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Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase. Nucleic Acids Res 2024:gkae500. [PMID: 38884215 DOI: 10.1093/nar/gkae500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/11/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The Orthoflavivirus NS3 helicase (NS3h) is crucial in virus replication, representing a potential drug target for pathogenesis. NS3h utilizes nucleotide triphosphate (ATP) for hydrolysis energy to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. Intermediate states along the ATP hydrolysis cycle and conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. Extensive molecular dynamics simulations of West Nile virus NS3h+ssRNA in the apo, ATP, ADP+Pi and ADP bound states were used to model the conformational ensembles along this cycle. Energetic and structural clustering analyses depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). Based on these results, MVIL mutants (D471L, D471N and D471E) were found to have a substantial reduction in ATPase activity and RNA replication compared to the wild-type. Simulations of the mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.
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Affiliation(s)
- Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
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Tu X, Yin S, Zang J, Zhang T, Lv C, Zhao G. Understanding the Role of Filamentous Actin in Food Quality: From Structure to Application. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11885-11899. [PMID: 38747409 DOI: 10.1021/acs.jafc.4c01877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Actin, a multifunctional protein highly expressed in eukaryotes, is widely distributed throughout cells and serves as a crucial component of the cytoskeleton. Its presence is integral to maintaining cell morphology and participating in various biological processes. As an irreplaceable component of myofibrillar proteins, actin, including G-actin and F-actin, is highly related to food quality. Up to now, purification of actin at a moderate level remains to be overcome. In this paper, we have reviewed the structures and functions of actin, the methods to obtain actin, and the relationships between actin and food texture, color, and flavor. Moreover, actin finds applications in diverse fields such as food safety, bioengineering, and nanomaterials. Developing an actin preparation method at the industrial level will help promote its further applications in food science, nutrition, and safety.
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Affiliation(s)
- Xinyi Tu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, People's Republic of China
| | - Shuhua Yin
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, People's Republic of China
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, People's Republic of China
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, People's Republic of China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, People's Republic of China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, People's Republic of China
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Ma Q, Surya W, He D, Yang H, Han X, Nai MH, Lim CT, Torres J, Miao Y. Spa2 remodels ADP-actin via molecular condensation under glucose starvation. Nat Commun 2024; 15:4491. [PMID: 38802374 PMCID: PMC11130202 DOI: 10.1038/s41467-024-48863-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Actin nucleotide-dependent actin remodeling is essential to orchestrate signal transduction and cell adaptation. Rapid energy starvation requires accurate and timely reorganization of the actin network. Despite distinct treadmilling mechanisms of ADP- and ATP-actin filaments, their filament structures are nearly identical. How other actin-binding proteins regulate ADP-actin filament assembly is unclear. Here, we show that Spa2 which is the polarisome scaffold protein specifically remodels ADP-actin upon energy starvation in budding yeast. Spa2 triggers ADP-actin monomer nucleation rapidly through a dimeric core of Spa2 (aa 281-535). Concurrently, the intrinsically disordered region (IDR, aa 1-281) guides Spa2 undergoing phase separation and wetting on the surface of ADP-G-actin-derived F-actin and bundles the filaments. Both ADP-actin-specific nucleation and bundling activities of Spa2 are actin D-loop dependent. The IDR and nucleation core of Spa2 are evolutionarily conserved by coexistence in the fungus kingdom, suggesting a universal adaptation mechanism in the fungal kingdom in response to glucose starvation, regulating ADP-G-actin and ADP-F-actin with high nucleotide homogeneity.
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Affiliation(s)
- Qianqian Ma
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Danxia He
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Hanmeng Yang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Xiao Han
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Mui Hoon Nai
- Department of Biomedical Engineering, National University of Singapore, 117583, Singapore, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, 117583, Singapore, Singapore
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, 119276, Singapore, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore, Singapore.
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Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569434. [PMID: 38077049 PMCID: PMC10705498 DOI: 10.1101/2023.11.30.569434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The flavivirus NS3 helicase (NS3h), a highly conserved protein, plays a pivotal role in virus replication and thus represents a potential drug target for flavivirus pathogenesis. NS3h utilizes nucleotide triphosphate, such as ATP, for hydrolysis energy (ATPase) to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. The intermediate states along the ATP binding and hydrolysis cycle, as well as the conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. We use extensive molecular dynamics simulations of apo, ATP, ADP+Pi, and ADP bound to WNV NS3h+ssRNA to model the conformational ensembles along this cycle. Energetic and structural clustering analyses on these trajectories depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). These findings were experimentally corroborated using viral replicons encoding three mutations at the D471 position. Replication assays using these mutants demonstrated a substantial reduction in viral replication compared to the wild-type. Molecular simulations of the D471 mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.
