1
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Asghari P, Scriven DR, Shahrasebi S, Valdivia HH, Alsina KM, Valdivia CR, Navarro-Garcia JA, Wehrens XH, Moore ED. Phosphorylation of RyR2 simultaneously expands the dyad and rearranges the tetramers. J Gen Physiol 2024; 156:e202213108. [PMID: 38385988 PMCID: PMC10883851 DOI: 10.1085/jgp.202213108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 01/23/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
We have previously demonstrated that type II ryanodine receptors (RyR2) tetramers can be rapidly rearranged in response to a phosphorylation cocktail. The cocktail modified downstream targets indiscriminately, making it impossible to determine whether phosphorylation of RyR2 was an essential element of the response. Here, we used the β-agonist isoproterenol and mice homozygous for one of the following clinically relevant mutations: S2030A, S2808A, S2814A, or S2814D. We measured the length of the dyad using transmission electron microscopy (TEM) and directly visualized RyR2 distribution using dual-tilt electron tomography. We found that the S2814D mutation, by itself, significantly expanded the dyad and reorganized the tetramers, suggesting a direct link between the phosphorylation state of the tetramer and its microarchitecture. S2808A and S2814A mutant mice, as well as wild types, had significant expansions of their dyads in response to isoproterenol, while S2030A mutants did not. In agreement with functional data from these mutants, S2030 and S2808 were necessary for a complete β-adrenergic response, unlike S2814 mutants. Additionally, all mutants had unique effects on the organization of their tetramer arrays. Lastly, the correlation of structural with functional changes suggests that tetramer-tetramer contacts play an important functional role. We thus conclude that both the size of the dyad and the arrangement of the tetramers are linked to the state of the channel tetramer and can be dynamically altered by a β-adrenergic receptor agonist.
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Affiliation(s)
- Parisa Asghari
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - David R.L. Scriven
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Saba Shahrasebi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Hector H. Valdivia
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Carmen R. Valdivia
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - J. Alberto Navarro-Garcia
- Department of Integrative Physiology, Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Xander H.T. Wehrens
- Department of Integrative Physiology, Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Edwin D.W. Moore
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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2
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Xu J, Liao C, Yin CC, Li G, Zhu Y, Sun F. In situ structural insights into the excitation-contraction coupling mechanism of skeletal muscle. Sci Adv 2024; 10:eadl1126. [PMID: 38507485 PMCID: PMC10954225 DOI: 10.1126/sciadv.adl1126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
Excitation-contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules sense excitation signals and then cause calcium release from the sarcoplasmic reticulum via coupling to type 1 ryanodine receptors (RyR1s), inducing the subsequent contraction of muscle filaments. However, the molecular mechanism remains unclear due to the lack of structural details. Here, we explored the architecture of triad junction by cryo-electron tomography, solved the in situ structure of RyR1 in complex with FKBP12 and calmodulin with the resolution of 16.7 Angstrom, and found the intact RyR1-DHPR supercomplex. RyR1s arrange into two rows on the terminal cisternae membrane by forming right-hand corner-to-corner contacts, and tetrads of DHPRs bind to RyR1s in an alternating manner, forming another two rows on the transverse tubule membrane. This unique arrangement is important for synergistic calcium release and provides direct evidence of physical coupling in ECC.
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Affiliation(s)
- Jiashu Xu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyi Liao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chang-Cheng Yin
- Department of Biophysics, The Health Science Center, Peking University, Beijing 100191, China
- Electron Microscopy Analysis Laboratory, The Health Science Center, Peking University, Beijing 100191, China
- Center for Protein Science, Peking University, Beijing 100871, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yun Zhu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, China
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3
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Hua X, Yao J, Liu X, Liu Q, Deng Y, Li S, Valdivia CR, Wang F, Pozzolini M, Shou Z, Valdivia HH, Xiao L. Comparison of the structure-function of five newly members of the calcin family. Int J Biol Macromol 2024; 260:129424. [PMID: 38219929 DOI: 10.1016/j.ijbiomac.2024.129424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
Calcins are a group of scorpion toxin peptides specifically binding to ryanodine receptors (RyRs) with high affinity, and have the ability to activate and stabilize RyR in a long-lasting subconductance state. Five newly calcins synthesized compounds exhibit typical structural characteristics of a specific family through chemical synthesis and virtual analysis. As the calcins from the same species, Petersiicalcin1 and Petersiicalcin2, Jendekicalcin2 and Jendekicalcin3, have only one residue difference. Both Petersiicalcin1 and Petersiicalcin2 exhibited different affinities in stimulating [3H]ryanodine binding, but the residue mutation resulted in a 2.7 folds difference. Other calcins also exhibited a stimulatory effect on [3H]ryanodine binding to RyR1, however, their affinities were significantly lower than that of Petersiiicalcin1 and Petersiiicalcin2. The channel domain of RyR1 was found to be capable of binding with the basic residues of these calcins, which also exhibited interactions with the S6 helices on RyR1. Dynamic simulations were conducted for Petersiicalcin1 and Petersiicalcin2, which demonstrated their ability to form a highly stable conformation and resulting in an asymmetric tetramer structure of RyR1. The discovery of five newly calcins further enriches the diversity of the natural calcin family, which provides more native peptides for the structure-function analysis between calcin and RyRs.
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Affiliation(s)
- Xiaoyu Hua
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Jinchi Yao
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China; School of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Xinyan Liu
- Department of Traditional Chinese Medicine Surgery, the First Affiliated Hospital of the Navy Medical University, Shanghai, 200433, China
| | - Qing Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Shanxi, Taigu 030801, China
| | - Yuchen Deng
- Department of Dermatology, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Songhua Li
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Carmen R Valdivia
- Department of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
| | - Fei Wang
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Marina Pozzolini
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy.
| | - Zhaoyong Shou
- Faculty of Health Service, Nacal Medical University (Second Military Medical University), Shanghai 200433, China.
| | - Héctor H Valdivia
- Department of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
| | - Liang Xiao
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China.
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4
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Chirasani VR, Elferdink M, Kral M, Carter JS, Heitmann S, Meissner G, Yamaguchi N. Structural and functional interactions between the EF hand domain and S2-S3 loop in the type-1 ryanodine receptor ion channel. J Biol Chem 2024; 300:105606. [PMID: 38159862 PMCID: PMC10832476 DOI: 10.1016/j.jbc.2023.105606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
Previous cryo-electron micrographs suggested that the skeletal muscle Ca2+ release channel, ryanodine receptor (RyR)1, is regulated by intricate interactions between the EF hand Ca2+ binding domain and the cytosolic loop (S2-S3 loop). However, the precise molecular details of these interactions and functional consequences of the interactions remain elusive. Here, we used molecular dynamics simulations to explore the specific amino acid pairs involved in hydrogen bond interactions within the EF hand-S2-S3 loop interface. Our simulations unveiled two key interactions: (1) K4101 (EF hand) with D4730 (S2-S3 loop) and (2) E4075, Q4078, and D4079 (EF hand) with R4736 (S2-S3 loop). To probe the functional significance of these interactions, we constructed mutant RyR1 complementary DNAs and expressed them in HEK293 cells for [3H]ryanodine binding assays. Our results demonstrated that mutations in the EF hand, specifically K4101E and K4101M, resulted in reduced affinities for Ca2+/Mg2+-dependent inhibitions. Interestingly, the K4101E mutation increased the affinity for Ca2+-dependent activation. Conversely, mutations in the S2-S3 loop, D4730K and D4730N, did not significantly change the affinities for Ca2+/Mg2+-dependent inhibitions. Our previous finding that skeletal disease-associated RyR1 mutations, R4736Q and R4736W, impaired Ca2+-dependent inhibition, is consistent with the current results. In silico mutagenesis analysis aligned with our functional data, indicating altered hydrogen bonding patterns upon mutations. Taken together, our findings emphasize the critical role of the EF hand-S2-S3 loop interaction in Ca2+/Mg2+-dependent inhibition of RyR1 and provide insights into potential therapeutic strategies targeting this domain interaction for the treatment of skeletal myopathies.
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Affiliation(s)
- Venkat R Chirasani
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; R.L. Juliano Structural Bioinformatics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Millar Elferdink
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA; College of Charleston Honors College, Charleston, South Carolina, USA
| | - MacKenzie Kral
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA; College of Charleston Honors College, Charleston, South Carolina, USA
| | - Jordan S Carter
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA
| | - Savannah Heitmann
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Naohiro Yamaguchi
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA; Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, South Carolina, USA.
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5
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Yao J, Hua X, Huo W, Xiao L, Wang Y, Tang Q, Valdivia CR, Valdivia HH, Dong W, Xiao L. The Effect of Acidic Residues on the Binding between Opicalcin1 and Ryanodine Receptor from the Structure-Functional Analysis. J Nat Prod 2024; 87:104-112. [PMID: 38128916 PMCID: PMC10825818 DOI: 10.1021/acs.jnatprod.3c00821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/26/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Calcin is a group ligand with high affinity and specificity for the ryanodine receptors (RyRs). Little is known about the effect of its acidic residues on the spacial structure as well as the interaction with RyRs. We screened the opicalcin1 acidic mutants and investigated the effect of mutation on activity. The results indicated that all acidic mutants maintained the structural features, but their surface charge distribution underwent significant changes. Molecular docking and dynamics simulations were used to analyze the interaction between opicalcin1 mutants and RyRs, which demonstrated that all opicalcin1 mutants effectively bound to the channel domain of RyR1. This stable binding induced a pronounced asymmetry in the structure of the RyR tetramer, exhibiting a high degree of structural dissimilarity. [3H]Ryanodine binding to RyR1 was enhanced in D2A and D15A, which was similar to opicalcin1, but that effect was suppressed in E12A and E29A and reversed for the DE-4A, thereby inhibiting ryanodine binding. Opicalcin1 and DE-4A also exhibited the ability to form stable docking structures with RyR2. Acidic residues play a crucial role in the structure of calcin and its functional interaction with RyRs that is beneficial for the calcin optimization to develop more active peptide lead compounds for RyR-related diseases.
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Affiliation(s)
- Jinchi Yao
- School
of Life Sciences, Liaoning Normal University, Dalian116081, China
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
| | - Xiaoyu Hua
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
| | - Wenjing Huo
- The
305 Hospital of PLA, Beijing 100017, China
| | - Li Xiao
- Department
of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53188, United States
- Department
of Forensic Toxicological Analysis, West China School of Basic Medical
Sciences and Forensic Medicine, Sichuan
University, Chengdu 610017, China
| | - Yongfang Wang
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
| | - Qinglong Tang
- Central
Medical District of Chinese, PLA General Hospital, Beijing 100120, China
| | - Carmen R. Valdivia
- Department
of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53188, United States
| | - Héctor H. Valdivia
- Department
of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53188, United States
| | - Weibing Dong
- School
of Life Sciences, Liaoning Normal University, Dalian116081, China
| | - Liang Xiao
- Department
of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical
University), Shanghai 200433, China
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6
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Šeflová J, Schwarz JA, Smith AN, Svensson B, Blackwell DJ, Phillips TA, Nikolaienko R, Bovo E, Rebbeck RT, Zima AV, Thomas DD, Van Petegem F, Knollmann BC, Johnston JN, Robia SL, Cornea RL. RyR2 Binding of an Antiarrhythmic Cyclic Depsipeptide Mapped Using Confocal Fluorescence Lifetime Detection of FRET. ACS Chem Biol 2023; 18:2290-2299. [PMID: 37769131 DOI: 10.1021/acschembio.3c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Hyperactivity of cardiac sarcoplasmic reticulum (SR) ryanodine receptor (RyR2) Ca2+-release channels contributes to heart failure and arrhythmias. Reducing the RyR2 activity, particularly during cardiac relaxation (diastole), is a desirable therapeutic goal. We previously reported that the unnatural enantiomer (ent) of an insect-RyR activator, verticilide, inhibits porcine and mouse RyR2 at diastolic (nanomolar) Ca2+ and has in vivo efficacy against atrial and ventricular arrhythmia. To determine the ent-verticilide structural mode of action on RyR2 and guide its further development via medicinal chemistry structure-activity relationship studies, here, we used fluorescence lifetime (FLT)-measurements of Förster resonance energy transfer (FRET) in HEK293 cells expressing human RyR2. For these studies, we used an RyR-specific FRET molecular-toolkit and computational methods for trilateration (i.e., using distances to locate a point of interest). Multiexponential analysis of FLT-FRET measurements between four donor-labeled FKBP12.6 variants and acceptor-labeled ent-verticilide yielded distance relationships placing the acceptor probe at two candidate loci within the RyR2 cryo-EM map. One locus is within the Ry12 domain (at the corner periphery of the RyR2 tetrameric complex). The other locus is sandwiched at the interface between helical domain 1 and the SPRY3 domain. These findings document RyR2-target engagement by ent-verticilide, reveal new insight into the mechanism of action of this new class of RyR2-targeting drug candidate, and can serve as input in future computational determinations of the ent-verticilide binding site on RyR2 that will inform structure-activity studies for lead optimization.
