1
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Hantz ER, Tikunova SB, Belevych N, Davis JP, Reiser PJ, Lindert S. Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship. J Chem Inf Model 2023; 63:3462-3473. [PMID: 37204863 PMCID: PMC10496875 DOI: 10.1021/acs.jcim.3c00196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite large investments from academia and industry, heart failure, which results from a disruption of the contractile apparatus, remains a leading cause of death. Cardiac muscle contraction is a calcium-dependent mechanism, which is regulated by the troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium-binding subunit (cNTnC). There is an increasing need for the development of small molecules that increase calcium sensitivity without altering the systolic calcium concentration, thereby strengthening the cardiac function. Here, we examined the effect of our previously identified calcium-sensitizing small molecule, ChemBridge compound 7930079, in the context of several homologous muscle systems. The effect of this molecule on force generation in isolated cardiac trabeculae and slow skeletal muscle fibers was measured. Furthermore, we explored the use of Gaussian accelerated molecular dynamics in sampling highly predictive receptor conformations based on NMR-derived starting structures. Additionally, we took a rational computational approach for lead optimization based on lipophilic diphenyl moieties. This integrated structural-biochemical-physiological approach led to the identification of three novel low-affinity binders, which had similar binding affinities to the known positive inotrope trifluoperazine. The most potent identified calcium sensitizer was compound 16 with an apparent affinity of 117 ± 17 μM.
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Affiliation(s)
- Eric R. Hantz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| | - Svetlana B. Tikunova
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Natalya Belevych
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Jonathan P. Davis
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Peter J. Reiser
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
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2
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Cool AM, Lindert S. Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations. J Chem Inf Model 2023; 63:3534-3543. [PMID: 37261389 PMCID: PMC10506665 DOI: 10.1021/acs.jcim.3c00388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The cardiac thin filament comprises F-actin, tropomyosin, and troponin (cTn). cTn is composed of three subunits: troponin C (cTnC), troponin I (cTnI), and troponin T (cTnT). To computationally study the effect of the thin filament on cTn activation events, we employed targeted molecular dynamics followed by umbrella sampling using a model of the thin filament to measure the thermodynamics of cTn transition events. Our simulations revealed that the thin filament causes an increase in the free energy required to open the cTnC hydrophobic patch and causes a more favorable interaction between this region and the cTnI switch peptide. Mutations to the cTn complex can lead to cardiomyopathy, a collection of diseases that present clinically with symptoms of hypertrophy or dilation of the cardiac muscle, leading to impairment of the heart's ability to function normally and ultimately myocardial infarction or heart failure. Upon introduction of cardiomyopathic mutations to R145 of cTnI, we observed a general decrease in the free energy of opening the cTnC hydrophobic patch, which is on par with previous experimental results. These mutations also exhibited a decrease in electrostatic interactions between cTnI-R145 and actin-E334. After introduction of a small molecule to the wild-type cTnI-actin interface to intentionally disrupt intersubunit contacts, we successfully observed similar thermodynamic consequences and disruptions to the same protein-protein contacts as observed with the cardiomyopathic mutations. Computational studies utilizing the cTn complex in isolation would have been unable to observe these effects, highlighting the importance of using a more physiologically relevant thin-filament model to investigate the global consequences of cardiomyopathic mutations to the cTn complex.
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Affiliation(s)
- Austin M. Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
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3
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Hantz ER, Tikunova SB, Belevych N, Davis JP, Reiser PJ, Lindert S. Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscle and Structure Activity Relationship. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527323. [PMID: 36798160 PMCID: PMC9934531 DOI: 10.1101/2023.02.06.527323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Despite large investments from academia and industry, heart failure, which results from a disruption of the contractile apparatus, remains a leading cause of death. Cardiac muscle contraction is a calcium-dependent mechanism, which is regulated by the troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium binding subunit (cNTnC). There is an increasing need for the development of small molecules that increase calcium sensitivity without altering systolic calcium concentration, thereby strengthening cardiac function. Here, we examined the effect of our previously identified calcium sensitizing small molecule, ChemBridge compound 7930079, in the context of several homologous muscle systems. The effect of this molecule on force generation in isolated cardiac trabeculae and slow skeletal muscle fibers was measured. Furthermore, we explored the use of Gaussian accelerated molecular dynamics in sampling highly predictive receptor conformations based on NMR derived starting structures. Additionally, we took a rational computational approach for lead optimization based on lipophilic diphenyl moieties. This led to the identification of three novel low affinity binders, which had similar binding affinities to known positive inotrope trifluoperazine. The most potent identified calcium sensitizer was compound 16 with an apparent affinity of 117 ± 17 μM .
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Affiliation(s)
- Eric R. Hantz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| | - Svetlana B. Tikunova
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Natalya Belevych
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Jonathan P. Davis
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Peter J. Reiser
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210,Correspondence to: Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 W. 18th Avenue, Columbus, OH 43210, 614-292-8284 (office), 614-292-1685 (fax),
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4
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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5
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Hantz ER, Lindert S. Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C. J Chem Inf Model 2022; 62:6201-6208. [PMID: 36383927 PMCID: PMC10497304 DOI: 10.1021/acs.jcim.2c01132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Calcium-dependent heart muscle contraction is regulated by the cardiac troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium binding subunit (cNTnC). cNTnC contains one calcium binding site (site II), and altered calcium binding in this site has been studied for decades. It has been previously shown that cNTnC mutants, which increase calcium sensitization may have therapeutic benefits, such as restoring cardiac muscle contractility and functionality post-myocardial infarction events. Here, we computationally characterized eight mutations for their potential effects on calcium binding affinity in site II of cNTnC. We utilized two distinct methods to estimate calcium binding: adaptive steered molecular dynamics (ASMD) and thermodynamic integration (TI). We observed a sensitizing trend for all mutations based on the employed ASMD methodology. The TI results showed excellent agreement with experimentally known calcium binding affinities in wild-type cNTnC. Based on the TI results, five mutants were predicted to increase calcium sensitivity in site II. This study presents an interesting comparison of the two computational methods, which have both been shown to be valuable tools in characterizing the impacts of calcium sensitivity in mutant cNTnC systems.
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Affiliation(s)
- Eric R. Hantz
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210
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6
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Cool AM, Lindert S. Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin. J Chem Inf Model 2022; 62:5666-5674. [PMID: 36283742 PMCID: PMC9712266 DOI: 10.1021/acs.jcim.2c00508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cardiac troponin (cTn) complex is an important regulatory protein in heart contraction. Upon binding of Ca2+, cTn undergoes a conformational shift that allows the troponin I switch peptide (cTnISP) to be released from the actin filament and bind to the troponin C hydrophobic patch (cTnCHP). Mutations and modifications to this complex can change its sensitivity to Ca2+ and alter the energetics of the transition from the Ca2+-unbound, cTnISP-unbound form to the Ca2+-bound, cTnISP-bound form. We utilized targeted molecular dynamics (TMD) to obtain a trajectory of this transition pathway, followed by umbrella sampling to estimate the free energy associated with the cTnISP-cTnCHP binding and the cTnCHP opening events for wild-type (WT) cTn. We were able to reproduce experimental values for the cTnISP-cTnCHP binding event and obtain cTnCHP opening free energies in agreement with previous computational measurements of smaller cTnC systems. This excellent agreement for WT cTn demonstrated the strength of computational methods in studying the dynamics and energetics of the cTn complex. We then introduced mutations to the cTn complex that cause cardiomyopathy or alter its Ca2+ sensitivity and observed a general decrease in the free energy of opening the cTnCHP. For these same mutations, we observed no general trend in the effect on the cTnISP-cTnCHP binding event. Our method sets the stage for future computational studies on this system that predict the consequences of yet uncharacterized mutations on cTn dynamics and energetics.
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Affiliation(s)
- Austin M Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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7
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Keyt LK, Duran JM, Bui QM, Chen C, Miyamoto MI, Silva Enciso J, Tardiff JC, Adler ED. Thin filament cardiomyopathies: A review of genetics, disease mechanisms, and emerging therapeutics. Front Cardiovasc Med 2022; 9:972301. [PMID: 36158814 PMCID: PMC9489950 DOI: 10.3389/fcvm.2022.972301] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
All muscle contraction occurs due to the cyclical interaction between sarcomeric thin and thick filament proteins within the myocyte. The thin filament consists of the proteins actin, tropomyosin, Troponin C, Troponin I, and Troponin T. Mutations in these proteins can result in various forms of cardiomyopathy, including hypertrophic, restrictive, and dilated phenotypes and account for as many as 30% of all cases of inherited cardiomyopathy. There is significant evidence that thin filament mutations contribute to dysregulation of Ca2+ within the sarcomere and may have a distinct pathomechanism of disease from cardiomyopathy associated with thick filament mutations. A number of distinct clinical findings appear to be correlated with thin-filament mutations: greater degrees of restrictive cardiomyopathy and relatively less left ventricular (LV) hypertrophy and LV outflow tract obstruction than that seen with thick filament mutations, increased morbidity associated with heart failure, increased arrhythmia burden and potentially higher mortality. Most therapies that improve outcomes in heart failure blunt the neurohormonal pathways involved in cardiac remodeling, while most therapies for hypertrophic cardiomyopathy involve use of negative inotropes to reduce LV hypertrophy or septal reduction therapies to reduce LV outflow tract obstruction. None of these therapies directly address the underlying sarcomeric dysfunction associated with thin-filament mutations. With mounting evidence that thin filament cardiomyopathies occur through a distinct mechanism, there is need for therapies targeting the unique, underlying mechanisms tailored for each patient depending on a given mutation.
