the inner leaflet of the cytoplasmic membrane through a direct interaction with FtsA, a widely conserved actin homolog. The Z-ring is comprised of polymers of tubulin-like FtsZ and has been suggested to provide the force for constriction. Here, we demonstrate that FtsA exerts force on membranes causing redistribution of membrane architecture, robustly hydrolyzes ATP and directly engages FtsZ polymers in a reconstituted system. Phospholipid reorganization by FtsA occurs rapidly and is mediated by insertion of a C-terminal membrane targeting sequence (MTS) into the bilayer and further promoted by a nucleotide-dependent conformational change relayed to the MTS. FtsA also recruits FtsZ to phospholipid vesicles via a direct interaction with the FtsZ C-terminus and regulates FtsZ assembly kinetics. These results implicate the actin homolog FtsA in establishment of a Z-ring scaffold, while directly remodeling the membrane and provide mechanistic insight into localized cell wall remodeling, invagination and constriction at the onset of division.
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Affiliation(s)
| | | | - Jodi L Camberg
- Departments of Cell and Molecular Biology.,Nutrition and Food Sciences, The University of Rhode Island, Kingston, RI 02881, USA
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27
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Tikhomirova TS, Ievlev RS, Suvorina MY, Bobyleva LG, Vikhlyantsev IM, Surin AK, Galzitskaya OV. Search for Functionally Significant Motifs and Amino Acid Residues of Actin. Mol Biol 2018. [DOI: 10.1134/s0026893318010193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Therapeutic Potentials of Synapses after Traumatic Brain Injury: A Comprehensive Review. Neural Plast 2017; 2017:4296075. [PMID: 28491479 PMCID: PMC5405590 DOI: 10.1155/2017/4296075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/09/2017] [Accepted: 03/14/2017] [Indexed: 12/26/2022] Open
Abstract
Massive studies have focused on the understanding of the pathobiology of cellular and molecular changes and injury mechanisms after traumatic brain injury (TBI), but very few studies have specially discussed the role of synapses in the context of TBI. This paper specifically highlights the role and therapeutic potentials of synapses after TBI. First, we review and conclude how synapses interact with constant structural, metabolic, neuroendocrine, and inflammatory mechanisms after TBI. Second, we briefly describe several key synaptic proteins involved in neuroplasticity, which may be novel neuronal targets for specific intervention. Third, we address therapeutic interventions in association with synapses after TBI. Finally, we concisely discuss the study gaps in the synapses after TBI, in hopes that this would provide more insights for future studies. Synapses play an important role in TBI; while the understandings on the synaptic participation in the treatments and prognosis of TBI are lacking, more studies in this area are warranted.
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29
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Sun R, Sode O, Dama JF, Voth GA. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics. J Chem Theory Comput 2017; 13:2332-2341. [PMID: 28345907 PMCID: PMC5425946 DOI: 10.1021/acs.jctc.7b00077] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from computationally demanding electronic structure calculations such as QM/MM simulations. Therefore, the combination of QM/MM molecular dynamics with the recently developed transition-tempered metadynamics (TTMetaD), an enhanced sampling method that can provide a high-quality free energy estimate at an early stage in a simulation, is an ideal approach to address the biomolecular nucleoside triphosphate hydrolysis problem. In this work the ATP hydrolysis process in monomeric and filamentous actin is studied as an example application of the combined methodology. The performance of TTMetaD in these demanding QM/MM simulations is compared with that of the more conventional well-tempered metadynamics (WTMetaD). Our results show that TTMetaD exhibits much better exploration of the hydrolysis reaction free energy surface in two key collective variables (CVs) during the early stages of the QM/MM simulation than does WTMetaD. The TTMetaD simulations also reveal that a key third degree of freedom, the O-H bond-breaking and proton transfer from the lytic water, must be biased for TTMetaD to converge fully. To perturb the NTP hydrolysis dynamics to the least extent and to properly focus the MetaD free energy sampling, we also adopt here the recently developed metabasin metadynamics (MBMetaD) to construct a self-limiting bias potential that only applies to the lytic water after its nucleophilic attack of the phosphate of ATP. With these new, state-of-the-art enhanced sampling metadynamics techniques, we present an effective and accurate computational strategy for combining QM/MM molecular dynamics simulation with free energy sampling methodology, including a means to analyze the convergence of the calculations through robust numerical criteria.