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Affiliation(s)
- Jaroslava Šeflová
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Jacob A Schwarz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Abigail N Smith
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Bengt Svensson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel J Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Taylor A Phillips
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Roman Nikolaienko
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Elisa Bovo
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Aleksey V Zima
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Björn C Knollmann
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey N Johnston
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Răzvan L Cornea
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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7
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Cholak S, Saville JW, Zhu X, Berezuk AM, Tuttle KS, Haji-Ghassemi O, Alvarado FJ, Van Petegem F, Subramaniam S. Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives. Structure 2023; 31:790-800.e4. [PMID: 37192614 PMCID: PMC10569317 DOI: 10.1016/j.str.2023.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/22/2023] [Accepted: 04/19/2023] [Indexed: 05/18/2023]
Abstract
The coordinated release of Ca2+ from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the SR membrane. In skeletal muscle, activity of RyR1 is regulated by metabolites such as ATP, which upon binding increase channel open probability (Po). To obtain structural insights into the mechanism of RyR1 priming by ATP, we determined several cryo-EM structures of RyR1 bound individually to ATP-γ-S, ADP, AMP, adenosine, adenine, and cAMP. We demonstrate that adenine and adenosine bind RyR1, but AMP is the smallest ATP derivative capable of inducing long-range (>170 Å) structural rearrangements associated with channel activation, establishing a structural basis for key binding site interactions that are the threshold for triggering quaternary structural changes. Our finding that cAMP also induces these structural changes and results in increased channel opening suggests its potential role as an endogenous modulator of RyR1 conductance.
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Affiliation(s)
- Spencer Cholak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Omid Haji-Ghassemi
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Francisco J Alvarado
- Department of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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8
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Du S, Hu X. Comprehensive Overview of Diamide Derivatives Acting as Ryanodine Receptor Activators. J Agric Food Chem 2023; 71:3620-3638. [PMID: 36791236 DOI: 10.1021/acs.jafc.2c08414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The world's hunger is continuously rising due to conflicts, climate change, pandemics (such as the recent COVID-19), and crop pests and diseases. It is widely accepted that zero hunger is impossible without using agrochemicals to control crop pests and diseases. Diamide insecticides are one of the widely used green insecticides developed in recent years and play important roles in controlling lepidopteran pests. Currently, eight diamine insecticides have been commercialized, which target the insect ryanodine receptors. This review summarizes the development and optimization processes of diamide derivatives acting as ryanodine receptor activators. The review also discusses pest resistance to diamide derivatives and possible solutions to overcome the limitations posed by the resistance. Thus, with reference to structural biology, this study provides an impetus for designing and developing diamide insecticides with improved insecticidal activities.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Xueping Hu
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, P. R. China
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9
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Iyer KA, Barnakov V, Samsó M. Three-dimensional perspective on ryanodine receptor mutations causing skeletal and cardiac muscle-related diseases. Curr Opin Pharmacol 2023; 68:102327. [PMID: 36516687 PMCID: PMC9908851 DOI: 10.1016/j.coph.2022.102327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/18/2022] [Accepted: 11/12/2022] [Indexed: 12/14/2022]
Abstract
Mutations in RyR alter the cell's Ca2+ homeostasis and can cause serious health problems for which few effective therapies are available. Until recently, there was little structural context for the hundreds of mutations linked to muscular disorders reported for this large channel. Growing knowledge of the three-dimensional structure of RyR starts to illustrate the fine control of Ca2+ release. Current efforts directed towards understanding how disease mutations impinge in such processes will be crucial for future design of novel therapies. In this review article we discuss the up-to-date information about mutations according to their role in the 3D structure, and classified them to provide context from a structural perspective.
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Affiliation(s)
- Kavita A Iyer
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Vadim Barnakov
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Montserrat Samsó
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.
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10
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Urabe T, Miyoshi H, Narasaki S, Yanase Y, Uchida K, Noguchi S, Hide M, Tsutsumi YM, Sakai N. Characterization of intracellular calcium mobilization induced by remimazolam, a newly approved intravenous anesthetic. PLoS One 2022; 17:e0263395. [PMID: 35104283 PMCID: PMC8806057 DOI: 10.1371/journal.pone.0263395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/18/2022] [Indexed: 01/12/2023] Open
Abstract
Many anesthetics, including Propofol, have been reported to induce elevation of intracellular calcium, and we were interested to investigate the possible contribution of calcium elevation to the mechanism of the newly approved remimazolam actions. Remimazolam is an intravenous anesthetic first approved in Japan in July 2020, and is thought to exert its anesthetic actions via γ-aminobutyric acid A (GABAA) receptors; however, the precise mechanisms of how remimazolam elevates intracellular calcium levels remains unclear. We examined the remimazolam-induced elevation of intracellular calcium using SHSY-5Y neuroblastoma cells, COS-7 cells, HEK293 cells, HeLa cells, and human umbilical vein endothelial cells (HUVECs) loaded with fluorescent dyes for live imaging. We confirmed that high concentrations of remimazolam (greater than 300 μM) elevated intracellular calcium in a dose-dependent manner in these cells tested. This phenomenon was not influenced by elimination of extracellular calcium. The calcium elevation was abolished when intracellular or intraendoplasmic reticulum (ER) calcium was depleted by BAPTA-AM or thapsigargin, respectively, suggesting that calcium was mobilized from the ER. Inhibitors of G-protein coupled receptors (GPCRs)-mediated signals, including U-73122, a phospholipase C (PLC) inhibitor and xestospongin C, an inositol 1,4,5-triphosphate receptors (IP3R) antagonist, significantly suppressed remimazolam-induced calcium elevation, whereas dantrolene, a ryanodine receptor antagonist, did not influence remimazolam-induced calcium elevation. Meanwhile, live imaging of ER during remimazolam stimulation using ER-tracker showed no morphological changes. These results suggest that high doses of remimazolam increased intracellular calcium concentration in a dose-dependent manner in each cell tested, which was predicted to be caused by calcium mobilization from the ER. In addition, our studies using various inhibitors revealed that this calcium elevation might be mediated by the GPCRs-IP3 pathway. However, further studies are required to identify which type of GPCRs is involved.
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Affiliation(s)
- Tomoaki Urabe
- Department of Anesthesiology and Critical Care, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hirotsugu Miyoshi
- Department of Anesthesiology and Critical Care, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
- * E-mail:
| | - Soshi Narasaki
- Department of Anesthesiology and Critical Care, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuhki Yanase
- Department of Pharmacotherapy, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazue Uchida
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Soma Noguchi
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Michihiro Hide
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuo M. Tsutsumi
- Department of Anesthesiology and Critical Care, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Norio Sakai
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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11
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Chirasani VR, Pasek DA, Meissner G. Structural and functional interactions between the Ca 2+-, ATP-, and caffeine-binding sites of skeletal muscle ryanodine receptor (RyR1). J Biol Chem 2021; 297:101040. [PMID: 34352272 PMCID: PMC8408527 DOI: 10.1016/j.jbc.2021.101040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/22/2022] Open
Abstract
Ryanodine receptor type 1 (RyR1) releases Ca2+ ions from the sarcoplasmic reticulum of skeletal muscle cells to initiate muscle contraction. Multiple endogenous and exogenous effectors regulate RyR1, such as ATP, Ca2+, caffeine (Caf), and ryanodine. Cryo-EM identified binding sites for the three coactivators Ca2+, ATP, and Caf. However, the mechanism of coregulation and synergy between these activators remains to be determined. Here, we used [3H]ryanodine ligand-binding assays and molecular dynamics simulations to test the hypothesis that both the ATP- and Caf-binding sites communicate with the Ca2+-binding site to sensitize RyR1 to Ca2+. We report that either phosphomethylphosphonic acid adenylate ester (AMPPCP), a nonhydrolyzable ATP analog, or Caf can activate RyR1 in the absence or the presence of Ca2+. However, enhanced RyR1 activation occurred in the presence of Ca2+, AMPPCP, and Caf. In the absence of Ca2+, Na+ inhibited [3H]ryanodine binding without impairing RyR1 activation by AMPPCP and Caf. Computational analysis suggested that Ca2+-, ATP-, and Caf-binding sites modulate RyR1 protein stability through interactions with the carboxyterminal domain and other domains in the activation core. In the presence of ATP and Caf but the absence of Ca2+, Na+ is predicted to inhibit RyR1 by interacting with the Ca2+-binding site. Our data suggested that ATP and Caf binding affected the conformation of the Ca2+-binding site, and conversely, Ca2+ binding affected the conformation of the ATP- and Caf-binding sites. We conclude that Ca2+, ATP, and Caf regulate RyR1 through a network of allosteric interactions involving the Ca2+-, ATP-, and Caf-binding sites.
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Affiliation(s)
- Venkat R Chirasani
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA.
| | - Daniel A Pasek
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
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12
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Guo W, Wei J, Estillore JP, Zhang L, Wang R, Sun B, Chen SRW. RyR2 disease mutations at the C-terminal domain intersubunit interface alter closed-state stability and channel activation. J Biol Chem 2021; 297:100808. [PMID: 34022226 PMCID: PMC8214192 DOI: 10.1016/j.jbc.2021.100808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/19/2022] Open
Abstract
Ryanodine receptors (RyRs) are ion channels that mediate the release of Ca2+ from the sarcoplasmic reticulum/endoplasmic reticulum, mutations of which are implicated in a number of human diseases. The adjacent C-terminal domains (CTDs) of cardiac RyR (RyR2) interact with each other to form a ring-like tetrameric structure with the intersubunit interface undergoing dynamic changes during channel gating. This mobile CTD intersubunit interface harbors many disease-associated mutations. However, the mechanisms of action of these mutations and the role of CTD in channel function are not well understood. Here, we assessed the impact of CTD disease-associated mutations P4902S, P4902L, E4950K, and G4955E on Ca2+− and caffeine-mediated activation of RyR2. The G4955E mutation dramatically increased both the Ca2+-independent basal activity and Ca2+-dependent activation of [3H]ryanodine binding to RyR2. The P4902S and E4950K mutations also increased Ca2+ activation but had no effect on the basal activity of RyR2. All four disease mutations increased caffeine-mediated activation of RyR2 and reduced the threshold for activation and termination of spontaneous Ca2+ release. G4955D dramatically increased the basal activity of RyR2, whereas G4955K mutation markedly suppressed channel activity. Similarly, substitution of P4902 with a negatively charged residue (P4902D), but not a positively charged residue (P4902K), also dramatically increased the basal activity of RyR2. These data suggest that electrostatic interactions are involved in stabilizing the CTD intersubunit interface and that the G4955E disease mutation disrupts this interface, and thus the stability of the closed state. Our studies shed new insights into the mechanisms of action of RyR2 CTD disease mutations.
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Affiliation(s)
- Wenting Guo
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Jinhong Wei
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - John Paul Estillore
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Lin Zhang
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Ruiwu Wang
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Bo Sun
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Medical School, Kunming University of Science and Technology, Kunming, China.
| | - S R Wayne Chen
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada.
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13
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Abstract
Photoresponsive ligands are powerful tool compounds for studying receptor function with spatiotemporal resolution. However, to the best of our knowledge, such a ligand is not available for the ryanodine receptor (RyR). Herein, we present a photochromic ligand (PCL) for insect RyR by decorating chlorantraniliprole (CHL) with photoswitchable azobenzene (AB). We demonstrated that one potent ligand, named ABCHL13, shows light-induced reversible trans-cis isomerization and 3.5-fold insecticidal activity decrease toward oriental armyworm (Mythimna separata) after UV-light irradiation, that is, trans-ABCH13 has higher activity than the cis-ABCH13. ABCHL13 enables optical control over intracellular Ca2+ release in dorsal unpaired median (DUM) neurons of M. separata and American cockroach (Periplaneta americana) and cardiac function of P. americana. Our results provide a first photopharmacological toolkit that is applicable to light-dependent regulation of RyR and heart beating.
