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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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Cai F, Kampourakis T, Parijat P, Cockburn KT, Sykes BD. Conversion of a Cardiac Muscle Modulator from an Inhibitor to an Activator. ACS Med Chem Lett 2023; 14:530-533. [PMID: 37077384 PMCID: PMC10108394 DOI: 10.1021/acsmedchemlett.3c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The binding of calcium to cardiac troponin C (cTnC) enhances the binding of troponin I (cTnI) switch region to the regulatory domain of cTnC (cNTnC) and triggers muscle contraction. Several molecules alter the response of the sarcomere by targeting this interface; virtually all have an aromatic core that binds to the hydrophobic pocket of cNTnC and an aliphatic tail that interacts with the switch region of cTnI. W7 has been extensively studied, and the positively charged tail has been shown to be important for its inhibitory action. Herein we investigate the importance of the aromatic core of W7 by synthesizing compounds that have the core region of calcium activator dfbp-o with various lengths of the same tail (D-series). These compounds all bind more tightly to cNTnC-cTnI chimera (cChimera) than the analogous W-series compounds and show increased calcium sensitivity of force generation and ATPase activity, demonstrating that the cardiovascular system is tightly balanced.
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Affiliation(s)
- Fangze Cai
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Thomas Kampourakis
- Randall
Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Priyanka Parijat
- Randall
Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Kieran T. Cockburn
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Brian D. Sykes
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
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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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Cai F, Kampourakis T, Cockburn KT, Sykes BD. Drugging the Sarcomere, a Delicate Balance: Position of N-Terminal Charge of the Inhibitor W7. ACS Chem Biol 2022; 17:1495-1504. [PMID: 35649123 DOI: 10.1021/acschembio.2c00126] [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: 11/30/2022]
Abstract
W7 is a sarcomere inhibitor that decreases the calcium sensitivity of force development in cardiac muscle. W7 binds to the interface of the regulatory domain of cardiac troponin C (cNTnC) and the switch region of troponin I (cTnI), decreasing the binding of cTnI to cNTnC, presumably by electrostatic repulsion between the -NH3+ group of W7 and basic amino acids in cTnI. W7 analogs with a -CO2- tail are inactive. To evaluate the importance of the location of the charged -NH3+, we used a series of compounds W4, W6, W8, and W9, which have three less, one less, one more, and two more methylene groups in the tail region than W7. W6, W8, and W9 all bind tighter to cNTnC-cTnI chimera (cChimera) than W7, while W4 binds weaker. W4 and, strikingly, W6 have no effect on calcium sensitivity of force generation, while W8 and W9 decrease calcium sensitivity, but less than W7. The structures of the cChimera-W6 and cChimera-W8 complexes reveal that W6 and W8 bind to the same hydrophobic cleft as W7, with the aliphatic tail taking a similar route to the surface. NMR relaxation data show that internal flexibility in the tail of W7 is very limited. Alignment of the cChimera-W7 structure with the recent cryoEM structures of the cardiac sarcomere in the diastolic and systolic states reveals the critical location of the amino group. Small molecule induced structural changes can therefore affect the tightly balanced equilibrium between tethered components required for rapid contraction.
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Affiliation(s)
- Fangze Cai
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Thomas Kampourakis
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - Kieran T Cockburn
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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5
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Rasmi Y, Mosa OF, Alipour S, Heidari N, Javanmard F, Golchin A, Gholizadeh-Ghaleh Aziz S. Significance of Cardiac Troponins as an Identification Tool in COVID-19 Patients Using Biosensors: An Update. Front Mol Biosci 2022; 9:821155. [PMID: 35281265 PMCID: PMC8912935 DOI: 10.3389/fmolb.2022.821155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/17/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has rapidly developed as a global health emergency. Respiratory diseases are significant causes of morbidity and mortality in these patients with a spectrum of different diseases, from asymptomatic subclinical infection to the progression of severe pneumonia and subsequent acute respiratory distress syndrome. Individuals with cardiovascular disease are more likely to become infected with SARS-CoV-2 and develop severe symptoms. Hence, patients with underlying cardiovascular disease mortality rate are over three times. Furthermore, note that patients with a history of cardiovascular disease are more likely to have higher cardiac biomarkers, especially cardiac troponins, than infected patients, especially those with severe disease, making these patients more susceptible to cardiac damage caused by SARS-2-CoV. Biomarkers are important in decision-making to facilitate the efficient allocation of resources. Viral replication in the heart muscle can lead to a cascade of inflammatory processes that lead to fibrosis and, ultimately, cardiac necrosis. Elevated troponin may indicate damage to the heart muscle and may predict death. After the first Chinese analysis, increased cardiac troponin value was observed in a significant proportion of patients, suggesting that myocardial damage is a possible pathogenic mechanism leading to severe disease and death. However, the prognostic performance of troponin and whether its value is affected by different comorbidities present in COVID-19 patients are not known. This review aimed to assess the diagnostic value of troponin to offer insight into pathophysiological mechanisms and reported new assessment methods, including new biosensors for troponin in patients with COVID-19.