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Affiliation(s)
- Lucas K. Keyt
- Department of Internal Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jason M. Duran
- Department of Cardiology, University of California, San Diego, San Diego, CA, United States
| | - Quan M. Bui
- Department of Cardiology, University of California, San Diego, San Diego, CA, United States
| | - Chao Chen
- Department of Cardiology, University of California, San Diego, San Diego, CA, United States
| | | | - Jorge Silva Enciso
- Department of Cardiology, University of California, San Diego, San Diego, CA, United States
| | - Jil C. Tardiff
- Department of Medicine and Biomedical Engineering, University of Arizona, Tucson, AZ, United States
| | - Eric D. Adler
- Department of Cardiology, University of California, San Diego, San Diego, CA, United States
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Hassoun R, Budde H, Mügge A, Hamdani N. Cardiomyocyte Dysfunction in Inherited Cardiomyopathies. Int J Mol Sci 2021; 22:11154. [PMID: 34681814 PMCID: PMC8541428 DOI: 10.3390/ijms222011154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 01/10/2023] Open
Abstract
Inherited cardiomyopathies form a heterogenous group of disorders that affect the structure and function of the heart. Defects in the genes encoding sarcomeric proteins are associated with various perturbations that induce contractile dysfunction and promote disease development. In this review we aimed to outline the functional consequences of the major inherited cardiomyopathies in terms of myocardial contraction and kinetics, and to highlight the structural and functional alterations in some sarcomeric variants that have been demonstrated to be involved in the pathogenesis of the inherited cardiomyopathies. A particular focus was made on mutation-induced alterations in cardiomyocyte mechanics. Since no disease-specific treatments for familial cardiomyopathies exist, several novel agents have been developed to modulate sarcomere contractility. Understanding the molecular basis of the disease opens new avenues for the development of new therapies. Furthermore, the earlier the awareness of the genetic defect, the better the clinical prognostication would be for patients and the better the prevention of development of the disease.
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Affiliation(s)
- Roua Hassoun
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Cardiology, St. Josef-Hospital and Bergmannsheil, Ruhr University Bochum, 44801 Bochum, Germany
| | - Heidi Budde
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Cardiology, St. Josef-Hospital and Bergmannsheil, Ruhr University Bochum, 44801 Bochum, Germany
| | - Andreas Mügge
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Cardiology, St. Josef-Hospital and Bergmannsheil, Ruhr University Bochum, 44801 Bochum, Germany
| | - Nazha Hamdani
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Cardiology, St. Josef-Hospital and Bergmannsheil, Ruhr University Bochum, 44801 Bochum, Germany
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9
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Cool AM, Lindert S. Computational Methods Elucidate Consequences of Mutations and Post-translational Modifications on Troponin I Effective Concentration to Troponin C. J Phys Chem B 2021; 125:7388-7396. [PMID: 34213339 DOI: 10.1021/acs.jpcb.1c03844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ca2+ binding to cardiac troponin C (cTnC) causes a conformational shift that exposes a hydrophobic patch (cTnCHP) for binding of the cTnI switch peptide (cTnISP), ultimately resulting in contraction of the heart. The inhibitory peptide (cTnIIP), attached at the N-terminal end of the cTnISP, serves as a tether for the cTnISP to the rest of the troponin complex. Due to this tethered nature, the cTnISP remains within proximity of the hydrophobic patch region, resulting in the cTnCHP experiencing an elevated "effective concentration" of the cTnISP. Mutations to the cTnIIP region have been hypothesized to cause disease by affecting the ability of the cTnISP to "find" the hydrophobic patch, resulting in alterations to the heart's ability to contract normally. We tested this hypothesis using molecular dynamics (MD) simulations of the troponin complex using a model that contained all three subunits of troponin: C, I, and T. We developed methods that allowed us to quantitatively measure the effective concentration of the cTnISP from the simulations. A significant reduction in the cTnISP effective concentration was observed when the cTnIIP was removed from the system, showcasing the importance of a tethered cTnISP. Through accelerated MD methods, we proposed the minimum effective concentration of a tethered cTnISP to be approximately 21 mM. Modification of the cTnIIP via PKC-mediated phosphorylation of T143 was shown to significantly increase the estimated effective concentration of cTnISP, help the cTnISP find the cTnCHP more effectively, and maintain the relative shape of the cTnIIP when compared to the native model. All of these data indicate that pT143 may be able to help promote binding of cTnISP to the cTnCHP. We then tested six mutations within the cTnIIP region that are known cTnC Ca2+-sensitizing mutations and have been linked with cardiomyopathy. We did not observe a significant reduction in the effective concentration upon the introduction of these mutations; however, we did observe increased variability in the flexibility and dynamics of the cTnIIP region when compared to native. Our observations led us to hypothesize that the mechanism by which these cardiomyopathic mutations affect Ca2+ sensitivity is by altering the off rate of cTnISP from the hydrophobic patch.
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Affiliation(s)
- Austin M Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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10
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Immadisetty K, Sun B, Kekenes-Huskey PM. Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins. J Phys Chem B 2021; 125:6390-6405. [PMID: 34115511 PMCID: PMC8848088 DOI: 10.1021/acs.jpcb.1c01269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Members of the parvalbumin (PV) family of calcium (Ca2+) binding proteins (CBPs) share a relatively high level of sequence similarity. However, their Ca2+ affinities and selectivities against competing ions like Mg2+ can widely vary. We conducted molecular dynamics simulations of several α-parvalbumin (αPV) constructs with micromolar to nanomolar Ca2+ affinities to identify structural and dynamic features that contribute to their binding of ions. Specifically, we examined a D94S/G98E construct with a lower Ca2+ affinity (≈-18 kcal/mol) relative to the wild type (WT) (≈-22 kcal/mol) and an S55D/E59D variant with enhanced affinity (≈-24 kcal/mol). Additionally, we also examined the binding of Mg2+ to these isoforms, which is much weaker than Ca2+. We used mean spherical approximation (MSA) theory to evaluate ion binding thermodynamics within the proteins' EF-hand domains to account for the impact of ions' finite sizes and the surrounding electrolyte composition. While the MSA scores differentiated Mg2+ from Ca2+, they did not indicate that Ca2+ binding affinities at the binding loop differed between the PV isoforms. Instead, molecular mechanics generalized Born surface area (MM/GBSA) approximation energies, which we used to quantify the thermodynamic cost of structural rearrangement of the proteins upon binding ions, indicated that S55D/E59D αPV favored Ca2+ binding by -20 kcal/mol relative to WT versus 30 kcal/mol for D94S/G98E αPV. Meanwhile, Mg2+ binding was favored for the S55D/E59D αPV and D94S/G98E αPV variants by -18.32 and -1.65 kcal/mol, respectively. These energies implicate significant contributions to ion binding beyond oxygen coordination at the binding loop, which stemmed from changes in α-helicity, β-sheet character, and hydrogen bonding. Hence, Ca2+ affinity and selectivity against Mg2+ are emergent properties stemming from both local effects within the proteins' ion binding sites as well as non-local contributions elsewhere. Our findings broaden our understanding of the molecular bases governing αPV ion binding that are likely shared by members of the broad family of CBPs.
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Affiliation(s)
| | - Bin Sun
- Stritch School of Medicine, Maywood, Illinois 60153, United States
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11
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Hantz ER, Lindert S. Adaptative Steered Molecular Dynamics Study of Mutagenesis Effects on Calcium Affinity in the Regulatory Domain of Cardiac Troponin C. J Chem Inf Model 2021; 61:3052-3057. [PMID: 34080877 DOI: 10.1021/acs.jcim.1c00419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calcium-dependent cardiac muscle contraction is regulated by the protein complex troponin (cTn) and specifically by the regulatory N-terminal domain (N-cTnC) which contains one active Ca2+ binding site (site II). It has been previously shown that cardiac muscle contractility and functionality is affected by mutations in N-cTnC which alter calcium binding affinity. Here, we describe the application of adaptive steered molecular dynamics to characterize the influence of N-cTnC mutations on site II calcium binding affinity. We observed the correct trends for all of the studied calcium sensitizing and desensitizing mutants, in conjunction with loop II perturbations. Additionally, the potential of mean force accuracy was shown to increase substantially with increasingly slower speeds and using fewer trajectories. This study presents a novel approach to computationally estimate the Ca2+ binding affinity of N-cTnC structures and is a valuable potential tool to support the design and characterization of novel mutations with potential therapeutic benefits.