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Affiliation(s)
- Long Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Meijun Chen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Shanshan Xia
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhiping Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yuxin Li
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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14
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Zhao Y, Gao L, Li H, Sun P, Meng F, Zhang Y, Xie Y, Sun B, Zhou S, Ma Y, Xiong L, Yang N, Li Y, Li Z. Synthesis, Insecticidal Activities, and Structure-Activity Relationship of Phenylpyrazole Derivatives Containing a Fluoro-Substituted Benzene Moiety. J Agric Food Chem 2020; 68:11282-11289. [PMID: 32926621 DOI: 10.1021/acs.jafc.9b08090] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fluorinated organic compounds represent a growing and important family of commercial chemicals. Introduction of fluorine into active ingredients has become an effective way to develop modern crop protection products. Given the particular properties of fluorine and high efficiency and selectivity of diamide insecticides, we designed and synthesized 27 anthranilic diamides analogues containing fluoro-sustituted phenylpyrazole. A preliminary bioassay indicated that most target compounds exhibited good biological activity against Mythimna separata and Plutella xylostella. Compound IIIf containing a 2,4,6-trifluoro-substituted benzene ring showed 43% insecticidal activity against M. separata at 0.1 mg L-1, while the control chlorantraniliprole was 36%. The activity of IIIe against P. xylostella at 10-5 mg L-1 was 94%, compared with that of the control being 70%. Thus, introduction of fluorine into diamide insecticides was useful for increasing activity. Insect electrophysiology studies showed that the calcium concentration in the nerve cells of third M. separata larvae was elevated by IIIf, which further confirmed that ryanodine receptor (RyR) was its potential target.
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Affiliation(s)
- Yangyang Zhao
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Li Gao
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Huangong Li
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Pengwei Sun
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Fanfei Meng
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Yan Zhang
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Yongtao Xie
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University (NTU), Singapore 637371, Singapore
| | - Binqiao Sun
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Sha Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Yi Ma
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Lixia Xiong
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Na Yang
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Yuxin Li
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Zhengming Li
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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15
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Zhou Y, Wang W, Salauddin NM, Lin L, You M, You S, Yuchi Z. Crystal structure of the N-terminal domain of ryanodine receptor from the honeybee, Apis mellifera. Insect Biochem Mol Biol 2020; 125:103454. [PMID: 32781205 DOI: 10.1016/j.ibmb.2020.103454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Ryanodine receptors (RyRs) are the molecular target of diamides, a new chemical class of insecticides. Diamide insecticides are used to control lepidopteran pests and were considered relatively safe for mammals and non-targeted beneficial insects, including honey bees. However, recent studies showed that exposure to diamides could cause long-lasting locomotor deficits of bees. Here we report the crystal structure of RyR N-terminal domain A (NTD-A) from the honeybee, Apis mellifera, at 2.5 Å resolution. It shows a similar overall fold as the RyR NTD-A from mammals and the diamondback moth (DBM), Plutella xylostella, and still several loops located at the inter-domain interfaces show insect-specific or bee-specific structural features. A potential insecticide-binding pocket formed by loop9 and loop13 is conserved in lepidopteran but different in both mammals and bees, making it a good candidate targeting site for the development of pest-selective insecticides. Furthermore, a conserved intra-domain disulfide bond was observed in both DBM and bee RyR NTD-A crystal structures, which explains their higher thermal stability compared to mammalian RyR NTD-A. This work provides a basis for the development of novel insecticides with better selectivity between pests and bees by targeting a distinct site on pest RyRs, which would be a promising strategy to overcome the current toxicity problem.
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Affiliation(s)
- Yuanyuan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Wenlan Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Nahiyan Mohammad Salauddin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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16
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Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A. Retrieving functional pathways of biomolecules from single-particle snapshots. Nat Commun 2020; 11:4734. [PMID: 32948759 PMCID: PMC7501871 DOI: 10.1038/s41467-020-18403-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/17/2020] [Indexed: 11/18/2022] Open
Abstract
A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.
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Affiliation(s)
- Ali Dashti
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Mrinal Shekhar
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL, 61801, USA
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Danya Ben Hail
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA
| | - Salah Salah
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA
- Ph.D. Programs in Physics, Chemistry & Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA.
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA.
- Ph.D. Programs in Physics, Chemistry & Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA.
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, 2-221 Black Building, 650 West 168th Street, New York, NY, 10032, USA.
- Department of Biological Sciences, Columbia University, 600 Fairchild Center, New York, NY, 10027, USA.
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA.
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17
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Bauerová-Hlinková V, Hajdúchová D, Bauer JA. Structure and Function of the Human Ryanodine Receptors and Their Association with Myopathies-Present State, Challenges, and Perspectives. Molecules 2020; 25:molecules25184040. [PMID: 32899693 PMCID: PMC7570887 DOI: 10.3390/molecules25184040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 01/28/2023] Open
Abstract
Cardiac arrhythmias are serious, life-threatening diseases associated with the dysregulation of Ca2+ influx into the cytoplasm of cardiomyocytes. This dysregulation often arises from dysfunction of ryanodine receptor 2 (RyR2), the principal Ca2+ release channel. Dysfunction of RyR1, the skeletal muscle isoform, also results in less severe, but also potentially life-threatening syndromes. The RYR2 and RYR1 genes have been found to harbor three main mutation “hot spots”, where mutations change the channel structure, its interdomain interface properties, its interactions with its binding partners, or its dynamics. In all cases, the result is a defective release of Ca2+ ions from the sarcoplasmic reticulum into the myocyte cytoplasm. Here, we provide an overview of the most frequent diseases resulting from mutations to RyR1 and RyR2, briefly review some of the recent experimental structural work on these two molecules, detail some of the computational work describing their dynamics, and summarize the known changes to the structure and function of these receptors with particular emphasis on their N-terminal, central, and channel domains.
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18
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Wu C, Yu X, Wang B, Liu J, Meng F, Zhao Y, Xiong L, Yang N, Li Y, Li Z. Synthesis, Insecticidal Evaluation, and 3D-QASR of Novel Anthranilic Diamide Derivatives Containing N-Arylpyrrole as Potential Ryanodine Receptor Activators. J Agric Food Chem 2020; 68:9319-9328. [PMID: 32786854 DOI: 10.1021/acs.jafc.0c04157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To cope with the global food shortage and insect pest, there is an urgent need to discover new pesticides with novel modes of actions. Ryanodine receptor (RyR) insecticides showed great promise in integrated pest management. Herein, we report the synthesis of novel anthranilic diamide derivatives incorporating pyrrole moieties targeting at insect RyRs. The structures were confirmed by 1H NMR, 13C NMR, 19F NMR, and high-resolution mass spectrometry. The preliminary bioassay results indicated that most of the title compounds showed good to excellent insecticidal activities against the oriental armyworm (Mythimna separata) and diamondback moth (Plutella xylostella). For the oriental armyworm, Ij displayed the same level of larvicidal activity as the positive control chlorantraniliprole, with an LC50 value of 0.21 mg/L. For the diamondback moth, In, Io, Ip, and Iq exhibited higher insecticidal activities than chlorantraniliprole. In particular, In had 50% larvicidal activity at 0.00001 mg/L. The calcium imaging technique was applied to study the effect of Ij, In, and Ip on the intracellular calcium ion concentration ([Ca2+]i) in central neurons isolated from the oriental armyworm. The results indicated that the tested compounds, such as chlorantraniliprole, could activate the insect RyRs. Furthermore, comparative molecular field analysis and density functional theory calculations were carried out to study the structure-activity relationship.
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Affiliation(s)
- Changchun Wu
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaobo Yu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Baolei Wang
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Jingbo Liu
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Fanfei Meng
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Yangyang Zhao
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Lixia Xiong
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Na Yang
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Yuxin Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha 410125, China
| | - Zhengming Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
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Sanchez RM, Zhang Y, Chen W, Dietrich L, Kudryashev M. Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM. Nat Commun 2020; 11:3709. [PMID: 32709843 PMCID: PMC7381653 DOI: 10.1038/s41467-020-17466-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/30/2020] [Indexed: 11/09/2022] Open
Abstract
Cryo-electron tomography combined with subtomogram averaging (StA) has yielded high-resolution structures of macromolecules in their native context. However, high-resolution StA is not commonplace due to beam-induced sample drift, images with poor signal-to-noise ratios (SNR), challenges in CTF correction, and limited particle number. Here we address these issues by collecting tilt series with a higher electron dose at the zero-degree tilt. Particles of interest are then located within reconstructed tomograms, processed by conventional StA, and then re-extracted from the high-dose images in 2D. Single particle analysis tools are then applied to refine the 2D particle alignment and generate a reconstruction. Use of our hybrid StA (hStA) workflow improved the resolution for tobacco mosaic virus from 7.2 to 4.4 Å and for the ion channel RyR1 in crowded native membranes from 12.9 to 9.1 Å. These resolution gains make hStA a promising approach for other StA projects aimed at achieving subnanometer resolution.
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Affiliation(s)
- Ricardo M Sanchez
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany
| | - Yingyi Zhang
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany
| | - Wenbo Chen
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany
| | - Lea Dietrich
- Department of Structural Biology, Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
| | - Mikhail Kudryashev
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany.
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20
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Iyer KA, Hu Y, Nayak AR, Kurebayashi N, Murayama T, Samsó M. Structural mechanism of two gain-of-function cardiac and skeletal RyR mutations at an equivalent site by cryo-EM. Sci Adv 2020; 6:eabb2964. [PMID: 32832689 PMCID: PMC7439390 DOI: 10.1126/sciadv.abb2964] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/10/2020] [Indexed: 05/16/2023]
Abstract
Mutations in ryanodine receptors (RyRs), intracellular Ca2+ channels, are associated with deadly disorders. Despite abundant functional studies, the molecular mechanism of RyR malfunction remains elusive. We studied two single-point mutations at an equivalent site in the skeletal (RyR1 R164C) and cardiac (RyR2 R176Q) isoforms using ryanodine binding, Ca2+ imaging, and cryo-electron microscopy (cryo-EM) of the full-length protein. Loss of the positive charge had greater effect on the skeletal isoform, mediated via distortion of a salt bridge network, a molecular latch inducing rotation of a cytoplasmic domain, and partial progression to open-state traits of the large cytoplasmic assembly accompanied by alteration of the Ca2+ binding site, which concur with the major "hyperactive" feature of the mutated channel. Our cryo-EM studies demonstrated the allosteric effect of a mutation situated ~85 Å away from the pore and identified an isoform-specific structural effect.
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Affiliation(s)
- Kavita A. Iyer
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Yifan Hu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Ashok R. Nayak
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Nagomi Kurebayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Murayama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Montserrat Samsó
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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Huang 黄镜梅 JM, Rao 饶聪 C, Wang 王帅 S, He 何林凤 LF, Zhao 赵思琪 SQ, Zhou 周丽琪 LQ, Zhao 赵云霞 YX, Yang 杨凤霞 FX, Gao 高聪芬 CF, Wu 吴顺凡 SF. Multiple target-site mutations occurring in lepidopterans confer resistance to diamide insecticides. Insect Biochem Mol Biol 2020; 121:103367. [PMID: 32243905 DOI: 10.1016/j.ibmb.2020.103367] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Diamide resistant phenotypes have evolved in the field and the resistance has been attributed to target-site mutations in some lepidopteran pests. In this study, we documented the resistance status of Chilo suppressalis to chlorantraniliprole during 2016-2018 in seven provinces of China. To investigate the possible role of target-site mutations as known from lepidopterans, we sequenced respective domains of the RyR gene of C. suppressalis with different levels of diamide resistance. The results revealed that I4758M (corresponding to I4790M in P. xylostella), Y4667D/C (numbered according to C. suppressalis), G4915E (corresponding to G4946E in P. xylostella), and one novel Y4891F (numbered according to C. suppressalis) RyR target-site mutations were present. The contribution of these mutations was further investigated by diamide toxicity bioassays with eight genome modified Drosophila melanogaster lines. The study showed that genome modified flies bearing the Y4667D mutation (corresponding to the Y4667D and I4758M simultaneous mutation in C. suppressalis) exhibited high resistance ratios to chlorantraniliprole (1542.8-fold), cyantraniliprole (487.9-fold) and tetrachlorantraniliprole (290.1-fold). The M4758I and G4915E simultaneous mutations (corresponding to single G4915E mutation in C. suppressalis) showed high resistance ratios to chlorantraniliprole (153.1-fold) and cyantraniliprole (323.5-fold), and relatively low resistance to flubendiamide (28.9-fold) and tetrachlorantraniliprole (25.2-fold). These findings suggest that multiple point mutations in RyR confer diamide resistance of C. suppressalis. The results contribute to a better understanding of insect diamide resistance mechanisms and provide insights on the impact of RyR target-site mutations in insects.