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Affiliation(s)
- Rui Sun
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Olaseni Sode
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - James F Dama
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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30
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Deville C, Girard-Blanc C, Assrir N, Nhiri N, Jacquet E, Bontems F, Renault L, Petres S, van Heijenoort C. Mutations in actin used for structural studies partially disrupt β-thymosin/WH2 domains interaction. FEBS Lett 2016; 590:3690-3699. [PMID: 27680677 DOI: 10.1002/1873-3468.12423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 11/10/2022]
Abstract
Understanding the structural basis of actin cytoskeleton remodeling requires stabilization of actin monomers, oligomers, and filaments in complex with partner proteins, using various biochemical strategies. Here, we report a dramatic destabilization of the dynamic interaction with a model β-thymosin/WH2 domain induced by mutations in actin. This result underlines that mutant actins should be used with prudence to characterize interactions with intrinsically disordered partners as destabilization of dynamic interactions, although identifiable by NMR, may be invisible to other structural techniques. It also highlights how both β-thymosin/WH2 domains and actin tune local structure and dynamics in regulatory processes involving intrinsically disordered domains.
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Affiliation(s)
- Célia Deville
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Nadine Assrir
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Naïma Nhiri
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Eric Jacquet
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - François Bontems
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Louis Renault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Carine van Heijenoort
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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31
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Kudryashov DS, Reisler E. ATP and ADP actin states. Biopolymers 2016; 99:245-56. [PMID: 23348672 DOI: 10.1002/bip.22155] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/07/2012] [Indexed: 11/06/2022]
Abstract
This minireview is dedicated to the memory of Henryk Eisenberg and honors his major contributions to many areas of biophysics and to the analysis of macromolecular states and interactions in particular. This work reviews the ATP and ADP states of a ubiquitous protein, actins, and considers the present evidence for and against unique, nucleotide-dependent conformations of this protein. The effects of ATP and ADP on specific structural elements of actins, its loops and clefts, as revealed by mutational, crosslinking, spectroscopic, and EPR methods are discussed. It is concluded that the existing evidence points to dynamic equilibria of these structural elements among various conformational states in both ATP- and ADP-actins, with the nucleotides impacting the equilibria distributions.
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Affiliation(s)
- Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, the Ohio State University, Columbus, OH 43210.
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32
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Abstract
Seven decades of research have revealed much about actin structure, assembly, regulatory proteins, and cellular functions. However, some key information is still missing, so we do not understand the mechanisms of most processes that depend on actin. This chapter summarizes our current knowledge and explains some examples of work that will be required to fill these gaps and arrive at a mechanistic understanding of actin biology.
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Affiliation(s)
- Thomas D Pollard
- Department of Molecular Cellular and Developmental Biology, Yale University, 208103, New Haven, CT, 06520-8103, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, 208103, New Haven, CT, 06520-8103, USA. .,Department of Cell Biology, Yale University, 208103, New Haven, CT, 06520-8103, USA.