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Affiliation(s)
- Eric R Hantz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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12
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Marques MA, Landim-Vieira M, Moraes AH, Sun B, Johnston JR, Dieseldorff Jones KM, Cino EA, Parvatiyar MS, Valera IC, Silva JL, Galkin VE, Chase PB, Kekenes-Huskey PM, de Oliveira GAP, Pinto JR. Anomalous structural dynamics of minimally frustrated residues in cardiac troponin C triggers hypertrophic cardiomyopathy. Chem Sci 2021; 12:7308-7323. [PMID: 34163821 PMCID: PMC8171346 DOI: 10.1039/d1sc01886h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022] Open
Abstract
Cardiac TnC (cTnC) is highly conserved among mammals, and genetic variants can result in disease by perturbing Ca2+-regulation of myocardial contraction. Here, we report the molecular basis of a human mutation in cTnC's αD-helix (TNNC1-p.C84Y) that impacts conformational dynamics of the D/E central-linker and sampling of discrete states in the N-domain, favoring the "primed" state associated with Ca2+ binding. We demonstrate cTnC's αD-helix normally functions as a central hub that controls minimally frustrated interactions, maintaining evolutionarily conserved rigidity of the N-domain. αD-helix perturbation remotely alters conformational dynamics of the N-domain, compromising its structural rigidity. Transgenic mice carrying this cTnC mutation exhibit altered dynamics of sarcomere function and hypertrophic cardiomyopathy. Together, our data suggest that disruption of evolutionary conserved molecular frustration networks by a myofilament protein mutation may ultimately compromise contractile performance and trigger hypertrophic cardiomyopathy.
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Affiliation(s)
- Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Adolfo H Moraes
- Department of Chemistry, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago Maywood IL USA
| | - Jamie R Johnston
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Karissa M Dieseldorff Jones
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Elio A Cino
- Department of Biochemistry and Immunology, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Michelle S Parvatiyar
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Isela C Valera
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Vitold E Galkin
- Department of Physiological Sciences, Eastern Virginia Medical School Norfolk VA USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University Tallahassee FL USA
| | | | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
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13
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Kim SS, Alves MJ, Gygli P, Otero J, Lindert S. Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex. Curr Comput Aided Drug Des 2021; 17:57-68. [PMID: 31889491 DOI: 10.2174/1573409916666191231113055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Given the diverse roles of cyclin A2 both in cell cycle regulation and in DNA damage response, identifying small molecule regulators of cyclin A2 activity carries significant potential to regulate diverse cellular processes in both ageing/neurodegeneration and in cancer. OBJECTIVE Based on cyclin A2's recently discovered role in DNA repair, we hypothesized that small molecule inhibitors that were predicted to bind to both cyclin A2 and CDK2 will be useful as a radiosensitizer of cancer cells. In this study, we used structure-based drug discovery to find inhibitors that target both cyclin A2 and CDK2. METHODS Molecular dynamics simulations were used to generate diverse binding pocket conformations for application of the relaxed complex scheme. We then used structure-based virtual screening to find potential dual cyclin A2 and CDK2 inhibitors. Based on a consensus score of docked poses from Glide and AutoDock Vina, we identified about 40 promising hit compounds, where all PAINS scaffolds were removed from consideration. A biochemical luminescence assay of cyclin A2-CDK2 function was used for experimental verification. RESULTS Four lead inhibitors of cyclin A2-CDK2 complex have been identified using a relaxed complex scheme virtual screen have been verified in a biochemical luminescence assay of cyclin A2- CDK2 function. Two of the four lead inhibitors had inhibitory concentrations in the nanomolar range. CONCLUSION The four cyclin A2-CDK2 complex inhibitors are the first reported inhibitors that were specifically designed not to target the cyclin A2-CDK2 protein-protein interface. Overall, our results highlight the potential of combined advanced computational tools and biochemical verification to discover novel binding scaffolds.
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Affiliation(s)
- Stephanie S Kim
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
| | - Michele J Alves
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Patrick Gygli
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Jose Otero
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
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14
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Powers JD, Kooiker KB, Mason AB, Teitgen AE, Flint GV, Tardiff JC, Schwartz SD, McCulloch AD, Regnier M, Davis J, Moussavi-Harami F. Modulating the tension-time integral of the cardiac twitch prevents dilated cardiomyopathy in murine hearts. JCI Insight 2020; 5:142446. [PMID: 32931484 PMCID: PMC7605524 DOI: 10.1172/jci.insight.142446] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is often associated with sarcomere protein mutations that confer reduced myofilament tension–generating capacity. We demonstrated that cardiac twitch tension-time integrals can be targeted and tuned to prevent DCM remodeling in hearts with contractile dysfunction. We employed a transgenic murine model of DCM caused by the D230N-tropomyosin (Tm) mutation and designed a sarcomere-based intervention specifically targeting the twitch tension-time integral of D230N-Tm hearts using multiscale computational models of intramolecular and intermolecular interactions in the thin filament and cell-level contractile simulations. Our models predicted that increasing the calcium sensitivity of thin filament activation using the cardiac troponin C (cTnC) variant L48Q can sufficiently augment twitch tension-time integrals of D230N-Tm hearts. Indeed, cardiac muscle isolated from double-transgenic hearts expressing D230N-Tm and L48Q cTnC had increased calcium sensitivity of tension development and increased twitch tension-time integrals compared with preparations from hearts with D230N-Tm alone. Longitudinal echocardiographic measurements revealed that DTG hearts retained normal cardiac morphology and function, whereas D230N-Tm hearts developed progressive DCM. We present a computational and experimental framework for targeting molecular mechanisms governing the twitch tension of cardiomyopathic hearts to counteract putative mechanical drivers of adverse remodeling and open possibilities for tension-based treatments of genetic cardiomyopathies. Tuning the molecular mechanisms that govern the twitch tension of cardiomyopathic hearts counteracts mechanical drivers of adverse remodeling.
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Affiliation(s)
- Joseph D Powers
- Department of Bioengineering, College of Engineering and School of Medicine, University of Washington, Seattle, Washington, USA.,Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Kristina B Kooiker
- Division of Cardiology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Allison B Mason
- Department of Chemistry and Biochemistry, College of Science, and
| | - Abigail E Teitgen
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Galina V Flint
- Department of Bioengineering, College of Engineering and School of Medicine, University of Washington, Seattle, Washington, USA
| | - Jil C Tardiff
- Department of Biomedical Engineering, College of Engineering, University of Arizona, Tucson, Arizona, USA
| | | | - Andrew D McCulloch
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.,Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Michael Regnier
- Department of Bioengineering, College of Engineering and School of Medicine, University of Washington, Seattle, Washington, USA
| | - Jennifer Davis
- Department of Bioengineering, College of Engineering and School of Medicine, University of Washington, Seattle, Washington, USA.,Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA
| | - Farid Moussavi-Harami
- Division of Cardiology, School of Medicine, University of Washington, Seattle, Washington, USA
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15
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Lin YH, Yap J, Ramachandra CJ, Hausenloy DJ. New insights provided by myofibril mechanics in inherited cardiomyopathies. CONDITIONING MEDICINE 2019; 2:213-224. [PMID: 32133438 PMCID: PMC7055865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cardiomyopathies represent a heterogeneous group of cardiac disorders that perturb cardiac contraction and/or relaxation, and can result in arrhythmias, heart failure, and sudden cardiac death. Based on morphological and functional differences, cardiomyopathies have been classified into hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and restrictive cardiomyopathy (RCM). It has been well documented that mutations in genes encoding sarcomeric proteins are associated with the onset of inherited cardiomyopathies. However, correlating patient genotype to the clinical phenotype has been challenging because of the complex genetic backgrounds, environmental influences, and lifestyles of individuals. Thus, "scaling down" the focus to the basic contractile unit of heart muscle using isolated single myofibril function techniques is of great importance and may be used to understand the molecular basis of disease-causing sarcomeric mutations. Single myofibril bundles harvested from diseased human or experimental animal hearts, as well as cultured adult cardiomyocytes or human cardiomyocytes derived from induced pluripotent stem cells, can be used, thereby providing an ideal multi-level, cross-species platform to dissect sarcomeric function in cardiomyopathies. Here, we will review the myofibril function technique, and discuss alterations in myofibril mechanics, which are known to occur in sarcomeric genetic mutations linked to inherited HCM, DCM, and RCM, and describe the therapeutic potential for future target identification.