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Affiliation(s)
- Jing-Mei Huang 黄镜梅
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Cong Rao 饶聪
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Shuai Wang 王帅
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Lin-Feng He 何林凤
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Si-Qi Zhao 赵思琪
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Li-Qi Zhou 周丽琪
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Yun-Xia Zhao 赵云霞
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Feng-Xia Yang 杨凤霞
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Cong-Fen Gao 高聪芬
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China.
| | - Shun-Fan Wu 吴顺凡
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China.
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22
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Samurkas A, Fan X, Ma D, Sundarraj R, Lin L, Yao L, Ma R, Jiang H, Cao P, Gao Q, Yuchi Z. Discovery of Potential Species-Specific Green Insecticides Targeting the Lepidopteran Ryanodine Receptor. J Agric Food Chem 2020; 68:4528-4537. [PMID: 32207934 DOI: 10.1021/acs.jafc.0c01063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ryanodine receptors (RyRs) are homotetrameric intracellular calcium (Ca2+) release channels responsible for excitation-contraction coupling of muscle cells. Diamide insecticides specifically act on RyRs of Lepidoptera and Coleoptera pests and are safe for nontargeted organisms, generating big worldwide sales. Despite their popularity, several devastating agricultural pests have been reported to be resistant to them because of mutations in a small transmembrane region of their RyRs, hinting a binding pocket nearby. A potential solution to overcome resistance is to develop new insecticides targeting different binding sites in pest RyRs. Based on a high-resolution crystal structure of diamondback moth (DBM) RyR N-terminal domain (NTD) determined by our group, we carried out extensive structure-based insecticide screening targeting the intersubunit interface. We identified eight lead compounds that selectively target the open conformation of DBM RyR, which are predicted to act as channel activators similar to diamide insecticides. Binding mode analysis shows selective binding to a hydrophobic pocket of DBM NTD-A but not to the pocket of its mammalian counterpart. We tested three available compounds on the HEK293 cell lines stably expressing DBM or mammalian RyR, one of which shows good potency and selectivity against DBM RyR. The insecticidal effect of the compound was also confirmed using fruit flies. The detailed binding mode, toxicity, absorption, distribution, metabolism, and excretion, and reactivity of the compound were predicted by bioinformatic methods. Together, our study lays a foundation for developing a new class of selective RyR-targeting insecticides to control both wild-type and resistant pests.
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Affiliation(s)
- Arthur Samurkas
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Xiaona Fan
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Dan Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | | | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Li Yao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Ruifang Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Heng Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Peng Cao
- Key Laboratory of Drug Targets and Drug Leads for Degenerative Diseases, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Qingzhi Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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23
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Zhou Y, Ma D, Lin L, You M, Yuchi Z, You S. Crystal Structure of the Ryanodine Receptor SPRY2 Domain from the Diamondback Moth Provides Insights into the Development of Novel Insecticides. J Agric Food Chem 2020; 68:1731-1740. [PMID: 31951399 DOI: 10.1021/acs.jafc.9b08151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Diamide insecticides targeting ryanodine receptors (RyRs) are a major class of pesticides used to control a wide range of agricultural pests, but their efficacies have been reduced dramatically by the recent emergence of resistance mutations. There is a pressing need to develop novel insecticides, targeting distinct and novel binding sites within insect RyRs to overcome the resistance crisis; however, the limited structural information on insect RyRs is a major roadblock to our understanding of their molecular mechanisms. Here, we report the crystal structure of the RyR SPRY2 domain from the diamondback moth (DBM), Plutella xylostella, a destructive agricultural pest worldwide that has developed resistance to all classes of insecticide at 2.06 Å resolution. The overall fold of DBM SPRY2 is similar to its mammalian homolog, but it shows distinct conformations in several loops. Docking it into the recently published cryo-electron microscope structure of the full-length RyR reveals that two insect-specific loops interact with the BSol domain from the neighboring subunit. The SPRY2-BSol interface will change the conformation upon channel gating, indicating that it might be a potential targeting site for insect-specific insecticides. Interestingly, several previously identified disease-causing mutations also lie in the same interface, implying that this interface is important for channel gating. Another insect-specific loop located in the SPRY2-SPRY3 interface might indirectly affect another gating interface between SPRY3 and Repeat34.
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Affiliation(s)
- Yuanyuan Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology , Fujian Agriculture and Forestry University , Fuzhou 350002 , China
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology , Tianjin University , Tianjin 300072 , China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education , Fuzhou 350002 , China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture , Fuzhou 350002 , China
| | - Dan Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology , Tianjin University , Tianjin 300072 , China
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology , Tianjin University , Tianjin 300072 , China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology , Fujian Agriculture and Forestry University , Fuzhou 350002 , China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education , Fuzhou 350002 , China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture , Fuzhou 350002 , China
| | - Zhiguang Yuchi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology , Fujian Agriculture and Forestry University , Fuzhou 350002 , China
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology , Tianjin University , Tianjin 300072 , China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology , Fujian Agriculture and Forestry University , Fuzhou 350002 , China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education , Fuzhou 350002 , China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture , Fuzhou 350002 , China
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24
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Haji-Ghassemi O, Yuchi Z, Van Petegem F. The Cardiac Ryanodine Receptor Phosphorylation Hotspot Embraces PKA in a Phosphorylation-Dependent Manner. Mol Cell 2019; 75:39-52.e4. [PMID: 31078384 DOI: 10.1016/j.molcel.2019.04.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/05/2019] [Accepted: 04/11/2019] [Indexed: 12/22/2022]
Abstract
Ryanodine receptors (RyRs) are intracellular Ca2+ release channels controlling essential cellular functions. RyRs are targeted by cyclic AMP (cAMP)-dependent protein kinase A (PKA), a controversial regulation implicated in disorders ranging from heart failure to Alzheimer's. Using crystal structures, we show that the phosphorylation hotspot domain of RyR2 embraces the PKA catalytic subunit, with an extensive interface not seen in PKA complexes with peptides. We trapped an intermediary open-form PKA bound to the RyR2 domain and an ATP analog, showing that PKA can engage substrates in an open form. Phosphomimetics or prior phosphorylation at nearby sites in RyR2 either enhance or reduce the activity of PKA. Finally, we show that a phosphomimetic at S2813, a well-known target site for calmodulin-dependent kinase II, induces the formation of an alpha helix in the phosphorylation domain, resulting in increased interactions and PKA activity. This shows that the different phosphorylation sites in RyR2 are not independent.
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Affiliation(s)
- Omid Haji-Ghassemi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhiguang Yuchi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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25
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Roston TM, Haji-Ghassemi O, LaPage MJ, Batra AS, Bar-Cohen Y, Anderson C, Lau YR, Maginot K, Gebauer RA, Etheridge SP, Potts JE, Van Petegem F, Sanatani S. Catecholaminergic polymorphic ventricular tachycardia patients with multiple genetic variants in the PACES CPVT Registry. PLoS One 2018; 13:e0205925. [PMID: 30403697 PMCID: PMC6221297 DOI: 10.1371/journal.pone.0205925] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/03/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Catecholaminergic polymorphic ventricular tachycardia (CPVT) is often a life-threatening arrhythmia disorder with variable penetrance and expressivity. Little is known about the incidence or outcomes of CPVT patients with ≥2 variants. METHODS The phenotypes, genotypes and outcomes of patients in the Pediatric and Congenital Electrophysiology Society CPVT Registry with ≥2 variants in genes linked to CPVT were ascertained. The American College of Medical Genetics & Genomics (ACMG) criteria and structural mapping were used to predict the pathogenicity of variants (3D model of pig RyR2 in open-state). RESULTS Among 237 CPVT subjects, 193 (81%) had genetic testing. Fifteen patients (8%) with a median age of 9 years (IQR 5-12) had ≥2 variants. Sudden cardiac arrest occurred in 11 children (73%), although none died during a median follow-up of 4.3 years (IQR 2.5-6.1). Thirteen patients (80%) had at least two RYR2 variants, while the remaining two patients had RYR2 variants plus variants in other CPVT-linked genes. Among all variants identified, re-classification of the commercial laboratory interpretation using ACMG criteria led to the upgrade from variant of unknown significance (VUS) to pathogenic/likely pathogenic (P/LP) for 5 variants, and downgrade from P/LP to VUS for 6 variants. For RYR2 variants, 3D mapping using the RyR2 model suggested that 2 VUS by ACMG criteria were P/LP, while 2 variants were downgraded to likely benign. CONCLUSIONS This severely affected cohort demonstrates that a minority of CPVT cases are related to ≥2 variants, which may have implications on family-based genetic counselling. While multi-variant CPVT patients were at high-risk for sudden cardiac arrest, there are insufficient data to conclude that this genetic phenomenon has prognostic implications at present. Further research is needed to determine the significance and generalizability of this observation. This study also shows that a rigorous approach to variant re-classification using the ACMG criteria and 3D mapping is important in reaching an accurate diagnosis, especially in the multi-variant population.
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Affiliation(s)
- Thomas M. Roston
- Departments of Medicine, Pediatrics, and Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Omid Haji-Ghassemi
- Departments of Medicine, Pediatrics, and Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Martin J. LaPage
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, United States of America
| | - Anjan S. Batra
- Department of Pediatrics, University of California at Irvine Medical Center, Irvine, CA, United States of America
| | - Yaniv Bar-Cohen
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Chris Anderson
- Providence Sacred Heart Children’s Hospital, Spokane, WA, United States of America
| | - Yung R. Lau
- Division of Pediatric Cardiology, University of Alabama at Birmingham, Birmingham, AB, United States of America
| | - Kathleen Maginot
- Department of Pediatrics, University of Wisconsin School of Medicine & Public Health, Madison, WI, United States of America
| | - Roman A. Gebauer
- Department of Pediatric Cardiology, University of Leipzig, Leipzig, Germany
| | - Susan P. Etheridge
- Department of Pediatrics, University of Utah, and Primary Children’s Hospital, Salt Lake City, UT, United States of America
| | - James E. Potts
- Departments of Medicine, Pediatrics, and Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Departments of Medicine, Pediatrics, and Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Shubhayan Sanatani
- Departments of Medicine, Pediatrics, and Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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26
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Hernández-Ochoa EO, Schneider MF. Voltage sensing mechanism in skeletal muscle excitation-contraction coupling: coming of age or midlife crisis? Skelet Muscle 2018; 8:22. [PMID: 30025545 PMCID: PMC6053751 DOI: 10.1186/s13395-018-0167-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/26/2018] [Indexed: 11/10/2022] Open
Abstract
The process by which muscle fiber electrical depolarization is linked to activation of muscle contraction is known as excitation-contraction coupling (ECC). Our understanding of ECC has increased enormously since the early scientific descriptions of the phenomenon of electrical activation of muscle contraction by Galvani that date back to the end of the eighteenth century. Major advances in electrical and optical measurements, including muscle fiber voltage clamp to reveal membrane electrical properties, in conjunction with the development of electron microscopy to unveil structural details provided an elegant view of ECC in skeletal muscle during the last century. This surge of knowledge on structural and biophysical aspects of the skeletal muscle was followed by breakthroughs in biochemistry and molecular biology, which allowed for the isolation, purification, and DNA sequencing of the muscle fiber membrane calcium channel/transverse tubule (TT) membrane voltage sensor (Cav1.1) for ECC and of the muscle ryanodine receptor/sarcoplasmic reticulum Ca2+ release channel (RyR1), two essential players of ECC in skeletal muscle. In regard to the process of voltage sensing for controlling calcium release, numerous studies support the concept that the TT Cav1.1 channel is the voltage sensor for ECC, as well as also being a Ca2+ channel in the TT membrane. In this review, we present early and recent findings that support and define the role of Cav1.1 as a voltage sensor for ECC.
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Affiliation(s)
- Erick O. Hernández-Ochoa
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201 USA
| | - Martin F. Schneider
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201 USA
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27
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Heinz LP, Kopec W, de Groot BL, Fink RHA. In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways. Sci Rep 2018; 8:6886. [PMID: 29720700 PMCID: PMC5932038 DOI: 10.1038/s41598-018-25061-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/13/2018] [Indexed: 12/18/2022] Open
Abstract
The ryanodine receptor 1 is a large calcium ion channel found in mammalian skeletal muscle. The ion channel gained a lot of attention recently, after multiple independent authors published near-atomic cryo electron microscopy data. Taking advantage of the unprecedented quality of structural data, we performed molecular dynamics simulations on the entire ion channel as well as on a reduced model. We calculated potentials of mean force for Ba2+, Ca2+, Mg2+, K+, Na+ and Cl- ions using umbrella sampling to identify the key residues involved in ion permeation. We found two main binding sites for the cations, whereas the channel is strongly repulsive for chloride ions. Furthermore, the data is consistent with the model that the receptor achieves its ion selectivity by over-affinity for divalent cations in a calcium-block-like fashion. We reproduced the experimental conductance for potassium ions in permeation simulations with applied voltage. The analysis of the permeation paths shows that ions exit the pore via multiple pathways, which we suggest to be related to the experimental observation of different subconducting states.