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Affiliation(s)
- Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
| | - Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
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Oosterheert W, Blanc FEC, Roy A, Belyy A, Sanders MB, Hofnagel O, Hummer G, Bieling P, Raunser S. Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nat Struct Mol Biol 2023; 30:1774-1785. [PMID: 37749275 PMCID: PMC10643162 DOI: 10.1038/s41594-023-01101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/18/2023] [Indexed: 09/27/2023]
Abstract
The release of inorganic phosphate (Pi) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. The mechanisms underlying Pi release from the core and barbed end of actin filaments remain unclear. Here, using human and bovine actin isoforms, we combine cryo-EM with molecular-dynamics simulations and in vitro reconstitution to demonstrate how actin releases Pi through a 'molecular backdoor'. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and opens only transiently through concerted amino acid rearrangements. This explains why Pi escapes rapidly from the filament end but slowly from internal subunits. In a nemaline-myopathy-associated actin variant, the backdoor is predominantly open in filament-core subunits, resulting in accelerated Pi release and filaments with drastically shortened ADP-Pi caps. Our results provide the molecular basis for Pi release from actin and exemplify how a disease-linked mutation distorts the nucleotide-state distribution and atomic structure of the filament.
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Affiliation(s)
- Wout Oosterheert
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Florian E C Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ankit Roy
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alexander Belyy
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Micaela Boiero Sanders
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oliver Hofnagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute for Biophysics, Goethe University, Frankfurt am Main, Germany.
| | - Peter Bieling
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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Dahlstroem C, Paraschiakos T, Sun H, Windhorst S. Cryo-EM structures of actin binding proteins as tool for drug discovery. Biochem Pharmacol 2023:115680. [PMID: 37399949 DOI: 10.1016/j.bcp.2023.115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
Cellular actin dynamic is controlled by a plethora of actin binding proteins (ABPs), including actin nucleating, bundling, cross-linking, capping, and severing proteins. In this review, regulation of actin dynamics by ABPs will be introduced, and the role of the F-actin severing protein cofilin-1 and the F-actin bundling protein L-plastin in actin dynamics discussed in more detail. Since up-regulation of these proteins in different kinds of cancers is associated with malignant progression of cancer cells, we suggest the cryogenic electron microscopy (Cryo-EM) structure of F- actin with the respective ABP as template for in silico drug design to specifically disrupt the interaction of these ABPs with F-actin.
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Affiliation(s)
- Christian Dahlstroem
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg
| | - Themistoklis Paraschiakos
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leipniz-Forschungsinstitut für Moekulare Pharmakologie, Robert-Rössle-Strasse 10, D-13125, Berlin; Institute of Chemistry, Technical University of Berlin, D-10623, Berlin
| | - Sabine Windhorst
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg.
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Iwasa M, Takeda S, Narita A, Maéda Y, Oda T. Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis. Front Cell Dev Biol 2023; 11:1105460. [PMID: 37009486 PMCID: PMC10062479 DOI: 10.3389/fcell.2023.1105460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
The dynamic assembly of actin is controlled by the hydrolysis of ATP, bound to the center of the molecule. Upon polymerization, actin undergoes a conformational change from the monomeric G-form to the fibrous F-form, which is associated with the flipping of the side chain of His161 toward ATP. His161 flipping from the gauche-minus to gauche-plus conformation leads to a rearrangement of the active site water molecules, including ATP attacking water (W1), into an orientation capable of hydrolysis. We previously showed that by using a human cardiac muscle α-actin expression system, mutations in the Pro-rich loop residues (A108G and P109A) and in a residue that was hydrogen-bonded to W1 (Q137A) affect the rate of polymerization and ATP hydrolysis. Here, we report the crystal structures of the three mutant actins bound to AMPPNP or ADP-Pi determined at a resolution of 1.35–1.55 Å, which are stabilized in the F-form conformation with the aid of the fragmin F1 domain. In A108G, His161 remained non-flipped despite the global actin conformation adopting the F-form, demonstrating that the side chain of His161 is flipped to avoid a steric clash with the methyl group of A108. Because of the non-flipped His161, W1 was located away from ATP, similar to G-actin, which was accompanied by incomplete hydrolysis. In P109A, the absence of the bulky proline ring allowed His161 to be positioned near the Pro-rich loop, with a minor influence on ATPase activity. In Q137A, two water molecules replaced the side-chain oxygen and nitrogen of Gln137 almost exactly at their positions; consequently, the active site structure, including the W1 position, is essentially conserved. This seemingly contradictory observation to the reported low ATPase activity of the Q137A filament could be attributed to a high fluctuation of the active site water. Together, our results suggest that the elaborate structural design of the active site residues ensures the precise control of the ATPase activity of actin.
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Affiliation(s)
- Mitsusada Iwasa
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shuichi Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
- *Correspondence: Toshiro Oda, ; Shuichi Takeda,
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuichiro Maéda
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
| | - Toshiro Oda
- Faculty of Health and Welfare, Tokai Gakuin University, Kakamigahara, Japan
- *Correspondence: Toshiro Oda, ; Shuichi Takeda,
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Kurisaki I, Suzuki M. Simulation toolkits at the molecular scale for trans-scale thermal signaling. Comput Struct Biotechnol J 2023; 21:2547-2557. [PMID: 37102156 PMCID: PMC10123322 DOI: 10.1016/j.csbj.2023.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/28/2023] Open
Abstract
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.
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Affiliation(s)
- Ikuo Kurisaki
- Waseda Research Institute for Science and Engineering, Waseda University, Bldg. No.55, S Tower, 4th Floor, 3–4-1 Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Corresponding authors.
| | - Madoka Suzuki
- Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka 565–0871, Japan
- Corresponding authors.
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