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Affiliation(s)
- Yousef Rasmi
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Osama F Mosa
- Public Health Department, Health Sciences College at Lieth, Umm Al Qura University, Mecca, Saudi Arabia
- Biochemistry Department, Bukhara State Medical Institute Named After Abu Ali ibn Sino, Bukhara, Uzbekistan
| | - Shahriar Alipour
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Nadia Heidari
- Department of Clinical Biochemistry, Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Farzaneh Javanmard
- Department of Pathology, Urmia University of Medical Science, Urmia, Iran
| | - Ali Golchin
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Shiva Gholizadeh-Ghaleh Aziz
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
- Nephrology and Kidney Transplant Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
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6
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Yan C, Sack JS. X-ray structure of a human cardiac muscle troponin C/troponin I chimera in two crystal forms. Acta Crystallogr F Struct Biol Commun 2022; 78:17-24. [PMID: 34981771 PMCID: PMC8725003 DOI: 10.1107/s2053230x21012395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023] Open
Abstract
The X-ray crystal structure of a human cardiac muscle troponin C/troponin I chimera has been determined in two different crystal forms and shows a conformation of the complex that differs from that previously observed by NMR. The chimera consists of the N-terminal domain of troponin C (cTnC; residues 1-80) fused to the switch region of troponin I (cTnI; residues 138-162). In both crystal forms, the cTnI residues form a six-turn α-helix that lays across the hydrophobic groove of an adjacent cTnC molecule in the crystal structure. In contrast to previous models, the cTnI helix runs in a parallel direction relative to the cTnC groove and completely blocks the calcium desensitizer binding site of the cTnC-cTnI interface.
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Affiliation(s)
- Chunhong Yan
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - John S. Sack
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA,Correspondence e-mail:
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7
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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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8
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Li MX, Mercier P, Hartman JJ, Sykes BD. Structural Basis of Tirasemtiv Activation of Fast Skeletal Muscle. J Med Chem 2021; 64:3026-3034. [PMID: 33703886 DOI: 10.1021/acs.jmedchem.0c01412] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Troponin regulates the calcium-mediated activation of skeletal muscle. Muscle weakness in diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy occurs from diminished neuromuscular output. The first direct fast skeletal troponin activator, tirasemtiv, amplifies the response of muscle to neuromuscular input. Tirasemtiv binds selectively and strongly to fast skeletal troponin, slowing the rate of calcium release and sensitizing muscle to calcium. We report the solution NMR structure of tirasemtiv bound to a fast skeletal troponin C-troponin I chimera. The structure reveals that tirasemtiv binds in a hydrophobic pocket between the regulatory domain of troponin C and the switch region of troponin I, which overlaps with that of Anapoe in the X-ray structure of skeletal troponin. Multiple interactions stabilize the troponin C-troponin I interface, increase the affinity of troponin C for the switch region of fast skeletal troponin I, and drive the equilibrium toward the active state.
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Affiliation(s)
- Monica X Li
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Pascal Mercier
- National High Field NMR Centre, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - James J Hartman
- Cytokinetics, Inc., South San Francisco, California 94080, United States
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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9
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Parijat P, Kondacs L, Alexandrovich A, Gautel M, Cobb AJA, Kampourakis T. High Throughput Screen Identifies Small Molecule Effectors That Modulate Thin Filament Activation in Cardiac Muscle. ACS Chem Biol 2021; 16:225-235. [PMID: 33315370 DOI: 10.1021/acschembio.0c00908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Current therapeutic interventions for both heart disease and heart failure are largely insufficient and associated with undesired side effects. Biomedical research has emphasized the role of sarcomeric protein function for the normal performance and energy efficiency of the heart, suggesting that directly targeting the contractile myofilaments themselves using small molecule effectors has therapeutic potential and will likely result in greater drug efficacy and selectivity. In this study, we developed a robust and highly reproducible fluorescence polarization-based high throughput screening (HTS) assay that directly targets the calcium-dependent interaction between cardiac troponin C (cTnC) and the switch region of cardiac troponin I (cTnISP), with the aim of identifying small molecule effectors of the cardiac thin filament activation pathway. We screened a commercially available small molecule library and identified several hit compounds with both inhibitory and activating effects. We used a range of biophysical and biochemical methods to characterize hit compounds and identified fingolimod, a sphingosin-1-phosphate receptor modulator, as a new troponin-based small molecule effector. Fingolimod decreased the ATPase activity and calcium sensitivity of demembranated cardiac muscle fibers in a dose-dependent manner, suggesting that the compound acts as a calcium desensitizer. We investigated fingolimod's mechanism of action using a combination of computational studies, biophysical methods, and synthetic chemistry, showing that fingolimod bound to cTnC repels cTnISP via mainly electrostatic repulsion of its positively charged tail. These results suggest that fingolimod is a potential new lead compound/scaffold for the development of troponin-directed heart failure therapeutics.