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Affiliation(s)
- Leonard P Heinz
- Medical Biophysics Unit, Medical Faculty, Institute of Physiology and Pathophysiology, Heidelberg University, 69120, Heidelberg, Germany.
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Rainer H A Fink
- Medical Biophysics Unit, Medical Faculty, Institute of Physiology and Pathophysiology, Heidelberg University, 69120, Heidelberg, Germany
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Wu SF, Zhao DD, Huang JM, Zhao SQ, Zhou LQ, Gao CF. Molecular characterization and expression profiling of ryanodine receptor gene in the pink stem borer, Sesamia inferens (Walker). Pestic Biochem Physiol 2018; 146:1-6. [PMID: 29626986 DOI: 10.1016/j.pestbp.2018.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 12/21/2017] [Accepted: 01/10/2018] [Indexed: 06/08/2023]
Abstract
The susceptibilities of three field populations of pink stem borer (PSB), Sesamia inferens (walker) to diamide insecticides, chlorantraniliprole and flubendiamide, were evaluated in this study. The results showed that these PSB field populations were still sensitive to the two diamide insecticides after many years of exposure. To further understand PSB and diamide insecticide, the full-length ryanodine receptor (RyR) cDNA (named as SiRyR), the molecular target of diamide insecticides was cloned from PSB and characterized. The SiRyR gene contains an open reading frame of 15,420 nucleotides, encoding 5140 amino acid residues, which shares 77% to 98% sequence identity with RyR homologous of other insects. All hallmarks of RyR proteins are conserved in the SiRyR protein, including the conserved C-terminal domain with the consensus calcium-biding EF-hands (calcium-binding motif), the six transmembrane domains, as well as mannosyltransferase, IP3R and RyR (pfam02815) (MIR) domains. Real-time qPCR analysis revealed that the highest mRNA expression levels of SiRyR were observed in pupa and adults, especially in males. SiRyR was expressed at the highest level in thorax, and the lowest level in wing. The full genetic characterization of SiRyR could provide useful information for future functional expression studies and for discovery of new insecticides with selective insecticidal activity.
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Affiliation(s)
- Shun-Fan Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Dan-Dan Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Jing-Mei Huang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Si-Qi Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Li-Qi Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Cong-Fen Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China.
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Abstract
Ryanodine receptors (RyRs) are ubiquitous intracellular calcium (Ca2+) release channels required for the function of many organs including heart and skeletal muscle, synaptic transmission in the brain, pancreatic beta cell function, and vascular tone. In disease, defective function of RyRs due either to stress (hyperadrenergic and/or oxidative overload) or genetic mutations can render the channels leaky to Ca2+ and promote defective disease-causing signals as observed in heat failure, muscular dystrophy, diabetes mellitus, and neurodegerative disease. RyRs are massive structures comprising the largest known ion channel-bearing macromolecular complex and exceeding 3 million Daltons in molecular weight. RyRs mediate the rapid release of Ca2+ from the endoplasmic/sarcoplasmic reticulum (ER/SR) to stimulate cellular functions through Ca2+-dependent processes. Recent advances in single-particle cryogenic electron microscopy (cryo-EM) have enabled the determination of atomic-level structures for RyR for the first time. These structures have illuminated the mechanisms by which these critical ion channels function and interact with regulatory ligands. In the present chapter we discuss the structure, functional elements, gating and activation mechanisms of RyRs in normal and disease states.
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Affiliation(s)
- Gaetano Santulli
- The Wu Center for Molecular Cardiology, Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, USA
- The Wilf Family Cardiovascular Research Institute and the Einstein-Mount Sinai Diabetes Research Center, Department of Medicine, Albert Einstein College of Medicine - Montefiore University Hospital, New York, NY, USA
| | - Daniel Lewis
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Amedee des Georges
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, NY, USA
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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Lin L, Liu C, Qin J, Wang J, Dong S, Chen W, He W, Gao Q, You M, Yuchi Z. Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites. Insect Biochem Mol Biol 2018; 92:73-83. [PMID: 29191465 DOI: 10.1016/j.ibmb.2017.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/04/2017] [Accepted: 11/20/2017] [Indexed: 06/07/2023]
Abstract
Ryanodine receptors (RyRs) are large calcium-release channels located in sarcoplasmic reticulum membrane. They play a central role in excitation-contraction coupling of muscle cells. Three commercialized insecticides targeting pest RyRs generate worldwide sales over 2 billion U.S. dollars annually, but the structure of insect RyRs remains elusive, hindering our understanding of the mode of action of RyR-targeting insecticides and the development of insecticide resistance in pests. Here we present the crystal structure of RyR N-terminal domain (NTD) (residue 1-205) at 2.84 Å resolution from the diamondback moth (DBM), Plutella xylostella, a destructive pest devouring cruciferous crops all over the world. Similar to its mammalian homolog, DBM RyR NTD consists of a beta-trefoil folding motif and a flanking alpha helix. Interestingly, two regions in NTD interacting with neighboring domains showed distinguished conformations in DBM relative to mammalian RyRs. Using homology modeling and molecular dynamics simulation, we created a structural model of the N-terminal three domains, showing two unique binding pockets that could be targeted by potential species-specific insecticides. Thermal melt experiment showed that the stability of DBM RyR NTD was higher than mammalian RyRs, probably due to a stable intra-domain disulfide bond observed in the crystal structure. Previously DBM NTD was shown to be one of the two critical regions to interact with insecticide flubendiamide, but isothermal titration calorimetry experiments negated DBM NTD alone as a major binding site for flubendiamide.
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Affiliation(s)
- Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chen Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Juan Qin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jie Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shengjie Dong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Wei Chen
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiyi He
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingzhi Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Holland EB, Goldstone JV, Pessah IN, Whitehead A, Reid NM, Karchner SI, Hahn ME, Nacci DE, Clark BW, Stegeman JJ. Ryanodine receptor and FK506 binding protein 1 in the Atlantic killifish (Fundulus heteroclitus): A phylogenetic and population-based comparison. Aquat Toxicol 2017; 192:105-115. [PMID: 28942070 PMCID: PMC5662517 DOI: 10.1016/j.aquatox.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 05/12/2023]
Abstract
Non-dioxin-like polychlorinated biphenyls (NDL PCBs) activate ryanodine receptors (RyR), microsomal Ca2+ channels of broad significance. Teleost fish may be important models for NDL PCB neurotoxicity, and we used sequencing databases to characterize teleost RyR and FK506 binding protein 12 or 12.6kDa (genes FKBP1A; FKBP1B), which promote NDL PCB-triggered Ca2+ dysregulation. Particular focus was placed on describing genes in the Atlantic killifish (Fundulus heteroclitus) genome and searching available RNA-sequencing datasets for single nucleotide variants (SNV) between PCB tolerant killifish from New Bedford Harbor (NBH) versus sensitive killifish from Scorton Creek (SC), MA. Consistent with the teleost whole genome duplication (tWGD), killifish have six RyR genes, corresponding to a and b paralogs of mammalian RyR1, 2 and 3. The presence of six RyR genes was consistent in all teleosts investigated including zebrafish. Killifish have four FKBP1; one FKBP1b and three FKBP1a named FKBP1aa, FKBP1ab, likely from the tWGD and a single gene duplicate FKBP1a3 suggested to have arisen in Atherinomorphae. The RyR and FKBP1 genes displayed tissue and developmental stage-specific mRNA expression, and the previously uncharacterized RyR3, herein named RyR3b, and all FKBP1 genes were prominent in brain. We identified a SNV in RyR3b encoding missense mutation E1458D. In NBH killifish, 57% were heterozygous and 28% were homozygous for this SNV, whereas almost all SC killifish (94%) lacked the variant (n≥39 per population). The outlined sequence differences between mammalian and teleost RyR and FKBP1 together with outlined population differences in SNV frequency may contribute to our understanding of NDL PCB neurotoxicity.
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Affiliation(s)
- Erika B Holland
- Department of Biological Sciences, California State University of Long Beach, Long Beach, CA, USA; Department of Biology, Woods Hole Oceanographic Institution, Woods Hole MA, USA; Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
| | - Jared V Goldstone
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Isaac N Pessah
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew Whitehead
- Department of Environmental Toxicology, College of Agricultural and Environmental Sciences,University of California Davis, Davis, CA, USA
| | - Noah M Reid
- Department of Environmental Toxicology, College of Agricultural and Environmental Sciences,University of California Davis, Davis, CA, USA
| | - Sibel I Karchner
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Mark E Hahn
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Diane E Nacci
- Atlantic Ecology Division, Office of Research and Development, US Environmental Protection Agency, Narragansett, RI, USA
| | - Bryan W Clark
- Oak Ridge Institute for Science and Education at the United States Environmental Protection Agency, Office of Research and Development, Narragansett, RI, 02882, USA
| | - John J Stegeman
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole MA, USA
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Yuan GR, Wang KY, Mou X, Luo RY, Dou W, Wang JJ. Molecular cloning, mRNA expression and alternative splicing of a ryanodine receptor gene from the citrus whitefly, Dialeurodes citri (Ashmead). Pestic Biochem Physiol 2017; 142:59-66. [PMID: 29107248 DOI: 10.1016/j.pestbp.2017.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/07/2016] [Accepted: 01/04/2017] [Indexed: 06/07/2023]
Abstract
Insect ryanodine receptors are the main targets of diamide insecticides that have highly selective insecticidal activity but are less toxic to mammals. Therefore, these insecticides are ideal for pest control. Ryanodine receptors (RyRs) play a critical role in Ca2+ signaling in muscle and non-muscle cells. In this study, we cloned the complete cDNA (DcRyR) of the RyR from the citrus whitefly, Dialeurodes citri, a serious pest of citrus orchards in China. The open reading frame of RyR is 15,378bp long and encodes a protein with 5126 amino acids with a computed molecular weight of 579.523kDa. DcRyR shows a high amino acid sequence identity to RyRs from other insects (76%-95%) and low identity to those from nematodes and mammals (44%-52%). DcRyR shares many features of insect and vertebrate RyRs, including a MIR domain, two RIH domains, three SPRY domains, four copies of RyR repeat domain, RIH-associated domain at the N-terminus, two consensus calcium-binding EF-hands and six transmembrane domains at the C-terminus. The expression of DcRyR mRNA was the highest in the nymphs and lowest in eggs; DcRyR mRNA was 1.85-fold higher in the nymphs than in the eggs. Among the tissues, DcRyR mRNA expression was 4.18- and 4.02-fold higher in the adult head and thorax than in the abdomen. DcRyR had three alternative splice sites and the splice variants showed body part-specific expression and were developmentally regulated. These results may help investigate target-based resistance to diamide insecticides in D. citri.
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Affiliation(s)
- Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Ke-Yi Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Xing Mou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Ruo-Yu Luo
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
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Abstract
Ryanodine receptors (RyRs) are calcium release channels expressed in the sarcoendoplasmic reticula of many cell types including cardiac and skeletal muscle cells. In recent years Ca2+ leak through RyRs has been implicated as a major contributor to the development of diseases including heart failure, muscle myopathies, Alzheimer's disease, and diabetes, making it an important therapeutic target. Recent mammalian RyR1 cryoelectron microscopy (cryo-EM) structures of multiple functional states have clarified longstanding questions including the architecture of the transmembrane (TM) pore and cytoplasmic domains, the location and architecture of the channel gate, ligand-binding sites, and the gating mechanism. As we advance toward complete models of RyRs this new information enables the determination of domain-domain interfaces and the location and structural effects of disease-causing RyR mutations.
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Affiliation(s)
- Ran Zalk
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Wu Center for Molecular Cardiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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Vénien-Bryan C, Li Z, Vuillard L, Boutin JA. Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery. Acta Crystallogr F Struct Biol Commun 2017; 73:174-183. [PMID: 28368275 PMCID: PMC5379166 DOI: 10.1107/s2053230x17003740] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/08/2017] [Indexed: 02/06/2023] Open
Abstract
The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolution structure was an accomplishment less than a decade ago, it is now common to generate structures at sub-5 Å resolution and even better. It is becoming possible to relatively quickly obtain high-resolution structures of biological molecules, in particular large ones (>500 kDa) which, in some cases, have resisted more conventional methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Such newly resolved structures may, for the first time, shed light on the precise mechanisms that are essential for cellular physiological processes. The ability to attain atomic resolution may support the development of new drugs that target these proteins, allowing medicinal chemists to understand the intimacy of the relationship between their molecules and targets. In addition, recent developments in cryo-electron microscopy combined with image analysis can provide unique information on the conformational variability of macromolecular complexes. Conformational flexibility of macromolecular complexes can be investigated using cryo-electron microscopy and multiconformation reconstruction methods. However, the biochemical quality of the sample remains the major bottleneck to routine cryo-electron microscopy-based determination of structures at very high resolution.