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Affiliation(s)
- Ying-Hsi Lin
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
- Cardiovascular & Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore
| | - Jonathan Yap
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, USA
| | - Chrishan J.A. Ramachandra
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
- Cardiovascular & Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore
| | - Derek J. Hausenloy
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
- Cardiovascular & Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore
- Yong Loo Lin School of Medicine, National University Singapore, Singapore
- The Hatter Cardiovascular Institute, University College London, London, UK
- The National Institute of Health Research University College London Hospitals
- Biomedical Research Centre, Research & Development, London, UK
- Tecnologico de Monterrey, Centro de Biotecnologia-FEMSA, Nuevo Leon, Mexico
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16
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Bowman JD, Lindert S. Computational Studies of Cardiac and Skeletal Troponin. Front Mol Biosci 2019; 6:68. [PMID: 31448287 PMCID: PMC6696891 DOI: 10.3389/fmolb.2019.00068] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022] Open
Abstract
Troponin is a key regulatory protein in muscle contraction, consisting of three subunits troponin C (TnC), troponin I (TnI), and troponin T (TnT). Calcium association to TnC initiates contraction by causing a series of dynamic and conformational changes that allow the switch peptide of TnI to bind and subsequently cross bridges to form between the thin and thick filament of the sarcomere. Owing to its pivotal role in contraction regulation, troponin has been the focus of numerous computational studies over the last decade. These studies elegantly supplemented a large volume of experimental work and focused on the structure, dynamics and function of the whole troponin complex, individual subunits, and even on segments of the thin filament. Molecular dynamics, Brownian dynamics, and free energy simulations have been used to elucidate the conformational dynamics and underlying free energy landscape of troponin, calcium, and switch peptide binding, as well as the effect of disease mutations, small molecules and post-translational modifications such as phosphorylation. Frequently, simulations have been used to confirm or explain experimental observations. Computer-aided drug discovery tools have been employed to identify novel potential calcium sensitizing agents binding to the TnC-TnI interface. Finally, Markov modeling has contributed to simulating contraction within the sarcomere on the mesoscale. Here we are reviewing and classifying the existing computational work on troponin and its subunits, outline current gaps in simulations elucidating troponin's role in contraction and suggest potential future developments in the field.
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Affiliation(s)
- Jacob D Bowman
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States
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17
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Marston S, Zamora JE. Troponin structure and function: a view of recent progress. J Muscle Res Cell Motil 2019; 41:71-89. [PMID: 31030382 PMCID: PMC7109197 DOI: 10.1007/s10974-019-09513-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/12/2019] [Indexed: 12/15/2022]
Abstract
The molecular mechanism by which Ca2+ binding and phosphorylation regulate muscle contraction through Troponin is not yet fully understood. Revealing the differences between the relaxed and active structure of cTn, as well as the conformational changes that follow phosphorylation has remained a challenge for structural biologists over the years. Here we review the current understanding of how Ca2+, phosphorylation and disease-causing mutations affect the structure and dynamics of troponin to regulate the thin filament based on electron microscopy, X-ray diffraction, NMR and molecular dynamics methodologies.
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Affiliation(s)
- Steven Marston
- NHLI and Chemistry Departments, Imperial College London, W12 0NN, London, UK.
| | - Juan Eiros Zamora
- NHLI and Chemistry Departments, Imperial College London, W12 0NN, London, UK
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18
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Moving beyond simple answers to complex disorders in sarcomeric cardiomyopathies: the role of integrated systems. Pflugers Arch 2019; 471:661-671. [PMID: 30848350 DOI: 10.1007/s00424-019-02269-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/01/2019] [Indexed: 12/26/2022]
Abstract
The classic clinical definition of hypertrophic cardiomyopathy (HCM) as originally described by Teare is deceptively simple, "left ventricular hypertrophy in the absence of any identifiable cause." Longitudinal studies, however, including a seminal study performed by Frank and Braunwald in 1968, clearly described the disorder much as we know it today, a complex, progressive, and highly variable cardiomyopathy affecting ~ 1/500 individuals worldwide. Subsequent genetic linkage studies in the early 1990s identified mutations in virtually all of the protein components of the cardiac sarcomere as the primary molecular cause of HCM. In addition, a substantial proportion of inherited dilated cardiomyopathy (DCM) has also been linked to sarcomeric protein mutations. Despite our deep understanding of the overall function of the sarcomere as the primary driver of cardiac contractility, the ability to use genotype in patient management remains elusive. A persistent challenge in the field from both the biophysical and clinical standpoints is how to rigorously link high-resolution protein dynamics and mechanics to the long-term cardiovascular remodeling process that characterizes these complex disorders. In this review, we will explore the depth of the problem from both the standpoint of a multi-subunit, highly conserved and dynamic "machine" to the resultant clinical and structural human phenotype with an emphasis on new, integrative approaches that can be widely applied to identify both novel disease mechanisms and new therapeutic targets for these primary biophysical disorders of the cardiac sarcomere.
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19
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Bailey KE, MacGowan GA, Tual-Chalot S, Phillips L, Mohun TJ, Henderson DJ, Arthur HM, Bamforth SD, Phillips HM. Disruption of embryonic ROCK signaling reproduces the sarcomeric phenotype of hypertrophic cardiomyopathy. JCI Insight 2019; 5:125172. [PMID: 30835717 PMCID: PMC6538384 DOI: 10.1172/jci.insight.125172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Sarcomeric disarray is a hallmark of gene mutations in patients with hypertrophic cardiomyopathy (HCM). However, it is unknown when detrimental sarcomeric changes first occur and whether they originate in the developing embryonic heart. Furthermore, Rho kinase (ROCK) is a serine/threonine protein kinase that is critical for regulating the function of several sarcomeric proteins, and therefore, our aim was to determine whether disruption of ROCK signaling during the earliest stages of heart development would disrupt the integrity of sarcomeres, altering heart development and function. Using a mouse model in which the function of ROCK is specifically disrupted in embryonic cardiomyocytes, we demonstrate a progressive cardiomyopathy that first appeared as sarcomeric disarray during cardiogenesis. This led to abnormalities in the structure of the embryonic ventricular wall and compensatory cardiomyocyte hypertrophy during fetal development. This sarcomeric disruption and hypertrophy persisted throughout adult life, triggering left ventricular concentric hypertrophy with systolic dysfunction, and reactivation of fetal gene expression and cardiac fibrosis, all typical features of HCM. Taken together, our findings establish a mechanism for the developmental origin of the sarcomeric phenotype of HCM and suggest that variants in the ROCK genes or disruption of ROCK signaling could, in part, contribute to its pathogenesis. Disruption of ROCK activity in embryonic cardiomyocytes revealed a developmental origin for hypertrophic cardiomyopathy.
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Affiliation(s)
- Kate E Bailey
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Guy A MacGowan
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon Tual-Chalot
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lauren Phillips
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Deborah J Henderson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen M Arthur
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon D Bamforth
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen M Phillips
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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20
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van der Velden J, Stienen GJM. Cardiac Disorders and Pathophysiology of Sarcomeric Proteins. Physiol Rev 2019; 99:381-426. [PMID: 30379622 DOI: 10.1152/physrev.00040.2017] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The sarcomeric proteins represent the structural building blocks of heart muscle, which are essential for contraction and relaxation. During recent years, it has become evident that posttranslational modifications of sarcomeric proteins, in particular phosphorylation, tune cardiac pump function at rest and during exercise. This delicate, orchestrated interaction is also influenced by mutations, predominantly in sarcomeric proteins, which cause hypertrophic or dilated cardiomyopathy. In this review, we follow a bottom-up approach starting from a description of the basic components of cardiac muscle at the molecular level up to the various forms of cardiac disorders at the organ level. An overview is given of sarcomere changes in acquired and inherited forms of cardiac disease and the underlying disease mechanisms with particular reference to human tissue. A distinction will be made between the primary defect and maladaptive/adaptive secondary changes. Techniques used to unravel functional consequences of disease-induced protein changes are described, and an overview of current and future treatments targeted at sarcomeric proteins is given. The current evidence presented suggests that sarcomeres not only form the basis of cardiac muscle function but also represent a therapeutic target to combat cardiac disease.