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33
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Mechanisms of leiomodin 2-mediated regulation of actin filament in muscle cells. Proc Natl Acad Sci U S A 2015; 112:12687-92. [PMID: 26417072 DOI: 10.1073/pnas.1512464112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Leiomodin (Lmod) is a class of potent tandem-G-actin-binding nucleators in muscle cells. Lmod mutations, deletion, or instability are linked to lethal nemaline myopathy. However, the lack of high-resolution structures of Lmod nucleators in action severely hampered our understanding of their essential cellular functions. Here we report the crystal structure of the actin-Lmod2162-495 nucleus. The structure contains two actin subunits connected by one Lmod2162-495 molecule in a non-filament-like conformation. Complementary functional studies suggest that the binding of Lmod2 stimulates ATP hydrolysis and accelerates actin nucleation and polymerization. The high level of conservation among Lmod proteins in sequence and functions suggests that the mechanistic insights of human Lmod2 uncovered here may aid in a molecular understanding of other Lmod proteins. Furthermore, our structural and mechanistic studies unraveled a previously unrecognized level of regulation in mammalian signal transduction mediated by certain tandem-G-actin-binding nucleators.
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34
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Clark L, Zahm JA, Ali R, Kukula M, Bian L, Patrie SM, Gardner KH, Rosen MK, Rosenbaum DM. Methyl labeling and TROSY NMR spectroscopy of proteins expressed in the eukaryote Pichia pastoris. JOURNAL OF BIOMOLECULAR NMR 2015; 62:239-45. [PMID: 26025061 PMCID: PMC4496254 DOI: 10.1007/s10858-015-9939-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/27/2015] [Indexed: 05/03/2023]
Abstract
(13)C Methyl TROSY NMR spectroscopy has emerged as a powerful method for studying the dynamics of large systems such as macromolecular assemblies and membrane proteins. Specific (13)C labeling of aliphatic methyl groups and perdeuteration has been limited primarily to proteins expressed in E. coli, preventing studies of many eukaryotic proteins of physiological and biomedical significance. We demonstrate the feasibility of efficient (13)C isoleucine δ1-methyl labeling in a deuterated background in an established eukaryotic expression host, Pichia pastoris, and show that this method can be used to label the eukaryotic protein actin, which cannot be expressed in bacteria. This approach will enable NMR studies of previously intractable targets.
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Affiliation(s)
- Lindsay Clark
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas TX 75390 USA
| | - Jacob A. Zahm
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas TX 75390 USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Rustam Ali
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas TX 75390 USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Maciej Kukula
- Shimadzu Center for Advanced Analytical Chemistry, University of Texas at Arlington, Arlington TX 76019 USA
| | - Liangqiao Bian
- Shimadzu Center for Advanced Analytical Chemistry, University of Texas at Arlington, Arlington TX 76019 USA
| | - Steven M. Patrie
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas TX 75390 USA
| | - Kevin H. Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Michael K. Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas TX 75390 USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Daniel M. Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas TX 75390 USA
- Corresponding Author
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35
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Galkin VE, Orlova A, Vos MR, Schröder GF, Egelman EH. Near-atomic resolution for one state of F-actin. Structure 2014; 23:173-182. [PMID: 25533486 DOI: 10.1016/j.str.2014.11.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 11/03/2014] [Accepted: 11/14/2014] [Indexed: 01/15/2023]
Abstract
Actin functions as a helical polymer, F-actin, but attempts to build an atomic model for this filament have been hampered by the fact that the filament cannot be crystallized and by structural heterogeneity. We have used a direct electron detector, cryo-electron microscopy, and the forces imposed on actin filaments in thin films to reconstruct one state of the filament at 4.7 Å resolution, which allows for building a reliable pseudo-atomic model of F-actin. We also report a different state of the filament where actin protomers adopt a conformation observed in the crystal structure of the G-actin-profilin complex with an open ATP-binding cleft. Comparison of the two structural states provides insights into ATP-hydrolysis and filament dynamics. The atomic model provides a framework for understanding why every buried residue in actin has been under intense selective pressure.
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Affiliation(s)
- Vitold E Galkin
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
| | - Albina Orlova
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908-0733, USA
| | - Matthijn R Vos
- FEI Company, Nanoport Europe, 5651 GG Eindhoven, the Netherlands
| | - Gunnar F Schröder
- Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908-0733, USA.