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Affiliation(s)
- Catherine Vénien-Bryan
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, UPMC, IRD, MNHN, 4 Place Jussieu, 75005 Paris, France
| | - Zhuolun Li
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, UPMC, IRD, MNHN, 4 Place Jussieu, 75005 Paris, France
| | - Laurent Vuillard
- Chimie des Protéines, Pôle d’Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean Albert Boutin
- Pôle d’Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
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Roditakis E, Steinbach D, Moritz G, Vasakis E, Stavrakaki M, Ilias A, García-Vidal L, Martínez-Aguirre MDR, Bielza P, Morou E, Silva JE, Silva WM, Siqueira ΗAA, Iqbal S, Troczka BJ, Williamson MS, Bass C, Tsagkarakou A, Vontas J, Nauen R. Ryanodine receptor point mutations confer diamide insecticide resistance in tomato leafminer, Tuta absoluta (Lepidoptera: Gelechiidae). Insect Biochem Mol Biol 2017; 80:11-20. [PMID: 27845250 DOI: 10.1016/j.ibmb.2016.11.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 10/14/2016] [Accepted: 11/11/2016] [Indexed: 06/06/2023]
Abstract
Insect ryanodine receptors (RyR) are the molecular target-site for the recently introduced diamide insecticides. Diamides are particularly active on Lepidoptera pests, including tomato leafminer, Tuta absoluta (Lepidoptera: Gelechiidae). High levels of diamide resistance were recently described in some European populations of T. absoluta, however, the mechanisms of resistance remained unknown. In this study the molecular basis of diamide resistance was investigated in a diamide resistant strain from Italy (IT-GELA-SD4), and additional resistant field populations collected in Greece, Spain and Brazil. The genetics of resistance was investigated by reciprocally crossing strain IT-GELA-SD4 with a susceptible strain and revealed an autosomal incompletely recessive mode of inheritance. To investigate the possible role of target-site mutations as known from diamondback moth (Plutella xylostella), we sequenced respective domains of the RyR gene of T. absoluta. Genotyping of individuals of IT-GELA-SD4 and field-collected strains showing different levels of diamide resistance revealed the presence of G4903E and I4746M RyR target-site mutations. These amino acid substitutions correspond to those recently described for diamide resistant diamondback moth, i.e. G4946E and I4790M. We also detected two novel mutations, G4903V and I4746T, in some of the resistant T. absoluta strains. Radioligand binding studies with thoracic membrane preparations of the IT-GELA-SD4 strain provided functional evidence that these mutations alter the affinity of the RyR to diamides. In combination with previous work on P. xylostella our study highlights the importance of position G4903 (G4946 in P. xylostella) of the insect RyR in defining sensitivity to diamides. The discovery of diamide resistance mutations in T. absoluta populations of diverse geographic origin has serious implications for the efficacy of diamides under applied conditions. The implementation of appropriate resistance management strategies is strongly advised to delay the further spread of resistance.
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Affiliation(s)
- Emmanouil Roditakis
- Hellenic Agricultural Organisation - 'Demeter', Institute of Olive Tree, Subtropical Crops and Viticulture, Heraklion, Crete, Greece.
| | - Denise Steinbach
- Bayer CropScience, R&D Pest Control, Monheim, Germany; Department of Biology, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Gerald Moritz
- Department of Biology, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Emmanouil Vasakis
- Hellenic Agricultural Organisation - 'Demeter', Institute of Olive Tree, Subtropical Crops and Viticulture, Heraklion, Crete, Greece
| | - Marianna Stavrakaki
- Hellenic Agricultural Organisation - 'Demeter', Institute of Olive Tree, Subtropical Crops and Viticulture, Heraklion, Crete, Greece
| | - Aris Ilias
- Hellenic Agricultural Organisation - 'Demeter', Institute of Olive Tree, Subtropical Crops and Viticulture, Heraklion, Crete, Greece
| | - Lidia García-Vidal
- Departamento de Producción Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | | | - Pablo Bielza
- Departamento de Producción Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Evangelia Morou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece
| | - Jefferson E Silva
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco - UFRPE, Recife, Brazil
| | - Wellington M Silva
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco - UFRPE, Recife, Brazil
| | - Ηerbert A A Siqueira
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco - UFRPE, Recife, Brazil
| | | | | | | | - Chris Bass
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Anastasia Tsagkarakou
- Hellenic Agricultural Organisation - 'Demeter', Institute of Olive Tree, Subtropical Crops and Viticulture, Heraklion, Crete, Greece
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece; Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Ralf Nauen
- Bayer CropScience, R&D Pest Control, Monheim, Germany.
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Sasaki K, Makiyama T, Yoshida Y, Wuriyanghai Y, Kamakura T, Nishiuchi S, Hayano M, Harita T, Yamamoto Y, Kohjitani H, Hirose S, Chen J, Kawamura M, Ohno S, Itoh H, Takeuchi A, Matsuoka S, Miura M, Sumitomo N, Horie M, Yamanaka S, Kimura T. Patient-Specific Human Induced Pluripotent Stem Cell Model Assessed with Electrical Pacing Validates S107 as a Potential Therapeutic Agent for Catecholaminergic Polymorphic Ventricular Tachycardia. PLoS One 2016; 11:e0164795. [PMID: 27764147 PMCID: PMC5072719 DOI: 10.1371/journal.pone.0164795] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 09/30/2016] [Indexed: 12/21/2022] Open
Abstract
Introduction Human induced pluripotent stem cells (hiPSCs) offer a unique opportunity for disease modeling. However, it is not invariably successful to recapitulate the disease phenotype because of the immaturity of hiPSC-derived cardiomyocytes (hiPSC-CMs). The purpose of this study was to establish and analyze iPSC-based model of catecholaminergic polymorphic ventricular tachycardia (CPVT), which is characterized by adrenergically mediated lethal arrhythmias, more precisely using electrical pacing that could promote the development of new pharmacotherapies. Method and Results We generated hiPSCs from a 37-year-old CPVT patient and differentiated them into cardiomyocytes. Under spontaneous beating conditions, no significant difference was found in the timing irregularity of spontaneous Ca2+ transients between control- and CPVT-hiPSC-CMs. Using Ca2+ imaging at 1 Hz electrical field stimulation, isoproterenol induced an abnormal diastolic Ca2+ increase more frequently in CPVT- than in control-hiPSC-CMs (control 12% vs. CPVT 43%, p<0.05). Action potential recordings of spontaneous beating hiPSC-CMs revealed no significant difference in the frequency of delayed afterdepolarizations (DADs) between control and CPVT cells. After isoproterenol application with pacing at 1 Hz, 87.5% of CPVT-hiPSC-CMs developed DADs, compared to 30% of control-hiPSC-CMs (p<0.05). Pre-incubation with 10 μM S107, which stabilizes the closed state of the ryanodine receptor 2, significantly decreased the percentage of CPVT-hiPSC-CMs presenting DADs to 25% (p<0.05). Conclusions We recapitulated the electrophysiological features of CPVT-derived hiPSC-CMs using electrical pacing. The development of DADs in the presence of isoproterenol was significantly suppressed by S107. Our model provides a promising platform to study disease mechanisms and screen drugs.
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MESH Headings
- Action Potentials/drug effects
- Adult
- Animals
- Anti-Asthmatic Agents/chemistry
- Anti-Asthmatic Agents/pharmacology
- Anti-Asthmatic Agents/therapeutic use
- Calcium/metabolism
- Calreticulin/genetics
- Calreticulin/metabolism
- Calsequestrin/genetics
- Calsequestrin/metabolism
- Cell Differentiation/drug effects
- Cells, Cultured
- Electric Stimulation
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Humans
- Induced Pluripotent Stem Cells/cytology
- Induced Pluripotent Stem Cells/metabolism
- Isoproterenol/pharmacology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Models, Biological
- Myocytes, Cardiac/cytology
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/transplantation
- Ryanodine/pharmacology
- Ryanodine Receptor Calcium Release Channel/chemistry
- Ryanodine Receptor Calcium Release Channel/genetics
- Ryanodine Receptor Calcium Release Channel/metabolism
- Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics
- Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism
- Tachycardia, Ventricular/drug therapy
- Tachycardia, Ventricular/pathology
- Tachycardia, Ventricular/therapy
- Thiazepines/chemistry
- Thiazepines/pharmacology
- Thiazepines/therapeutic use
- Transplantation, Heterologous
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Affiliation(s)
- Kenichi Sasaki
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- * E-mail: (TM); (Y. Yoshida)
| | - Yoshinori Yoshida
- Kyoto University iPS Cell Research and Application, Kyoto, Japan
- * E-mail: (TM); (Y. Yoshida)
| | - Yimin Wuriyanghai
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Tsukasa Kamakura
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Suguru Nishiuchi
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mamoru Hayano
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeshi Harita
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuta Yamamoto
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirohiko Kohjitani
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sayako Hirose
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jiarong Chen
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mihoko Kawamura
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Seiko Ohno
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Hideki Itoh
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Ayako Takeuchi
- Department of Integrative and Systems Physiology, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Satoshi Matsuoka
- Department of Integrative and Systems Physiology, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Masaru Miura
- Division of Cardiology, Tokyo Metropolitan Children’s Medical Center, Tokyo, Japan
| | - Naokata Sumitomo
- Department of Pediatric Cardiology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Minoru Horie
- Department of Cardiovascular and Respiratory Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Shinya Yamanaka
- Kyoto University iPS Cell Research and Application, Kyoto, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
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37
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Sato D, Shannon TR, Bers DM. Sarcoplasmic Reticulum Structure and Functional Properties that Promote Long-Lasting Calcium Sparks. Biophys J 2016; 110:382-390. [PMID: 26789761 DOI: 10.1016/j.bpj.2015.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/07/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Calcium (Ca) sparks are the fundamental sarcoplasmic reticulum (SR) Ca release events in cardiac myocytes, and they have a typical duration of 20-40 ms. However, when a fraction of ryanodine receptors (RyRs) are blocked by tetracaine or ruthenium red, Ca sparks lasting hundreds of milliseconds have been observed experimentally. The fundamental mechanism underlying these extremely prolonged Ca sparks is not understood. In this study, we use a physiologically detailed mathematical model of subcellular Ca cycling to examine how Ca spark duration is influenced by the number of functional RyRs in a junctional cluster (which is reduced by tetracaine or ruthenium red) and other SR Ca handling properties. One RyR cluster contains a few to several hundred RyRs, and we use a four-state Markov RyR gating model. Each RyR opens stochastically and is regulated by cytosolic and luminal Ca. We varied the number of functional RyRs in the single cluster, diffusion within the SR network, diffusion between network and junctional SR, cytosolic Ca diffusion, SERCA uptake activity, and RyR open probability. For long-lasting Ca release events, opening events within the cluster must occur continuously because the typical open time of the RyR is only a few milliseconds. We found the following: 1) if the number of RyRs is too small, it is difficult to maintain consecutive openings and stochastic attrition terminates the release; 2) if the number of RyRs is too large, the depletion of Ca from the junctional SR terminates the release; and 3) very long release events require relatively small-sized RyR clusters (reducing flux as seen experimentally with tetracaine) and sufficiently rapid intra-SR Ca diffusion, such that local junctional intra-SR [Ca] can be maintained by intra-SR diffusion and overall SR Ca reuptake.
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Affiliation(s)
- Daisuke Sato
- Department of Pharmacology, University of California, Davis, Davis, California.
| | - Thomas R Shannon
- Molecular Biophysics and Physiology, Rush University, Chicago, Illinois
| | - Donald M Bers
- Department of Pharmacology, University of California, Davis, Davis, California
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38
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Abstract
Ryanodine receptors (RyRs) are intracellular cation channels that mediate the rapid and voluminous release of Ca2+ from the sarcoplasmic reticulum (SR) as required for excitation-contraction coupling in cardiac and skeletal muscle. Understanding of the architecture and gating of RyRs has advanced dramatically over the past two years, due to the publication of high resolution cryo-electron microscopy (cryoEM) reconstructions and associated atomic models of multiple functional states of the skeletal muscle receptor, RyR1. Here we review recent advances in our understanding of RyR architecture and gating, and highlight remaining gaps in understanding which we anticipate will soon be filled.