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Affiliation(s)
- Jolanda van der Velden
- Amsterdam UMC, Vrije Universiteit Amsterdam, Physiology, Amsterdam Cardiovascular Sciences, Amsterdam , The Netherlands ; and Department of Physiology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Ger J M Stienen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Physiology, Amsterdam Cardiovascular Sciences, Amsterdam , The Netherlands ; and Department of Physiology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
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21
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Mortazavi MMT, Ganjpour Sales J, Nouri-Vaskeh M, Parish M, Abdolhosseynzadeh S. Perioperative Cardiac Troponin I Levels in Patients Undergoing Total Hip and Total Knee Arthroplasty: A Single Center Study. Anesth Pain Med 2018; 8:e84228. [PMID: 30719421 PMCID: PMC6347731 DOI: 10.5812/aapm.84228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/20/2018] [Accepted: 11/10/2018] [Indexed: 11/16/2022] Open
Abstract
Background Cardiac injury is one of the significant perioperative complications in major orthopedic surgeries and its early diagnosis is useful in the reduction of postoperative comorbidity. The cardiac troponin is a sensitive and specific biomarker for detecting this damage. Objectives The aim of this study was to evaluate the levels of perioperative cardiac troponin I (cTnI) before and after arthroplasty in patients undergoing total hip arthroplasty (THA) and total knee arthroplasty (TKA). The effects of related variables and probable major cardiac complications were evaluated in this study. Methods For one year, in a prospective, cross-sectional study, the serum levels of cTnI before and 48 hours after arthroplasty were evaluated in 52 patients. Possible contributing factors including age, gender, body mass index (BMI), daily activity, history of hospitalization due to cardiovascular diseases, underlying illness, and medications were recorded. The Chi-square test, Pearson correlation, and Spearman test were used to examine the relationship between variables. Results The mean cTnI increased significantly after arthroplasty (P < 0.001). There was no significant relationship between age (P = 0.708), gender (P = 0.225), BMI (P = 0.195), daily activity (0.441), underlying illness (P = 0.244), and cTnI levels after arthroplasty. Linear regression showed BMI was significantly correlated with troponin changes (P = 0.006). Five patients had heart palpitations and one had chest pain, but none of the patients had any findings in favor of cardiac injury. Conclusions cTnI levels after THA and TKA increased significantly, but this elevation was in the normal range. In addition, none of them had a new cardiac complication after arthroplasty.
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Affiliation(s)
- Mir Mohammad Taghi Mortazavi
- Department of Anesthesiology and Critical Care, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Ganjpour Sales
- Department of Orthopedics Surgery, Shohada Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Nouri-Vaskeh
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Medical Philosophy and History Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Corresponding Author: Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Postal Code: 5166614756, Tabriz, Iran.
| | - Masoud Parish
- Department of Anesthesiology and Critical Care, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Corresponding Author: Department of Anesthesiology and Critical Care, Faculty of Medicine, Tabriz University of Medical Sciences, Postal Code: 5166614756, Tabriz, Iran.
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22
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Bowman JD, Lindert S. Molecular Dynamics and Umbrella Sampling Simulations Elucidate Differences in Troponin C Isoform and Mutant Hydrophobic Patch Exposure. J Phys Chem B 2018; 122:7874-7883. [PMID: 30070845 DOI: 10.1021/acs.jpcb.8b05435] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Troponin C (TnC) facilitates muscle contraction through calcium-binding within its N-terminal region (NTnC). As previously observed using molecular dynamics (MD) simulations, this calcium-binding event leads to an increase in the dynamics of helices lining a hydrophobic patch on TnC. Simulation times of multiple microseconds were required to even see a partial opening of the hydrophobic patch, limiting the ability to thoroughly and quantitatively investigate these rare events. Here we describe the application of umbrella sampling to probe the TnC hydrophobic patch opening in a more targeted and quantitative fashion. Umbrella sampling was utilized to investigate the differences in the free energy of opening between cardiac (cTnC) and fast skeletal TnC (sTnC). We found that, in agreement with previous reports, holo (calcium-bound) sTnC had a lower free energy of opening compared with holo cTnC. Additionally, differences in the free energy of opening of hypertrophic (HCM) and dilated cardiomyopathy (DCM) cTnC systems were investigated. MD simulations and umbrella sampling revealed a lower free energy of opening for the HCM mutations A8V and A31S, as well as the calcium-sensitizing mutation L48Q. The DCM mutations, Y5H, Q50R, and E59D/D75Y, all exhibited a higher free energy of opening. An umbrella sampling simulation of cTnI-bound holo cTnC exhibited the lowest free energy in the open configuration, in agreement with experimental data. In conclusion, this study presents a novel and successful protocol for applying umbrella sampling simulations to quantitatively study the molecular basis of muscle contraction and proposes a mechanism by which HCM and DCM-associated mutations influence contraction.
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Affiliation(s)
- Jacob D Bowman
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
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23
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In silico investigation of the molecular effects caused by R123H variant in secretory phospholipase A2-IIA associated with ARDS. J Mol Graph Model 2018. [PMID: 29529495 DOI: 10.1016/j.jmgm.2018.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phospholipase A2-IIA catalyzes the hydrolysis of the sn-2 ester of glycerophospholipids. A rare c.428G > A (p.Arg143His) variant in PLA2G2A gene was found in two infants affected by acute respiratory distress syndrome (ARDS) by whole coding region and exon/intron boundaries sequencing. To obtain insights into the possible molecular effects of the rare R123H mutation in secretory PLA2-IIA (sPLA2-IIA), molecular modelling, molecular dynamics (MD) using principal component analysis (PCA) and continuum electrostatic calculations were conducted on the crystal structure of the wild type protein and on a generated model structure of the R123H mutant. Analysis of MD trajectories indicate that the overall stability of the protein is not affected by this mutation but nevertheless the catalytically crucial H-bond between Tyr51 and Asp91 as well as main electrostatic interactions in the region close to the mutation site are altered. PCA results indicate that the R123H replacement alter the internal molecular motions of the enzyme and that collective motions are increased. Electrostatic surface potential studies suggest that after mutation the interfacial binding to anionic phospholipid membranes and anionic proteins may be changed. The strengthening of electrostatic interactions may be propagated into the active site region thus potentially affecting the substrate recognition and enzymatic activity. Our findings provide the basis for further investigation and advances our understanding of the effects of mutations on sPLA2 structure and function.
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24
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Matsuo T, Tominaga T, Kono F, Shibata K, Fujiwara S. Modulation of the picosecond dynamics of troponin by the cardiomyopathy-causing mutation K247R of troponin T observed by quasielastic neutron scattering. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1781-1789. [PMID: 28923663 DOI: 10.1016/j.bbapap.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/18/2017] [Accepted: 09/14/2017] [Indexed: 11/16/2022]
Abstract
Troponin (Tn), consisting of three subunits (TnC, TnI, and TnT), regulates cardiac muscle contraction in a Ca2+-dependent manner. Various point mutations of human cardiac Tn are known to cause familial hypertrophic cardiomyopathy due to aberration of the regulatory function. In this study, we investigated the effects of one of these mutations, K247R of TnT, on the picosecond dynamics of the Tn core domain (Tn-CD), consisting of TnC, TnI and TnT2 (183-288 residues of TnT), by carrying out the quasielastic neutron scattering measurements on the reconstituted Tn-CD containing either the wild-type TnT2 (wtTn-CD) or the mutant TnT2 (K247R-Tn-CD) in the absence and presence of Ca2+. It was found that Ca2+-binding to the wtTn-CD decreases the residence time of atomic motions in the Tn-CD with slight changes in amplitudes, suggesting that the regulatory function mainly requires modulation of frequency of atomic motions. On the other hand, the K247R-Tn-CD shows different dynamic behavior from that of the wtTn-CD both in the absence and presence of Ca2+. In particular, the K247R-Tn-CD exhibits a larger amplitude than the wtTn-CD in the presence of Ca2+, suggesting that the mutant can explore larger conformational space than the wild-type. This increased flexibility should be relevant to the functional aberration of this mutant.
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Affiliation(s)
- Tatsuhito Matsuo
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Tokai, Ibaraki 319-1106, Japan
| | - Fumiaki Kono
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Kaoru Shibata
- Neutron Science Section, J-PARC Center, Tokai, Ibaraki 319-1195, Japan
| | - Satoru Fujiwara
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan.