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Affiliation(s)
- Priyanka Parijat
- Randall Centre for Cell and Molecular Biophysics, King’s College London, and British Heart Foundation Centre of Research Excellence, London SE1 1UL, United Kingdom
| | - Laszlo Kondacs
- Department of Chemistry, King’s College London, 7 Trinity Street, London, SE1 1DB, United Kingdom
| | - Alexander Alexandrovich
- Randall Centre for Cell and Molecular Biophysics, King’s College London, and British Heart Foundation Centre of Research Excellence, London SE1 1UL, United Kingdom
| | - Mathias Gautel
- Randall Centre for Cell and Molecular Biophysics, King’s College London, and British Heart Foundation Centre of Research Excellence, London SE1 1UL, United Kingdom
| | - Alexander J. A. Cobb
- Department of Chemistry, King’s College London, 7 Trinity Street, London, SE1 1DB, United Kingdom
| | - Thomas Kampourakis
- Randall Centre for Cell and Molecular Biophysics, King’s College London, and British Heart Foundation Centre of Research Excellence, London SE1 1UL, United Kingdom
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10
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A comprehensive guide to genetic variants and post-translational modifications of cardiac troponin C. J Muscle Res Cell Motil 2020; 42:323-342. [PMID: 33179204 DOI: 10.1007/s10974-020-09592-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/24/2020] [Indexed: 02/07/2023]
Abstract
Familial cardiomyopathy is an inherited disease that affects the structure and function of heart muscle and has an extreme range of phenotypes. Among the millions of affected individuals, patients with hypertrophic (HCM), dilated (DCM), or left ventricular non-compaction (LVNC) cardiomyopathy can experience morphologic changes of the heart which lead to sudden death in the most detrimental cases. TNNC1, the gene that codes for cardiac troponin C (cTnC), is a sarcomere gene associated with cardiomyopathies in which probands exhibit young age of presentation and high death, transplant or ventricular fibrillation events relative to TNNT2 and TNNI3 probands. Using GnomAD, ClinVar, UniProt and PhosphoSitePlus databases and published literature, an extensive list to date of identified genetic variants in TNNC1 and post-translational modifications (PTMs) in cTnC was compiled. Additionally, a recent cryo-EM structure of the cardiac thin filament regulatory unit was used to localize each functionally studied amino acid variant and each PTM (acetylation, glycation, s-nitrosylation, phosphorylation) in the structure of cTnC. TNNC1 has a large number of variants (> 100) relative to other genes of the same transcript size. Surprisingly, the mapped variant amino acids and PTMs are distributed throughout the cTnC structure. While many cardiomyopathy-associated variants are localized in α-helical regions of cTnC, this was not statistically significant χ2 (p = 0.72). Exploring the variants in TNNC1 and PTMs of cTnC in the contexts of cardiomyopathy association, physiological modulation and potential non-canonical roles provides insights into the normal function of cTnC along with the many facets of TNNC1 as a cardiomyopathic gene.
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11
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Cai F, Robertson IM, Kampourakis T, Klein BA, Sykes BD. The Role of Electrostatics in the Mechanism of Cardiac Thin Filament Based Sensitizers. ACS Chem Biol 2020; 15:2289-2298. [PMID: 32633482 DOI: 10.1021/acschembio.0c00519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Heart muscle contraction is regulated by calcium binding to cardiac troponin C. This induces troponin I (cTnI) switch region binding to the regulatory domain of troponin C (cNTnC), pulling the cTnI inhibitory region off actin and triggering muscle contraction. Small molecules targeting this cNTnC-cTnI interface have potential in the treatment of heart disease. Most of these have an aromatic core which binds to the hydrophobic core of cNTnC, and a polar and often charged 'tail'. The calmodulin antagonist W7 is unique in that it acts as calcium desensitizer. W7 binds to the interface of cNTnC and cTnI switch region and weakens cTnI binding, possibly by electrostatic repulsion between the positively charged terminal amino group of W7 and the positively charged RRVR144-147 region of cTnI. To evaluate the role of electrostatics, we synthesized A7, where the amino group of W7 was replaced with a carboxyl group. We determined the high-resolution solution NMR structure of A7 bound to a cNTnC-cTnI chimera. The structure shows that A7 does not change the overall conformation of the cNTnC-cTnI interface, and the naphthalene ring of A7 sits in the same hydrophobic pocket as that of W7, but the charged tail takes a different route to the surface of the complex, especially with respect to the position of the switch region of cTnI. We measured the affinities of A7 for cNTnC and the cNTnC-cTnI complex and that of the cTnI switch peptide for the cNTnC-A7 complex. We also compared the binding of W7 and A7 for two cNTnC-cTnI chimeras, differing in the presence or absence of the RRVR region of cTnI. A7 decreased the binding affinity of cTnI to cNTnC substantially less than W7 and bound more tightly to the more positively charged chimera. We tested the effects of W7 and A7 on the force-calcium relation of demembranated rat right ventricular trabeculae and demonstrated that A7 has a much weaker desensitization effect than W7. We also synthesized A6, which has one less methylene group on the hydrocarbon chain than A7. A6 did not affect binding of cTnI switch peptide nor change the calcium sensitivity of ventricular trabeculae. These results suggest that the negative inotropic effect of W7 may result from a combination of electrostatic repulsion and steric hindrance with cTnI.