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36
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Nucleotide regulation of the structure and dynamics of G-actin. Biophys J 2014; 106:1710-20. [PMID: 24739170 DOI: 10.1016/j.bpj.2014.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/17/2014] [Accepted: 03/06/2014] [Indexed: 11/24/2022] Open
Abstract
Actin, a highly conserved cytoskeletal protein found in all eukaryotic cells, facilitates cell motility and membrane remodeling via a directional polymerization cycle referred to as treadmilling. The nucleotide bound at the core of each actin subunit regulates this process. Although the biochemical kinetics of treadmilling has been well characterized, the atomistic details of how the nucleotide affects polymerization remain to be definitively determined. There is increasing evidence that the nucleotide regulation (and other characteristics) of actin cannot be fully described from the minimum energy structure, but rather depends on a dynamic equilibrium between conformations. In this work we explore the conformational mobility of the actin monomer (G-actin) in a coarse-grained subspace using umbrella sampling to bias all-atom molecular-dynamics simulations along the variables of interest. The results reveal that ADP-bound actin subunits are more conformationally mobile than ATP-bound subunits. We used a multiscale analysis method involving coarse-grained and atomistic representations of these simulations to characterize how the nucleotide affects the low-energy states of these systems. The interface between subdomains SD2-SD4, which is important for polymerization, is stabilized in an actin filament-like (F-actin) conformation in ATP-bound G-actin. Additionally, the nucleotide modulates the conformation of the SD1-SD3 interface, a region involved in the binding of several actin-binding proteins.
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37
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Robust and low cost uniform 15N-labeling of proteins expressed in Drosophila S2 cells and Spodoptera frugiperda Sf9 cells for NMR applications. J Struct Biol 2014; 188:71-8. [DOI: 10.1016/j.jsb.2014.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/15/2014] [Accepted: 08/15/2014] [Indexed: 12/11/2022]
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38
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McCullagh M, Saunders MG, Voth GA. Unraveling the mystery of ATP hydrolysis in actin filaments. J Am Chem Soc 2014; 136:13053-8. [PMID: 25181471 PMCID: PMC4183606 DOI: 10.1021/ja507169f] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Actin
performs its myriad cellular functions by the growth and
disassembly of its filamentous form. The hydrolysis of ATP in the
actin filament has been shown to modulate properties of the filament,
thus making it a pivotal regulator of the actin life cycle. Actin
has evolved to selectively hydrolyze ATP in the filamentous form,
F-actin, with an experimentally observed rate increase over the monomeric
form, G-actin, of 4.3 × 104. The cause of this dramatic
increase in rate is investigated in this paper using extensive QM/MM
simulations of both G- and F-actin. To compute the free energy of
hydrolysis in both systems, metadynamics is employed along two collective
variables chosen to describe the reaction coordinates of hydrolysis.
F-actin is modeled as a monomer with restraints applied to coarse-grained
variables enforced to keep it in a filament-like conformation. The
simulations reveal a barrier height reduction for ATP hydrolysis in
F-actin as compared to G-actin of 8 ± 1 kcal/mol, in good agreement
with the experimentally measured barrier height reduction of 7 ±
1 kcal/mol. The barrier height reduction is influenced by an enhanced
rotational diffusion of water in F-actin as compared to G-actin and
shorter water wires between Asp154 and the nucleophilic water in F-actin,
leading to more rapid proton transport.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States
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39
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Rao JN, Madasu Y, Dominguez R. Mechanism of actin filament pointed-end capping by tropomodulin. Science 2014; 345:463-7. [PMID: 25061212 DOI: 10.1126/science.1256159] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteins that cap the ends of the actin filament are essential regulators of cytoskeleton dynamics. Whereas several proteins cap the rapidly growing barbed end, tropomodulin (Tmod) is the only protein known to cap the slowly growing pointed end. The lack of structural information severely limits our understanding of Tmod's capping mechanism. We describe crystal structures of actin complexes with the unstructured amino-terminal and the leucine-rich repeat carboxy-terminal domains of Tmod. The structures and biochemical analysis of structure-inspired mutants showed that one Tmod molecule interacts with three actin subunits at the pointed end, while also contacting two tropomyosin molecules on each side of the filament. We found that Tmod achieves high-affinity binding through several discrete low-affinity interactions, which suggests a mechanism for controlled subunit exchange at the pointed end.