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Affiliation(s)
- Oliver B Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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39
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Liu JB, Li YX, Zhang XL, Hua XW, Wu CC, Wei W, Wan YY, Cheng DD, Xiong LX, Yang N, Song HB, Li ZM. Novel Anthranilic Diamide Scaffolds Containing N-Substituted Phenylpyrazole as Potential Ryanodine Receptor Activators. J Agric Food Chem 2016; 64:3697-3704. [PMID: 27109555 DOI: 10.1021/acs.jafc.6b00380] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To discover potent insecticides targeting ryanodine receptors (RyRs), a series of novel anthranilic diamides analogues (12a-12u) containing N-substituted phenylpyrazole were designed and synthesized. These compounds were characterized by (1)H NMR, (13)C NMR, and HRMS, and the structure of compound 12u was confirmed by X-ray diffraction. Their insecticidal activities indicated that these compounds displayed moderate to excellent activities. In particular, 12i showed 100 and 37% larvicidal activities against oriental armyworm (Mythimna separata) at 0.25 and 0.05 mg L(-1), equivalent to that of chlorantraniliprole (100%, 0.25 mg L(-1); and 33%, 0.05 mg L(-1)). The activity of 12i against diamondback moth (Plutella xylostella) was 95% at 0.05 mg L(-1), whereas the control was 100% at 0.05 mg L(-1). The calcium-imaging technique experiment results showed that the effects of 12i on the intracellular calcium ion concentration ([Ca(2+)]i) in neurons were concentration-dependent. After the central neurons of Helicoverpa armigera were dyed by loading with fluo-5N and treated with 12i, the free calcium released in endoplasmic reticulum indicated the target of compound 12i is RyRs or IP3Rs. The activation of RyRs by natural ryanodine completely blocked the calcium release induced by 12i, which indicated that RyRs in the central neurons of H. armigera third-instar larvae is the possible target of compound 12i.
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Affiliation(s)
- Jing-Bo Liu
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Yu-Xin Li
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Xiu-Lan Zhang
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Xue-Wen Hua
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Chang-Chun Wu
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Wei Wei
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Ying-Ying Wan
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Dan-Dan Cheng
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Li-Xia Xiong
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Na Yang
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Hai-Bin Song
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
| | - Zheng-Ming Li
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
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40
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Gaburjakova J, Gaburjakova M. Cardiac ryanodine receptor: Selectivity for alkaline earth metal cations points to the EF-hand nature of luminal binding sites. Bioelectrochemistry 2016; 109:49-56. [PMID: 26849106 DOI: 10.1016/j.bioelechem.2016.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 01/21/2016] [Accepted: 01/24/2016] [Indexed: 11/18/2022]
Abstract
A growing body of evidence suggests that the regulation of cardiac ryanodine receptor (RYR2) by luminal Ca(2+) is mediated by luminal binding sites located on the RYR2 channel itself and/or its auxiliary protein, calsequestrin. The localization and structure of RYR2-resident binding sites are not known because of the lack of a high-resolution structure of RYR2 luminal regions. To obtain the first structural insight, we probed the RYR2 luminal face stripped of calsequestrin by alkaline earth metal divalents (M(2+): Mg(2+), Ca(2+), Sr(2+) or Ba(2+)). We show that the RYR2 response to caffeine at the single-channel level is significantly modified by the nature of luminal M(2+). Moreover, we performed competition experiments by varying the concentration of luminal M(2+) (Mg(2+), Sr(2+) or Ba(2+)) from 8 mM to 53 mM and investigated its ability to compete with 1mM luminal Ca(2+). We demonstrate that all tested M(2+) bind to exactly the same RYR2 luminal binding sites. Their affinities decrease in the order: Ca(2+)>Sr(2+)>Mg(2+)~Ba(2+), showing a strong correlation with the M(2+) affinity of the EF-hand motif. This indicates that the RYR2 luminal binding regions and the EF-hand motif likely share some structural similarities because the structure ties directly to the function.
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Affiliation(s)
- Jana Gaburjakova
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Health Sciences Pavilion, 840 05, Bratislava, Slovak Republic.
| | - Marta Gaburjakova
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Health Sciences Pavilion, 840 05, Bratislava, Slovak Republic.
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41
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Schilling R, Fink RHA, Fischer WB. Interaction of ions with the luminal sides of wild-type and mutated skeletal muscle ryanodine receptors. J Mol Model 2016; 22:37. [PMID: 26781665 DOI: 10.1007/s00894-015-2906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 12/28/2015] [Indexed: 12/22/2022]
Abstract
Ryanodine receptors (RyRs) are the largest known ion channels, and are of central importance for the release of Ca(2+) from the sarco/endoplasmic reticulum (SR/ER) in a variety of cells. In cardiac and skeletal muscle cells, contraction is triggered by the release of Ca(2+) into the cytoplasm and thus depends crucially on correct RyR function. In this work, in silico mutants of the RyR pore were generated and MD simulations were conducted to examine the impact of the mutations on the Ca(2+) distribution. The Ca(2+) distribution pattern on the luminal side of the RyR was most affected by G4898R, D4899Q, E4900Q, R4913E, and D4917A mutations. MD simulations with our wild-type model and various ion species showed a preference for Ca(2+) over other cations at the luminal pore entrance. This Ca(2+)-accumulating characteristic of the luminal RyR side may be essential to the conductance properties of the channel.
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Affiliation(s)
- Roman Schilling
- Medical Biophysics Group, Institute of Physiology and Pathophysiology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Rainer H A Fink
- Medical Biophysics Group, Institute of Physiology and Pathophysiology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Non St., Sec. 2, Taipei, 112, Taiwan.
- Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, 112, Taiwan.
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42
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Walker MA, Kohl T, Lehnart SE, Greenstein JL, Lederer WJ, Winslow RL. On the Adjacency Matrix of RyR2 Cluster Structures. PLoS Comput Biol 2015; 11:e1004521. [PMID: 26545234 PMCID: PMC4636394 DOI: 10.1371/journal.pcbi.1004521] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023] Open
Abstract
In the heart, electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells. This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors (RyR2). Their openings cause cell-wide release of Ca2+, which in turn causes muscle contraction and the generation of the mechanical force required to pump blood. In resting myocytes, RyR2s can also open spontaneously giving rise to spatially-confined Ca2+ release events known as "sparks." RyR2s are organized in a lattice to form clusters in the junctional sarcoplasmic reticulum membrane. Our recent work has shown that the spatial arrangement of RyR2s within clusters strongly influences the frequency of Ca2+ sparks. We showed that the probability of a Ca2+ spark occurring when a single RyR2 in the cluster opens spontaneously can be predicted from the precise spatial arrangements of the RyR2s. Thus, "function" follows from "structure." This probability is related to the maximum eigenvalue (λ1) of the adjacency matrix of the RyR2 cluster lattice. In this work, we develop a theoretical framework for understanding this relationship. We present a stochastic contact network model of the Ca2+ spark initiation process. We show that λ1 determines a stability threshold for the formation of Ca2+ sparks in terms of the RyR2 gating transition rates. We recapitulate these results by applying the model to realistic RyR2 cluster structures informed by super-resolution stimulated emission depletion (STED) microscopy. Eigendecomposition of the linearized mean-field contact network model reveals functional subdomains within RyR2 clusters with distinct sensitivities to Ca2+. This work provides novel perspectives on the cardiac Ca2+ release process and a general method for inferring the functional properties of transmembrane receptor clusters from their structure.
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Affiliation(s)
- Mark A. Walker
- Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tobias Kohl
- Heart Research Center Göttingen, Clinic of Cardiology and Pulmonology, University Medical Center Göttingen, Göttingen, Germany
| | - Stephan E. Lehnart
- Heart Research Center Göttingen, Clinic of Cardiology and Pulmonology, University Medical Center Göttingen, Göttingen, Germany
- German Center for Cardiovascular Research site Göttingen, Germany
| | - Joseph L. Greenstein
- Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - W. J. Lederer
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Raimond L. Winslow
- Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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43
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Ryvkin AM, Zorin NM, Moskvin AS, Solovyova OE, Markhasin VS. [Interaction of Membrane and Calcium Oscillators in Cardiac Pacemaker Cells: Mathematical Modeling]. Biofizika 2015; 60:1138-1145. [PMID: 26841508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An integrative model of the calcium dynamics in cardiac pacemaker cells is developed taking into account a synergetic effect of the interaction between an outer membrane oscillator and an intracellular calcium oscillator ("membrane and Ca(2+)-clock"). The main feature of the model is a description of the stochastic dynamics of Ca2+ release units within the electron-conformational mechanism of the functioning of ryanodine-sensitive calcium channels. It is shown that interaction of two cellular oscillators provides a stable action potential generation in the cardiac pacemaker cells even in the case of the stochastic Ca2+ dynamics. We studied in detail the effect of ryanodine channels sensitivity to an increase in the intracellular calcium concentration in sarcoplasmic reticulum and in the dyadic space on the behavior of calcium-release system. A parametric analysis of the integrative model of pacemaker cells is performed.
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44
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Xiao Z, Guo W, Yuen SMWK, Wang R, Zhang L, Van Petegem F, Chen SRW. The H29D Mutation Does Not Enhance Cytosolic Ca2+ Activation of the Cardiac Ryanodine Receptor. PLoS One 2015; 10:e0139058. [PMID: 26405799 PMCID: PMC4583508 DOI: 10.1371/journal.pone.0139058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/07/2015] [Indexed: 11/25/2022] Open
Abstract
The N-terminal domain of the cardiac ryanodine receptor (RyR2) harbors a large number of naturally occurring mutations that are associated with stress-induced ventricular tachyarrhythmia and sudden death. Nearly all these disease-associated N-terminal mutations are located at domain interfaces or buried within domains. Mutations at these locations would alter domain-domain interactions or the stability/folding of domains. Recently, a novel RyR2 mutation H29D associated with ventricular arrhythmia at rest was found to enhance the activation of single RyR2 channels by diastolic levels of cytosolic Ca2+. Unlike other N-terminal disease-associated mutations, the H29D mutation is located on the surface of the N-terminal domain. It is unclear how this surface-exposed H29D mutation that does not appear to interact with other parts of the RyR2 structure could alter the intrinsic properties of the channel. Here we carried out detailed functional characterization of the RyR2-H29D mutant at the molecular and cellular levels. We found that the H29D mutation has no effect on the basal level or the Ca2+ dependent activation of [3H]ryanodine binding to RyR2, the cytosolic Ca2+ activation of single RyR2 channels, or the cytosolic Ca2+- or caffeine-induced Ca2+ release in HEK293 cells. In addition, the H29D mutation does not alter the propensity for spontaneous Ca2+ release or the thresholds for Ca2+ release activation or termination. Furthermore, the H29D mutation does not have significant impact on the thermal stability of the N-terminal region (residues 1–547) of RyR2. Collectively, our data show that the H29D mutation exerts little or no effect on the function of RyR2 or on the folding stability of the N-terminal region. Thus, our results provide no evidence that the H29D mutation enhances the cytosolic Ca2+ activation of RyR2.