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Stevens CM, Rayani K, Singh G, Lotfalisalmasi B, Tieleman DP, Tibbits GF. Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca 2+-sensitizing mutations. J Biol Chem 2017; 292:11915-11926. [PMID: 28533433 DOI: 10.1074/jbc.m116.770776] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/07/2017] [Indexed: 12/31/2022] Open
Abstract
Cardiac troponin C (cTnC) is the regulatory protein that initiates cardiac contraction in response to Ca2+ TnC binding Ca2+ initiates a cascade of protein-protein interactions that begins with the opening of the N-terminal domain of cTnC, followed by cTnC binding the troponin I switch peptide (TnISW). We have evaluated, through isothermal titration calorimetry and molecular-dynamics simulation, the effect of several clinically relevant mutations (A8V, L29Q, A31S, L48Q, Q50R, and C84Y) on the Ca2+ affinity, structural dynamics, and calculated interaction strengths between cTnC and each of Ca2+ and TnISW Surprisingly the Ca2+ affinity measured by isothermal titration calorimetry was only significantly affected by half of these mutations including L48Q, which had a 10-fold higher affinity than WT, and the Q50R and C84Y mutants, each of which had affinities 3-fold higher than wild type. This suggests that Ca2+ affinity of the N-terminal domain of cTnC in isolation is insufficient to explain the pathogenicity of these mutations. Molecular-dynamics simulation was used to evaluate the effects of these mutations on Ca2+ binding, structural dynamics, and TnI interaction independently. Many of the mutations had a pronounced effect on the balance between the open and closed conformations of the TnC molecule, which provides an indirect mechanism for their pathogenic properties. Our data demonstrate that the structural dynamics of the cTnC molecule are key in determining myofilament Ca2+ sensitivity. Our data further suggest that modulation of the structural dynamics is the underlying molecular mechanism for many disease mutations that are far from the regulatory Ca2+-binding site of cTnC.
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Affiliation(s)
- Charles M Stevens
- Cardiovascular Sciences, British Columbia Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada; Departments of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kaveh Rayani
- Departments of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Gurpreet Singh
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Bairam Lotfalisalmasi
- Departments of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Glen F Tibbits
- Cardiovascular Sciences, British Columbia Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada; Departments of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; Departments of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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26
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Dewan S, McCabe KJ, Regnier M, McCulloch AD. Insights and Challenges of Multi-Scale Modeling of Sarcomere Mechanics in cTn and Tm DCM Mutants-Genotype to Cellular Phenotype. Front Physiol 2017; 8:151. [PMID: 28352236 PMCID: PMC5348544 DOI: 10.3389/fphys.2017.00151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/24/2017] [Indexed: 01/18/2023] Open
Abstract
Dilated Cardiomyopathy (DCM) is a leading cause of sudden cardiac death characterized by impaired pump function and dilatation of cardiac ventricles. In this review we discuss various in silico approaches to elucidating the mechanisms of genetic mutations leading to DCM. The approaches covered in this review focus on bridging the spatial and temporal gaps that exist between molecular and cellular processes. Mutations in sarcomeric regulatory thin filament proteins such as the troponin complex (cTn) and Tropomyosin (Tm) have been associated with DCM. Despite the experimentally-observed myofilament measures of contractility in the case of these mutations, the mechanisms by which the underlying molecular changes and protein interactions scale up to organ failure by these mutations remains elusive. The review highlights multi-scale modeling approaches and their applicability to study the effects of sarcomeric gene mutations in-silico. We discuss some of the insights that can be gained from computational models of cardiac biomechanics when scaling from molecular states to cellular level.
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Affiliation(s)
- Sukriti Dewan
- Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kimberly J McCabe
- Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael Regnier
- Departments of Bioengineering and Medicine, University of Washington Seattle, WA, USA
| | - Andrew D McCulloch
- Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA
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Molecular Basis of S100A1 Activation at Saturating and Subsaturating Calcium Concentrations. Biophys J 2016; 110:1052-63. [PMID: 26958883 DOI: 10.1016/j.bpj.2015.12.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/30/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022] Open
Abstract
The S100A1 protein mediates a wide variety of physiological processes through its binding of calcium (Ca(2+)) and endogenous target proteins. S100A1 presents two Ca(2+)-binding domains: a high-affinity "canonical" EF (cEF) hand and a low-affinity "pseudo" EF (pEF) hand. Accumulating evidence suggests that both Ca(2+)-binding sites must be saturated to stabilize an open state conducive to peptide recognition, yet the pEF hand's low affinity limits Ca(2+) binding at normal physiological concentrations. To understand the molecular basis of Ca(2+) binding and open-state stabilization, we performed 100 ns molecular dynamics simulations of S100A1 in the apo/holo (Ca(2+)-free/bound) states and a half-saturated state, for which only the cEF sites are Ca(2+)-bound. Our simulations indicate that the pattern of oxygen coordination about Ca(2+) in the cEF relative to the pEF site contributes to the former's higher affinity, whereas Ca(2+) binding strongly reshapes the protein's conformational dynamics by disrupting β-sheet coupling between EF hands. Moreover, modeling of the half-saturated configuration suggests that the open state is unstable and reverts toward a closed state in the absence of the pEF Ca(2+) ion. These findings indicate that Ca(2+) binding at the cEF site alone is insufficient to stabilize opening; thus, posttranslational modification of the protein may be required for target peptide binding at subsaturating intracellular Ca(2+) levels.
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28
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Papadaki M, Marston SB. The Importance of Intrinsically Disordered Segments of Cardiac Troponin in Modulating Function by Phosphorylation and Disease-Causing Mutations. Front Physiol 2016; 7:508. [PMID: 27853436 PMCID: PMC5089987 DOI: 10.3389/fphys.2016.00508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/17/2016] [Indexed: 11/18/2022] Open
Abstract
Troponin plays a central role in regulation of muscle contraction. It is the Ca2+ switch of striated muscles including the heart and in the cardiac muscle it is physiologically modulated by PKA-dependent phosphorylation at Ser22 and 23. Many cardiomyopathy-related mutations affect Ca2+ regulation and/or disrupt the relationship between Ca2+ binding and phosphorylation. Unlike the mechanism of heart activation, the modulation of Ca2+-sensitivity by phosphorylation of the cardiac specific N-terminal segment of TnI (1–30) is structurally subtle and has proven hard to investigate. The crystal structure of cardiac troponin describes only the relatively stable core of the molecule and the crucial mobile parts of the molecule are missing including TnI C-terminal region, TnI (1–30), TnI (134–149) (“inhibitory” peptide) and the C-terminal 28 amino acids of TnT that are intrinsically disordered. Recent studies have been performed to answer this matter by building structural models of cardiac troponin in phosphorylated and dephosphorylated states based on peptide NMR studies. Now these have been updated by more recent concepts derived from molecular dynamic simulations treating troponin as a dynamic structure. The emerging model confirms the stable core structure of troponin and the mobile structure of the intrinsically disordered segments. We will discuss how we can describe these segments in terms of dynamic transitions between a small number of states, with the probability distributions being altered by phosphorylation and by HCM or DCM-related mutations that can explain how Ca2+-sensitivity is modulated by phosphorylation and the effects of mutations.
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Affiliation(s)
- Maria Papadaki
- Department of Cell and Molecular Physiology, Loyola University of Chicago Maywood, IL, USA
| | - Steven B Marston
- Myocardial Function, National Heart and Lung Institute, Imperial College London London, UK
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Marques MDA, de Oliveira GAP. Cardiac Troponin and Tropomyosin: Structural and Cellular Perspectives to Unveil the Hypertrophic Cardiomyopathy Phenotype. Front Physiol 2016; 7:429. [PMID: 27721798 PMCID: PMC5033975 DOI: 10.3389/fphys.2016.00429] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/09/2016] [Indexed: 12/12/2022] Open
Abstract
Inherited myopathies affect both skeletal and cardiac muscle and are commonly associated with genetic dysfunctions, leading to the production of anomalous proteins. In cardiomyopathies, mutations frequently occur in sarcomeric genes, but the cause-effect scenario between genetic alterations and pathological processes remains elusive. Hypertrophic cardiomyopathy (HCM) was the first cardiac disease associated with a genetic background. Since the discovery of the first mutation in the β-myosin heavy chain, more than 1400 new mutations in 11 sarcomeric genes have been reported, awarding HCM the title of the “disease of the sarcomere.” The most common macroscopic phenotypes are left ventricle and interventricular septal thickening, but because the clinical profile of this disease is quite heterogeneous, these phenotypes are not suitable for an accurate diagnosis. The development of genomic approaches for clinical investigation allows for diagnostic progress and understanding at the molecular level. Meanwhile, the lack of accurate in vivo models to better comprehend the cellular events triggered by this pathology has become a challenge. Notwithstanding, the imbalance of Ca2+ concentrations, altered signaling pathways, induction of apoptotic factors, and heart remodeling leading to abnormal anatomy have already been reported. Of note, a misbalance of signaling biomolecules, such as kinases and tumor suppressors (e.g., Akt and p53), seems to participate in apoptotic and fibrotic events. In HCM, structural and cellular information about defective sarcomeric proteins and their altered interactome is emerging but still represents a bottleneck for developing new concepts in basic research and for future therapeutic interventions. This review focuses on the structural and cellular alterations triggered by HCM-causing mutations in troponin and tropomyosin proteins and how structural biology can aid in the discovery of new platforms for therapeutics. We highlight the importance of a better understanding of allosteric communications within these thin-filament proteins to decipher the HCM pathological state.