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Affiliation(s)
- Jampani Nageswara Rao
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yadaiah Madasu
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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40
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Pereira JH, Petchprayoon C, Hoepker AC, Moriarty NW, Fink SJ, Cecere G, Paterson I, Adams PD, Marriott G. Structural and biochemical studies of actin in complex with synthetic macrolide tail analogues. ChemMedChem 2014; 9:2286-93. [PMID: 25047814 DOI: 10.1002/cmdc.201402150] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 11/12/2022]
Abstract
The actin filament-binding and filament-severing activities of the aplyronine, kabiramide, and reidispongiolide families of marine macrolides are located within the hydrophobic tail region of the molecule. Two synthetic tail analogues of aplyronine C (SF-01 and GC-04) are shown to bind to G-actin with dissociation constants of (285±33) and (132±13) nM, respectively. The crystal structures of actin complexes with GC-04, SF-01, and kabiramide C reveal a conserved mode of tail binding within the cleft that forms between subdomains (SD) 1 and 3. Our studies support the view that filament severing is brought about by specific binding of the tail region to the SD1/SD3 cleft on the upper protomer, which displaces loop-D from the lower protomer on the same half-filament. With previous studies showing that the GC-04 analogue can sever actin filaments, it is argued that the shorter complex lifetime of tail analogues with F-actin would make them more effective at severing filaments compared with plasma gelsolin. Structure-based analyses are used to suggest more reactive or targetable forms of GC-04 and SF-01, which may serve to boost the capacity of the serum actin scavenging system, to generate antibody conjugates against tumor cell antigens, and to decrease sputum viscosity in children with cystic fibrosis.
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Affiliation(s)
- Jose H Pereira
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA)
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41
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Kang H, Bradley MJ, Elam WA, De La Cruz EM. Regulation of actin by ion-linked equilibria. Biophys J 2013; 105:2621-8. [PMID: 24359734 PMCID: PMC3882474 DOI: 10.1016/j.bpj.2013.10.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 10/25/2013] [Accepted: 10/29/2013] [Indexed: 11/22/2022] Open
Abstract
Actin assembly, filament mechanical properties, and interactions with regulatory proteins depend on the types and concentrations of salts in solution. Salts modulate actin through both nonspecific electrostatic effects and specific binding to discrete sites. Multiple cation-binding site classes spanning a broad range of affinities (nanomolar to millimolar) have been identified on actin monomers and filaments. This review focuses on discrete, low-affinity cation-binding interactions that drive polymerization, regulate filament-bending mechanics, and modulate interactions with regulatory proteins. Cation binding may be perturbed by actin post-translational modifications and linked equilibria. Partial cation occupancy under physiological and commonly used in vitro solution conditions likely contribute to filament mechanical heterogeneity and structural polymorphism. Site-specific cation-binding residues are conserved in Arp2 and Arp3, and may play a role in Arp2/3 complex activation and actin-filament branching activity. Actin-salt interactions demonstrate the relevance of ion-linked equilibria in the operation and regulation of complex biological systems.
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Affiliation(s)
- Hyeran Kang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Michael J Bradley
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - W Austin Elam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
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42
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Kapoor P, Shen X. Mechanisms of nuclear actin in chromatin-remodeling complexes. Trends Cell Biol 2013; 24:238-46. [PMID: 24246764 DOI: 10.1016/j.tcb.2013.10.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 10/04/2013] [Accepted: 10/22/2013] [Indexed: 10/26/2022]
Abstract
The mystery of nuclear actin has puzzled biologists for decades largely due to the lack of defined experimental systems. However, the development of actin-containing chromatin-modifying complexes as a defined genetic and biochemical system in the past decade has provided an unprecedented opportunity to dissect the mechanism of actin in the nucleus. Although the established functions of actin mostly rely on its dynamic polymerization, the novel finding of the mechanism of action of actin in the INO80 chromatin-remodeling complex suggests a conceptually distinct mode of actin that functions as a monomer. In this review we highlight the new paradigm and discuss how actin interaction with chromatin suggests a fundamental divergence between conventional cytoplasmic actin and nuclear actin. Furthermore, we provide how this framework could be applied to investigations of nuclear actin in other actin-containing chromatin-modifying complexes.