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Affiliation(s)
- Zhichao Xiao
- Libin Cardiovascular Institute of Alberta, Department of Physiology & Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Wenting Guo
- Libin Cardiovascular Institute of Alberta, Department of Physiology & Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Siobhan M. Wong King Yuen
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada V6T 1Z3
| | - Ruiwu Wang
- Libin Cardiovascular Institute of Alberta, Department of Physiology & Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Lin Zhang
- Libin Cardiovascular Institute of Alberta, Department of Physiology & Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada V6T 1Z3
| | - S. R. Wayne Chen
- Libin Cardiovascular Institute of Alberta, Department of Physiology & Pharmacology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- * E-mail:
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45
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Rajagopal V, Bass G, Walker CG, Crossman DJ, Petzer A, Hickey A, Siekmann I, Hoshijima M, Ellisman MH, Crampin EJ, Soeller C. Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes. PLoS Comput Biol 2015; 11:e1004417. [PMID: 26335304 PMCID: PMC4559435 DOI: 10.1371/journal.pcbi.1004417] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 06/26/2015] [Indexed: 11/18/2022] Open
Abstract
Spatio-temporal dynamics of intracellular calcium, [Ca2+]i, regulate the contractile function of cardiac muscle cells. Measuring [Ca2+]i flux is central to the study of mechanisms that underlie both normal cardiac function and calcium-dependent etiologies in heart disease. However, current imaging techniques are limited in the spatial resolution to which changes in [Ca2+]i can be detected. Using spatial point process statistics techniques we developed a novel method to simulate the spatial distribution of RyR clusters, which act as the major mediators of contractile Ca2+ release, upon a physiologically-realistic cellular landscape composed of tightly-packed mitochondria and myofibrils. We applied this method to computationally combine confocal-scale (~ 200 nm) data of RyR clusters with 3D electron microscopy data (~ 30 nm) of myofibrils and mitochondria, both collected from adult rat left ventricular myocytes. Using this hybrid-scale spatial model, we simulated reaction-diffusion of [Ca2+]i during the rising phase of the transient (first 30 ms after initiation). At 30 ms, the average peak of the simulated [Ca2+]i transient and of the simulated fluorescence intensity signal, F/F0, reached values similar to that found in the literature ([Ca2+]i ≈1 μM; F/F0≈5.5). However, our model predicted the variation in [Ca2+]i to be between 0.3 and 12.7 μM (~3 to 100 fold from resting value of 0.1 μM) and the corresponding F/F0 signal ranging from 3 to 9.5. We demonstrate in this study that: (i) heterogeneities in the [Ca2+]i transient are due not only to heterogeneous distribution and clustering of mitochondria; (ii) but also to heterogeneous local densities of RyR clusters. Further, we show that: (iii) these structure-induced heterogeneities in [Ca2+]i can appear in line scan data. Finally, using our unique method for generating RyR cluster distributions, we demonstrate the robustness in the [Ca2+]i transient to differences in RyR cluster distributions measured between rat and human cardiomyocytes. Calcium (Ca2+) acts as a signal for many functions in the heart cell, from its primary role in triggering contractions during the heartbeat to acting as a signal for cell growth. Cellular function is tightly coupled to its ultra-structural organization. Spatially-realistic and biophysics-based computational models can provide quantitative insights into structure-function relationships in Ca2+ signaling. We developed a novel computational model of a rat ventricular myocyte that integrates structural information from confocal and electron microscopy datasets that were independently acquired and includes: myofibrils (protein complexes that contract during the heartbeat), mitochondria (organelles that provide energy for contraction), and ryanodine receptors (RyR, ion channels that release the Ca2+ required to trigger myofibril contraction from intracellular stores). Using this model, we examined [Ca2+]i dynamics throughout the cell cross-section at a much higher resolution than previously possible. We estimated the size of structural maladaptation that would cause disease-related alterations in [Ca2+]i dynamics. Using our methods for data integration, we also tested whether reducing the density of RyRs in human cardiomyocytes (~40% relative to rat) would have a significant effect on [Ca2+]i. We found that Ca2+ release patterns between the two species are similar, suggesting Ca2+ dynamics are robust to variations in cell ultrastructure.
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Affiliation(s)
- Vijay Rajagopal
- Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
- Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, Australia
- * E-mail:
| | - Gregory Bass
- Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, Australia
| | - Cameron G. Walker
- Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - David J. Crossman
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Amorita Petzer
- School of Biological Sciences, University of Auckland, Auckland. New Zealand
| | - Anthony Hickey
- School of Biological Sciences, University of Auckland, Auckland. New Zealand
| | - Ivo Siekmann
- Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia
| | - Masahiko Hoshijima
- Department of Medicine, University of California San Diego, San Diego, United States of America
- National Center for Microscopy and Imaging Research, University of California San Diego, San Diego, United States of America
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, University of California San Diego, San Diego, United States of America
| | - Edmund J. Crampin
- Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia
- School of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, Australia
| | - Christian Soeller
- Department of Physiology, University of Auckland, Auckland, New Zealand
- Biomedical Physics, University of Exeter, Exeter, United Kingdom
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Gillespie D, Xu L, Meissner G. Selecting ions by size in a calcium channel: the ryanodine receptor case study. Biophys J 2014; 107:2263-73. [PMID: 25418295 PMCID: PMC4241444 DOI: 10.1016/j.bpj.2014.09.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022] Open
Abstract
Many calcium channels can distinguish between ions of the same charge but different size. For example, when cations are in direct competition with each other, the ryanodine receptor (RyR) calcium channel preferentially conducts smaller cations such as Li(+) and Na(+) over larger ones such as K(+) and Cs(+). Here, we analyze the physical basis for this preference using a previously established model of RyR permeation and selectivity. Like other calcium channels, RyR has four aspartate residues in its GGGIGDE selectivity filter. These aspartates have their terminal carboxyl group in the pore lumen, which take up much of the available space for permeating ions. We find that small ions are preferred by RyR because they can fit into this crowded environment more easily.
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Affiliation(s)
- Dirk Gillespie
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois.
| | - Le Xu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
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Borko Ľ, Bauerová-Hlinková V, Hostinová E, Gašperík J, Beck K, Lai FA, Zahradníková A, Ševčík J. Structural insights into the human RyR2 N-terminal region involved in cardiac arrhythmias. Acta Crystallogr D Biol Crystallogr 2014; 70:2897-912. [PMID: 25372681 PMCID: PMC4220973 DOI: 10.1107/s1399004714020343] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/10/2014] [Indexed: 01/11/2023]
Abstract
Human ryanodine receptor 2 (hRyR2) mediates calcium release from the sarcoplasmic reticulum, enabling cardiomyocyte contraction. The N-terminal region of hRyR2 (amino acids 1-606) is the target of >30 arrhythmogenic mutations and contains a binding site for phosphoprotein phosphatase 1. Here, the solution and crystal structures determined under near-physiological conditions, as well as a homology model of the hRyR2 N-terminal region, are presented. The N-terminus is held together by a unique network of interactions among its three domains, A, B and C, in which the central helix (amino acids 410-437) plays a prominent stabilizing role. Importantly, the anion-binding site reported for the mouse RyR2 N-terminal region is notably absent from the human RyR2. The structure concurs with the differential stability of arrhythmogenic mutations in the central helix (R420W, I419F and I419F/R420W) which are owing to disparities in the propensity of mutated residues to form energetically favourable or unfavourable contacts. In solution, the N-terminus adopts a globular shape with a prominent tail that is likely to involve residues 545-606, which are unresolved in the crystal structure. Docking the N-terminal domains into cryo-electron microscopy maps of the closed and open RyR1 conformations reveals C(α) atom movements of up to 8 Å upon channel gating, and predicts the location of the leucine-isoleucine zipper segment and the interaction site for spinophilin and phosphoprotein phosphatase 1 on the RyR surface.
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Affiliation(s)
- Ľubomír Borko
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Vladena Bauerová-Hlinková
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Eva Hostinová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Juraj Gašperík
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Konrad Beck
- Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY, Wales
| | - F. Anthony Lai
- Department of Cardiology, Wales Heart Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales
| | - Alexandra Zahradníková
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
- Department of Muscle Cell Research, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlárska 5, 833 34 Bratislava, Slovakia
| | - Jozef Ševčík
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
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López-Caamal F, Marquez-Lago TT. Exact probability distributions of selected species in stochastic chemical reaction networks. Bull Math Biol 2014; 76:2334-61. [PMID: 25155220 PMCID: PMC4153981 DOI: 10.1007/s11538-014-9985-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 06/05/2014] [Indexed: 10/29/2022]
Abstract
Chemical reactions are discrete, stochastic events. As such, the species' molecular numbers can be described by an associated master equation. However, handling such an equation may become difficult due to the large size of reaction networks. A commonly used approach to forecast the behaviour of reaction networks is to perform computational simulations of such systems and analyse their outcome statistically. This approach, however, might require high computational costs to provide accurate results. In this paper we opt for an analytical approach to obtain the time-dependent solution of the Chemical Master Equation for selected species in a general reaction network. When the reaction networks are composed exclusively of zeroth and first-order reactions, this analytical approach significantly alleviates the computational burden required by simulation-based methods. By building upon these analytical solutions, we analyse a general monomolecular reaction network with an arbitrary number of species to obtain the exact marginal probability distribution for selected species. Additionally, we study two particular topologies of monomolecular reaction networks, namely (i) an unbranched chain of monomolecular reactions with and without synthesis and degradation reactions and (ii) a circular chain of monomolecular reactions. We illustrate our methodology and alternative ways to use it for non-linear systems by analysing a protein autoactivation mechanism. Later, we compare the computational load required for the implementation of our results and a pure computational approach to analyse an unbranched chain of monomolecular reactions. Finally, we study calcium ions gates in the sarco/endoplasmic reticulum mediated by ryanodine receptors.
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Affiliation(s)
- Fernando López-Caamal
- Integrative Systems Biology Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa 904-0412 Japan
| | - Tatiana T. Marquez-Lago
- Integrative Systems Biology Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa 904-0412 Japan
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Zhou S, Jia Z, Xiong L, Yan T, Yang N, Wu G, Song H, Li Z. Chiral dicarboxamide scaffolds containing a sulfiliminyl moiety as potential ryanodine receptor activators. J Agric Food Chem 2014; 62:6269-6277. [PMID: 24949911 DOI: 10.1021/jf501727k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
To search for new environmentally benign insecticides with high activity, low toxicity, and low residue, novel chiral configurations introduced into dicarboxamide scaffolds containing N-cyano sulfiliminyl moieties were first studied. Four series of phthalamides with sulfur-containing side chains were designed, synthesized, and evaluated against oriental armyworm (Pseudaletia separata Walker) and diamondback moth (Plutella xylostella (L.)) for their insecticidal activities. All structures were characterized by (1)H NMR, (13)C NMR, and HRMS (or elemental analysis), and their configurations were confirmed by optical polarimetry. The biological assessment indicated that some title compounds exhibited significant insecticidal activities. For oriental armyworm, these stereoisomers exerted different impacts on biological activity following the sequence (Sc, Ss) ≥ (Sc, Rs) ≫ (Rc, Ss) > (Rc, Rs), and carbon chirality influenced the activities more strongly than sulfur. Compounds Ia and IIa reached as high an activity as commercial flubendiamide, with LC50 values of 0.0504 and 0.0699 mg L(-1), respectively, lower than that of flubendiamide (0.1230 mg L(-1)). For diamondback moth, the sequence of activity was (Sc, Ss) > (Sc, Rs), and the sulfur chirality influenced the activities more greatly than carbon. Compound IIe exhibited even higher activity than flubendiamide, whereas Ie and Ic,d reached the activity of the latter. The results indicated that the improvement of insecticidal activity probably required a coordination of both carbon and sulfur chirality. Comparative molecular field analysis calculation indicated that stereoisomers with Sc configurations containing strong electron-withdrawing groups such as as CN are important in maintaining the high activity. The chiral scaffolds containing the N-cyano sulfiliminyl moiety are also essential for high larvicidal activity. Some title compounds could be considered as potential candidates for ryanodine receptor activators.
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Affiliation(s)
- Sha Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin, China 300071
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50
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Shirvanyants D, Ramachandran S, Mei Y, Xu L, Meissner G, Dokholyan NV. Pore dynamics and conductance of RyR1 transmembrane domain. Biophys J 2014; 106:2375-84. [PMID: 24896116 PMCID: PMC4052289 DOI: 10.1016/j.bpj.2014.04.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/17/2014] [Indexed: 11/25/2022] Open
Abstract
Ryanodine receptors (RyR) are calcium release channels, playing a major role in the regulation of muscular contraction. Mutations in skeletal muscle RyR (RyR1) are associated with congenital diseases such as malignant hyperthermia and central core disease (CCD). The absence of high-resolution structures of RyR1 has limited our understanding of channel function and disease mechanisms at the molecular level. Previously, we have reported a hypothetical structure of the RyR1 pore-forming region, obtained by homology modeling and supported by mutational scans, electrophysiological measurements, and cryo-electron microscopy. Here, we utilize the expanded model encompassing six transmembrane helices to calculate the RyR1 pore region conductance, to analyze its structural stability, and to hypothesize the mechanism of the Ile4897 CCD-associated mutation. The calculated conductance of the wild-type RyR1 suggests that the proposed pore structure can sustain ion currents measured in single-channel experiments. We observe a stable pore structure on timescales of 0.2 μs, with multiple cations occupying the selectivity filter and cytosolic vestibule, but not the inner chamber. We further suggest that stability of the selectivity filter critically depends on the interactions between the I4897 residue and several hydrophobic residues of the neighboring subunit. Loss of these interactions in the case of polar substitution I4897T results in destabilization of the selectivity filter, a possible cause of the CCD-specific reduced Ca(2+) conductance.
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Affiliation(s)
- David Shirvanyants
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Srinivas Ramachandran
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Yingwu Mei
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Le Xu
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina.
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina.
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