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Affiliation(s)
- Mayra de A Marques
- Programa de Biologia Estrutural, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
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30
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Cheng Y, Lindert S, Oxenford L, Tu AY, McCulloch AD, Regnier M. Effects of Cardiac Troponin I Mutation P83S on Contractile Properties and the Modulation by PKA-Mediated Phosphorylation. J Phys Chem B 2016; 120:8238-53. [PMID: 27150586 PMCID: PMC5001945 DOI: 10.1021/acs.jpcb.6b01859] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
cTnI(P82S) (cTnI(P83S) in rodents) resides at the I-T arm of cardiac troponin I (cTnI) and was initially identified as a disease-causing mutation of hypertrophic cardiomyopathy (HCM). However, later studies suggested this may not be true. We recently reported that introduction of an HCM-associated mutation in either inhibitory-peptide (cTnI(R146G)) or cardiac-specific N-terminus (cTnI(R21C)) of cTnI blunts the PKA-mediated modulation on myofibril activation/relaxation kinetics by prohibiting formation of intrasubunit contacts between these regions. Here, we tested whether this also occurs for cTnI(P83S). cTnI(P83S) increased both Ca(2+) binding affinity to cTn (KCa) and affinity of cTnC for cTnI (KC-I), and eliminated the reduction of KCa and KC-I observed for phosphorylated-cTnI(WT). In isolated myofibrils, cTnI(P83S) maintained maximal tension (TMAX) and Ca(2+) sensitivity of tension (pCa50). For cTnI(WT) myofibrils, PKA-mediated phosphorylation decreased pCa50 and sped up the slow-phase relaxation (especially for those Ca(2+) conditions that heart performs in vivo). Those effects were blunted for cTnI(P83S) myofibrils. Molecular-dynamics simulations suggested cTnI(P83S) moderately inhibited an intrasubunit interaction formation between inhibitory-peptide and N-terminus, but this "blunting" effect was weaker than that with cTnI(R146G) or cTnI(R21C). In summary, cTnI(P83S) has similar effects as other HCM-associated cTnI mutations on troponin and myofibril function even though it is in the I-T arm of cTnI.
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Affiliation(s)
- Yuanhua Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
- National Biomedical Computation Resource, University of California San Diego, La Jolla, California 92093, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lucas Oxenford
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - An-yue Tu
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - Andrew D. McCulloch
- National Biomedical Computation Resource, University of California San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
- Center for Cardiovascular Biology, University of Washington, Seattle, Washington 98195, United States
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31
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Dvornikov AV, Smolin N, Zhang M, Martin JL, Robia SL, de Tombe PP. Restrictive Cardiomyopathy Troponin I R145W Mutation Does Not Perturb Myofilament Length-dependent Activation in Human Cardiac Sarcomeres. J Biol Chem 2016; 291:21817-21828. [PMID: 27557662 DOI: 10.1074/jbc.m116.746172] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/23/2016] [Indexed: 02/05/2023] Open
Abstract
The cardiac troponin I (cTnI) R145W mutation is associated with restrictive cardiomyopathy (RCM). Recent evidence suggests that this mutation induces perturbed myofilament length-dependent activation (LDA) under conditions of maximal protein kinase A (PKA) stimulation. Some cardiac disease-causing mutations, however, have been associated with a blunted response to PKA-mediated phosphorylation; whether this includes LDA is unknown. Endogenous troponin was exchanged in isolated skinned human myocardium for recombinant troponin containing either cTnI R145W, PKA/PKC phosphomimetic charge mutations (S23D/S24D and T143E), or various combinations thereof. Myofilament Ca2+ sensitivity of force, tension cost, LDA, and single myofibril activation/relaxation parameters were measured. Our results show that both R145W and T143E uncouple the impact of S23D/S24D phosphomimetic on myofilament function, including LDA. Molecular dynamics simulations revealed a marked reduction in interactions between helix C of cTnC (residues 56, 59, and 63), and cTnI (residue 145) in the presence of either cTnI RCM mutation or cTnI PKC phosphomimetic. These results suggest that the RCM-associated cTnI R145W mutation induces a permanent structural state that is similar to, but more extensive than, that induced by PKC-mediated phosphorylation of cTnI Thr-143. We suggest that this structural conformational change induces an increase in myofilament Ca2+ sensitivity and, moreover, uncoupling from the impact of phosphorylation of cTnI mediated by PKA at the Ser-23/Ser-24 target sites. The R145W RCM mutation by itself, however, does not impact LDA. These perturbed biophysical and biochemical myofilament properties are likely to significantly contribute to the diastolic cardiac pump dysfunction that is seen in patients suffering from a restrictive cardiomyopathy that is associated with the cTnI R145W mutation.
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Affiliation(s)
- Alexey V Dvornikov
- From the Department of Cell and Molecular Physiology, Health Sciences Division, Loyola University Chicago, Maywood, Illinois 60153
| | - Nikolai Smolin
- From the Department of Cell and Molecular Physiology, Health Sciences Division, Loyola University Chicago, Maywood, Illinois 60153
| | - Mengjie Zhang
- From the Department of Cell and Molecular Physiology, Health Sciences Division, Loyola University Chicago, Maywood, Illinois 60153
| | - Jody L Martin
- From the Department of Cell and Molecular Physiology, Health Sciences Division, Loyola University Chicago, Maywood, Illinois 60153
| | - Seth L Robia
- From the Department of Cell and Molecular Physiology, Health Sciences Division, Loyola University Chicago, Maywood, Illinois 60153
| | - Pieter P de Tombe
- From the Department of Cell and Molecular Physiology, Health Sciences Division, Loyola University Chicago, Maywood, Illinois 60153
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32
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Kucharski AN, Scott CE, Davis JP, Kekenes-Huskey PM. Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory. J Phys Chem B 2016; 120:8617-30. [PMID: 27267153 DOI: 10.1021/acs.jpcb.6b02666] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of PV sequence homologues and EF-hand-containing, Ca(2+) binding proteins.
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Affiliation(s)
- Amir N Kucharski
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Caitlin E Scott
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, Ohio State University , Columbus, Ohio 43210, United States
| | - Peter M Kekenes-Huskey
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
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33
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Cheng Y, Regnier M. Cardiac troponin structure-function and the influence of hypertrophic cardiomyopathy associated mutations on modulation of contractility. Arch Biochem Biophys 2016; 601:11-21. [PMID: 26851561 PMCID: PMC4899195 DOI: 10.1016/j.abb.2016.02.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/30/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022]
Abstract
Cardiac troponin (cTn) acts as a pivotal regulator of muscle contraction and relaxation and is composed of three distinct subunits (cTnC: a highly conserved Ca(2+) binding subunit, cTnI: an actomyosin ATPase inhibitory subunit, and cTnT: a tropomyosin binding subunit). In this mini-review, we briefly summarize the structure-function relationship of cTn and its subunits, its modulation by PKA-mediated phosphorylation of cTnI, and what is known about how these properties are altered by hypertrophic cardiomyopathy (HCM) associated mutations of cTnI. This includes recent work using computational modeling approaches to understand the atomic-based structural level basis of disease-associated mutations. We propose a viewpoint that it is alteration of cTnC-cTnI interaction (rather than the Ca(2+) binding properties of cTn) per se that disrupt the ability of PKA-mediated phosphorylation at cTnI Ser-23/24 to alter contraction and relaxation in at least some HCM-associated mutations. The combination of state of the art biophysical approaches can provide new insight on the structure-function mechanisms of contractile dysfunction resulting cTnI mutations and exciting new avenues for the diagnosis, prevention, and even treatment of heart diseases.
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Affiliation(s)
- Yuanhua Cheng
- University of Washington, Department of Bioengineering, Seattle, WA, USA
| | - Michael Regnier
- University of Washington, Department of Bioengineering, Seattle, WA, USA.