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Affiliation(s)
- Prabodh Kapoor
- Department of Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Xuetong Shen
- Department of Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA.
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43
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Bhargav SP, Vahokoski J, Kumpula EP, Kursula I. Crystallization and preliminary structural characterization of the two actin isoforms of the malaria parasite. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1171-6. [PMID: 24100575 PMCID: PMC3792683 DOI: 10.1107/s174430911302441x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 09/02/2013] [Indexed: 11/10/2022]
Abstract
Malaria is a devastating disease caused by apicomplexan parasites of the genus Plasmodium that use a divergent actin-powered molecular motor for motility and invasion. Plasmodium actin differs from canonical actins in sequence, structure and function. Here, the purification, crystallization and secondary-structure analysis of the two Plasmodium actin isoforms are presented. The recombinant parasite actins were folded and could be purified to homogeneity. Plasmodium actins I and II were crystallized in complex with the gelsolin G1 domain; the crystals diffracted to resolutions of 1.19 and 2.2 Å and belonged to space groups P2₁2₁2₁ and P2₁, respectively, each with one complex in the asymmetric unit.
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Affiliation(s)
| | - Juha Vahokoski
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Esa-Pekka Kumpula
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland
- Centre for Structural Systems Biology (CSSB), Helmholtz Centre for Infection Research and German Electron Synchrotron (DESY), Building 25b, Notkestrasse 85, 22607 Hamburg, Germany
| | - Inari Kursula
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland
- Centre for Structural Systems Biology (CSSB), Helmholtz Centre for Infection Research and German Electron Synchrotron (DESY), Building 25b, Notkestrasse 85, 22607 Hamburg, Germany
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44
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Chen X, Ni F, Tian X, Kondrashkina E, Wang Q, Ma J. Structural basis of actin filament nucleation by tandem W domains. Cell Rep 2013; 3:1910-20. [PMID: 23727244 DOI: 10.1016/j.celrep.2013.04.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 03/23/2013] [Accepted: 04/26/2013] [Indexed: 11/17/2022] Open
Abstract
Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mechanism of actin nucleation remains poorly understood. This is hindered largely by the fact that actin nucleus, once formed, rapidly polymerizes into filament, thus making it impossible to capture stable multisubunit actin nucleus. Here, we report an effective double-mutant strategy to stabilize actin nucleus by preventing further polymerization. Employing this strategy, we solved the crystal structure of AMPPNP-actin in complex with the first two tandem W domains of Cordon-bleu (Cobl), a potent actin filament nucleator. Further sequence comparison and functional studies suggest that the nucleation mechanism of Cobl is probably shared by the p53 cofactor JMY, but not Spire. Moreover, the double-mutant strategy opens the way for atomic mechanistic study of actin nucleation and polymerization.
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Affiliation(s)
- Xiaorui Chen
- Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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45
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Sagar A, Peddada N, Solanki AK, Choudhary V, Garg R, Ashish. Visualizing the elusive open shape of G-actin in solution by SAXS data analysis. Biochem Biophys Res Commun 2013; 435:740-4. [PMID: 23707938 DOI: 10.1016/j.bbrc.2013.05.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
Abstract
Though biochemical data upholds that ATP hydrolysis induces an opening of the nucleotide binding cleft, crystal structures of the G-actin in the absence of profillin represent the closed structure, regardless of the bound ATP/ADP. Analysis of small angle X-ray scattering (SAXS) intensities confirmed that ATP hydrolysis increases the radius of gyration (R(G)) and maximum linear dimension (D(max)) of G-actin molecules from 22.3 to 23.7 Ǻ and 70 to 78 Å, respectively. Kratky analysis confirmed that G-actin molecules behave like globular scattering particles regardless of the bound nucleotide state. Shape reconstruction using dummy residues and inertial axes overlay with known crystal structures confirmed that the ATP or AMP-PNP bound G-actin adopts a compact shape, and the nucleotide binding site opens up with ATP hydrolysis. Importantly, our ADP-state model resembled the open shape seen for β-actin and hexokinase.
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Affiliation(s)
- Amin Sagar
- CSIR-Institute of Microbial Technology, Chandigarh, India
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Fan J, Saunders MG, Voth GA. Coarse-graining provides insights on the essential nature of heterogeneity in actin filaments. Biophys J 2013; 103:1334-42. [PMID: 22995506 DOI: 10.1016/j.bpj.2012.08.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/21/2012] [Accepted: 08/08/2012] [Indexed: 10/27/2022] Open
Abstract
Experiments have shown that actin is structurally polymorphic, but knowledge of the details of molecular level heterogeneity in both the dynamics of a single subunit and the interactions between subunits is still lacking. Here, using atomistic molecular dynamics simulations of the actin filament, we identify domains of atoms that move in a correlated fashion, quantify interactions between these domains using coarse-grained (CG) analysis methods, and perform CG simulations to explore the importance of filament heterogeneity. The persistence length and torsional stiffness calculated from molecular dynamics simulation data agree with experimental values. We additionally observe that distinct actin conformations coexist in actin filaments. The filaments also exhibit random twist angles that are broadly distributed. CG analysis reveals that interactions between equivalent CG pairs vary from one subunit to another. To explore the importance of heterogeneity on filament dynamics, we perform CG simulations using different methods of parameterization to show that only by including heterogeneous interactions can we reproduce the twist angles and related properties. Free energy calculations further suggest that in general the actin filament is best represented as a set of subunits with differing CG sites and interactions, and the incorporating heterogeneity into the CG interactions is more important than including that in the CG sites. Our work therefore presents a systematic method to explore molecular level detail in this large and complex biopolymer.
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Affiliation(s)
- Jun Fan
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, University of Chicago, Chicago, Illinois, USA
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Identification of cation-binding sites on actin that drive polymerization and modulate bending stiffness. Proc Natl Acad Sci U S A 2012; 109:16923-7. [PMID: 23027950 DOI: 10.1073/pnas.1211078109] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The assembly of actin monomers into filaments and networks plays vital roles throughout eukaryotic biology, including intracellular transport, cell motility, cell division, determining cellular shape, and providing cells with mechanical strength. The regulation of actin assembly and modulation of filament mechanical properties are critical for proper actin function. It is well established that physiological salt concentrations promote actin assembly and alter the overall bending mechanics of assembled filaments and networks. However, the molecular origins of these salt-dependent effects, particularly if they involve nonspecific ionic strength effects or specific ion-binding interactions, are unknown. Here, we demonstrate that specific cation binding at two discrete sites situated between adjacent subunits along the long-pitch helix drive actin polymerization and determine the filament bending rigidity. We classify the two sites as "polymerization" and "stiffness" sites based on the effects that mutations at the sites have on salt-dependent filament assembly and bending mechanics, respectively. These results establish the existence and location of the cation-binding sites that confer salt dependence to the assembly and mechanics of actin filaments.