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34
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Genge CE, Stevens CM, Davidson WS, Singh G, Peter Tieleman D, Tibbits GF. Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC. Genome Biol Evol 2016; 8:994-1011. [PMID: 26979795 PMCID: PMC4860682 DOI: 10.1093/gbe/evw044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Gene duplication results in extra copies of genes that must coevolve with their interacting partners in multimeric protein complexes. The cardiac troponin (Tn) complex, containing TnC, TnI, and TnT, forms a distinct functional unit critical for the regulation of cardiac muscle contraction. In teleost fish, the function of the Tn complex is modified by the consequences of differential expression of paralogs in response to environmental thermal challenges. In this article, we focus on the interaction between TnI and TnC, coded for by genes that have independent evolutionary origins, but the co-operation of their protein products has necessitated coevolution. In this study, we characterize functional divergence of TnC and TnI paralogs, specifically the interrelated roles of regulatory subfunctionalization and structural subfunctionalization. We determined that differential paralog transcript expression in response to temperature acclimation results in three combinations of TnC and TnI in the zebrafish heart: TnC1a/TnI1.1, TnC1b/TnI1.1, and TnC1a/TnI1.5. Phylogenetic analysis of these highly conserved proteins identified functionally divergent residues in TnI and TnC. The structural and functional effect of these Tn combinations was modeled with molecular dynamics simulation to link divergent sites to changes in interaction strength. Functional divergence in TnI and TnC were not limited to the residues involved with TnC/TnI switch interaction, which emphasizes the complex nature of Tn function. Patterns in domain-specific divergent selection and interaction energies suggest that substitutions in the TnI switch region are crucial to modifying TnI/TnC function to maintain cardiac contraction with temperature changes. This integrative approach introduces Tn as a model of functional divergence that guides the coevolution of interacting proteins.
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Affiliation(s)
- Christine E Genge
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Charles M Stevens
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada Cardiovascular Sciences, Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - William S Davidson
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gurpreet Singh
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Alberta, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Alberta, Canada
| | - Glen F Tibbits
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada Cardiovascular Sciences, Child and Family Research Institute, Vancouver, British Columbia, Canada Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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35
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Abstract
Calcium binding and dissociation within the cardiac thin filament (CTF) is a fundamental regulator of normal contraction and relaxation. Although the disruption of this complex, allosterically mediated process has long been implicated in human disease, the precise atomic-level mechanisms remain opaque, greatly hampering the development of novel targeted therapies. To address this question, we used a fully atomistic CTF model to test both Ca(2+) binding strength and the energy required to remove Ca(2+) from the N-lobe binding site in WT and mutant troponin complexes that have been linked to genetic cardiomyopathies. This computational approach is combined with measurements of in vitro Ca(2+) dissociation rates in fully reconstituted WT and cardiac troponin T R92L and R92W thin filaments. These human disease mutations represent known substitutions at the same residue, reside at a significant distance from the calcium binding site in cardiac troponin C, and do not affect either the binding pocket affinity or EF-hand structure of the binding domain. Both have been shown to have significantly different effects on cardiac function in vivo. We now show that these mutations independently alter the interaction between the Ca(2+) ion and cardiac troponin I subunit. This interaction is a previously unidentified mechanism, in which mutations in one protein of a complex indirectly affect a third via structural and dynamic changes in a second to yield a pathogenic change in thin filament function that results in mutation-specific disease states. We can now provide atom-level insight that is potentially highly actionable in drug design.
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36
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Zamora JE, Papadaki M, Messer AE, Marston SB, Gould IR. Troponin structure: its modulation by Ca2+and phosphorylation studied by molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:20691-707. [DOI: 10.1039/c6cp02610a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The only available crystal structure of the human cardiac troponin molecule (cTn) in the Ca2+activated state does not include crucial segments, including the N-terminus of the cTn inhibitory subunit (cTnI).
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Affiliation(s)
- Juan Eiros Zamora
- Department of Chemistry
- Institute of Chemical Biology
- Imperial College London
- UK
| | - Maria Papadaki
- National Heart & Lung Institute
- Myocardial Function Section
- Imperial College London
- UK
| | - Andrew E. Messer
- National Heart & Lung Institute
- Myocardial Function Section
- Imperial College London
- UK
| | - Steven B. Marston
- National Heart & Lung Institute
- Myocardial Function Section
- Imperial College London
- UK
| | - Ian R. Gould
- Department of Chemistry
- Institute of Chemical Biology
- Imperial College London
- UK
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37
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Valimberti I, Tiberti M, Lambrughi M, Sarcevic B, Papaleo E. E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft. Sci Rep 2015; 5:14849. [PMID: 26463729 PMCID: PMC4604453 DOI: 10.1038/srep14849] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/19/2015] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation is a modification that offers a dynamic and reversible mechanism to regulate the majority of cellular processes. Numerous diseases are associated with aberrant regulation of phosphorylation-induced switches. Phosphorylation is emerging as a mechanism to modulate ubiquitination by regulating key enzymes in this pathway. The molecular mechanisms underpinning how phosphorylation regulates ubiquitinating enzymes, however, are elusive. Here, we show the high conservation of a functional site in E2 ubiquitin-conjugating enzymes. In catalytically active E2s, this site contains aspartate or a phosphorylatable serine and we refer to it as the conserved E2 serine/aspartate (CES/D) site. Molecular simulations of substrate-bound and -unbound forms of wild type, mutant and phosphorylated E2s, provide atomistic insight into the role of the CES/D residue for optimal E2 activity. Both the size and charge of the side group at the site play a central role in aligning the substrate lysine toward E2 catalytic cysteine to control ubiquitination efficiency. The CES/D site contributes to the fingerprint of the E2 superfamily. We propose that E2 enzymes can be divided into constitutively active or regulated families. E2s characterized by an aspartate at the CES/D site signify constitutively active E2s, whereas those containing a serine can be regulated by phosphorylation.
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Affiliation(s)
- Ilaria Valimberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Matteo Tiberti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Matteo Lambrughi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
| | - Boris Sarcevic
- Cell Cycle and Cancer Unit, St. Vincent's Institute of Medical Research and The Department of Medicine, St. Vincent's Hospital, The University of Melbourne, Fitzroy, Melbourne, Victoria 3065, Australia
| | - Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan (Italy)
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Cheng Y, Rao V, Tu AY, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation. J Biol Chem 2015; 290:27749-66. [PMID: 26391394 DOI: 10.1074/jbc.m115.683045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Indexed: 11/06/2022] Open
Abstract
Two hypertrophic cardiomyopathy-associated cardiac troponin I (cTnI) mutations, R146G and R21C, are located in different regions of cTnI, the inhibitory peptide and the cardiac-specific N terminus. We recently reported that these regions may interact when Ser-23/Ser-24 are phosphorylated, weakening the interaction of cTnI with cardiac TnC. Little is known about how these mutations influence the affinity of cardiac TnC for cTnI (KC-I) or contractile kinetics during β-adrenergic stimulation. Here, we tested how cTnI(R146G) or cTnI(R21C) influences contractile activation and relaxation and their response to protein kinase A (PKA). Both mutations significantly increased Ca(2+) binding affinity to cTn (KCa) and KC-I. PKA phosphorylation resulted in a similar reduction of KCa for all complexes, but KC-I was reduced only with cTnI(WT). cTnI(WT), cTnI(R146G), and cTnI(R21C) were complexed into cardiac troponin and exchanged into rat ventricular myofibrils, and contraction/relaxation kinetics were measured ± PKA phosphorylation. Maximal tension (Tmax) was maintained for cTnI(R146G)- and cTnI(R21C)-exchanged myofibrils, and Ca(2+) sensitivity of tension (pCa50) was increased. PKA phosphorylation decreased pCa50 for cTnI(WT)-exchanged myofibrils but not for either mutation. PKA phosphorylation accelerated the early slow phase relaxation for cTnI(WT) myofibrils, especially at Ca(2+) levels that the heart operates in vivo. Importantly, this effect was blunted for cTnI(R146G)- and cTnI(R21C)-exchanged myofibrils. Molecular dynamics simulations suggest both mutations inhibit formation of intra-subunit contacts between the N terminus and the inhibitory peptide of cTnI that is normally seen with WT-cTn upon PKA phosphorylation. Together, our results suggest that cTnI(R146G) and cTnI(R21C) blunt PKA modulation of activation and relaxation kinetics by prohibiting cardiac-specific N-terminal interaction with the cTnI inhibitory peptide.
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Affiliation(s)
- Yuanhua Cheng
- From the Department of Bioengineering, University of Washington, Seattle, Washington 98105, the National Biomedical Computational Resource and
| | - Vijay Rao
- From the Department of Bioengineering, University of Washington, Seattle, Washington 98105
| | - An-Yue Tu
- From the Department of Bioengineering, University of Washington, Seattle, Washington 98105
| | - Steffen Lindert
- Pharmacology, University of California at San Diego, La Jolla, California 92093, and
| | - Dan Wang
- From the Department of Bioengineering, University of Washington, Seattle, Washington 98105
| | - Lucas Oxenford
- From the Department of Bioengineering, University of Washington, Seattle, Washington 98105
| | - Andrew D McCulloch
- the National Biomedical Computational Resource and Departments of Bioengineering and
| | - J Andrew McCammon
- the National Biomedical Computational Resource and Pharmacology, University of California at San Diego, La Jolla, California 92093, and
| | - Michael Regnier
- From the Department of Bioengineering, University of Washington, Seattle, Washington 98105, the Center for Cardiovascular Biology, University of Washington, Seattle, Washington 98105
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