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48
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Durer ZAO, Kudryashov DS, Sawaya MR, Altenbach C, Hubbell W, Reisler E. Structural states and dynamics of the D-loop in actin. Biophys J 2012; 103:930-9. [PMID: 23009842 PMCID: PMC3433612 DOI: 10.1016/j.bpj.2012.07.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 07/09/2012] [Accepted: 07/13/2012] [Indexed: 01/07/2023] Open
Abstract
Conformational changes induced by ATP hydrolysis on actin are involved in the regulation of complex actin networks. Previous structural and biochemical data implicate the DNase I binding loop (D-loop) of actin in such nucleotide-dependent changes. Here, we investigated the structural and conformational states of the D-loop (in solution) using cysteine scanning mutagenesis and site-directed labeling. The reactivity of D-loop cysteine mutants toward acrylodan and the mobility of spin labels on these mutants do not show patterns of an α-helical structure in monomeric and filamentous actin, irrespective of the bound nucleotide. Upon transition from monomeric to filamentous actin, acrylodan emission spectra and electron paramagnetic resonance line shapes of labeled mutants are blue-shifted and more immobilized, respectively, with the central residues (residues 43-47) showing the most drastic changes. Moreover, complex electron paramagnetic resonance line shapes of spin-labeled mutants suggest several conformational states of the D-loop. Together with a new (to our knowledge) actin crystal structure that reveals the D-loop in a unique hairpin conformation, our data suggest that the D-loop equilibrates in F-actin among different conformational states irrespective of the nucleotide state of actin.
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Affiliation(s)
- Zeynep A Oztug Durer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA.
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Gaucher JF, Maugé C, Didry D, Guichard B, Renault L, Carlier MF. Interactions of isolated C-terminal fragments of neural Wiskott-Aldrich syndrome protein (N-WASP) with actin and Arp2/3 complex. J Biol Chem 2012; 287:34646-59. [PMID: 22847007 DOI: 10.1074/jbc.m112.394361] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Wiskott-Aldrich syndrome proteins (WASP) are a family of proteins that all catalyze actin filament branching with the Arp2/3 complex in a variety of actin-based motile processes. The constitutively active C-terminal domain, called VCA, harbors one or more WASP homology 2 (WH2) domains that bind G-actin, whereas the CA extension binds the Arp2/3 complex. The VCA·actin·Arp2/3 entity associates with a mother filament to form a branched junction from which a daughter filament is initiated. The number and function of WH2-bound actin(s) in the branching process are not known, and the stoichiometry of the VCA·actin·Arp2/3 complex is debated. We have expressed the tandem WH2 repeats of N-WASP, either alone (V) or associated with the C (VC) and CA (VCA) extensions. We analyzed the structure of actin in complex with V, VC, and VCA using protein crystallography and hydrodynamic and spectrofluorimetric methods. The partial crystal structure of the VC·actin 1:1 complex shows two actins in the asymmetric unit with extensive actin-actin contacts. In solution, each of the two WH2 domains in V, VC, and VCA binds G-actin in 1:2 complexes that participate in barbed end assembly. V, VC, and VCA enhance barbed end depolymerization like profilin but neither nucleate nor sever filaments, in contrast with other WH2 repeats. VCA binds the Arp2/3 complex in a 1:1 complex even in the presence of a large excess of VCA. VCA·Arp2/3 binds one actin in a latrunculin A-sensitive fashion, in a 1:1:1 complex, indicating that binding of the second actin to VCA is weakened in the ternary complex.
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Affiliation(s)
- Jean-François Gaucher
- Laboratoire de Cristallographie et RMN Biologiques CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
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Abstract
Cofilin/ADF proteins play key roles in the dynamics of actin, one of the most abundant and highly conserved eukaryotic proteins. We used cryoelectron microscopy to generate a 9-Å resolution three-dimensional reconstruction of cofilin-decorated actin filaments, the highest resolution achieved for a complex of F-actin with an actin-binding protein. We show that the cofilin-induced change in the filament twist is due to a unique conformation of the actin molecule unrelated to any previously observed state. The changes between the actin protomer in naked F-actin and in the actin-cofilin filament are greater than the conformational changes between G- and F-actin. Our results show the structural plasticity of actin, suggest that other actin-binding proteins may also induce large but different conformational changes, and show that F-actin cannot be described by a single molecular model.
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