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Affiliation(s)
- Fangze Cai
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Ian M. Robertson
- Ministry of Health, Government of Alberta, Edmonton, AB T5J 1S6, Canada
| | - Thomas Kampourakis
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Brittney A. Klein
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Brian D. Sykes
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
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12
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Coldren WH, Tikunova SB, Davis JP, Lindert S. Discovery of Novel Small-Molecule Calcium Sensitizers for Cardiac Troponin C: A Combined Virtual and Experimental Screening Approach. J Chem Inf Model 2020; 60:3648-3661. [PMID: 32633957 DOI: 10.1021/acs.jcim.0c00452] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Heart failure is a leading cause of death throughout the world and is triggered by a disruption of the cardiac contractile machinery. This machinery is regulated in a calcium-dependent manner by the protein complex troponin. Calcium binds to the N-terminal domain of cardiac troponin C (cNTnC) setting into motion the cascade of events leading to muscle contraction. Because of the severity and prevalence of heart failure, there is a strong need to develop small-molecule therapeutics designed to increase the calcium sensitivity of cardiac troponin in order to treat this devastating condition. Molecules that are able to stabilize an open configuration of cNTnC and additionally facilitate the binding of the cardiac troponin I (cTnI) switch peptide have the potential to enable increased calcium sensitization and strengthened cardiac function. Here, we employed a high throughput virtual screening methodology built upon the ability of computational docking to reproduce known experimental results and to accurately recognize cNTnC conformations conducive to small molecule binding using a receiver operator characteristic curve analysis. This approach combined with concurrent stopped-flow kinetic experimental verification led to the identification of a number of sensitizers, which slowed the calcium off-rate. An initial hit, compound 4, was identified with medium affinity (84 ± 30 μM). Through refinement, a calcium sensitizing agent, compound 5, with an apparent affinity of 1.45 ± 0.09 μM was discovered. This molecule is one of the highest affinity calcium sensitizers known to date.
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Affiliation(s)
- William H Coldren
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Svetlana B Tikunova
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan P Davis
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, 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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13
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Smith AS, Choi E, Gray K, Macadangdang J, Ahn EH, Clark EC, Laflamme MA, Wu JC, Murry CE, Tung L, Kim DH. NanoMEA: A Tool for High-Throughput, Electrophysiological Phenotyping of Patterned Excitable Cells. NANO LETTERS 2020; 20:1561-1570. [PMID: 31845810 PMCID: PMC7547911 DOI: 10.1021/acs.nanolett.9b04152] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Matrix nanotopographical cues are known to regulate the structure and function of somatic cells derived from human pluripotent stem cell (hPSC) sources. High-throughput electrophysiological analysis of excitable cells derived from hPSCs is possible via multielectrode arrays (MEAs) but conventional MEA platforms use flat substrates and do not reproduce physiologically relevant tissue-specific architecture. To address this issue, we developed a high-throughput nanotopographically patterned multielectrode array (nanoMEA) by integrating conductive, ion-permeable, nanotopographic patterns with 48-well MEA plates, and investigated the effect of substrate-mediated cytoskeletal organization on hPSC-derived cardiomyocyte and neuronal function at scale. Using our nanoMEA platform, we found patterned hPSC-derived cardiac monolayers exhibit both enhanced structural organization and greater sensitivity to treatment with calcium blocking or conduction inhibiting compounds when subjected to high-throughput dose-response studies. Similarly, hPSC-derived neurons grown on nanoMEA substrates exhibit faster migration and neurite outgrowth speeds, greater colocalization of pre- and postsynaptic markers, and enhanced cell-cell communication only revealed through examination of data sets derived from multiple technical replicates. The presented data highlight the nanoMEA as a new tool to facilitate high-throughput, electrophysiological analysis of ordered cardiac and neuronal monolayers, which can have important implications for preclinical analysis of excitable cell function.
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Affiliation(s)
- Alec S.T. Smith
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Eunpyo Choi
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Department of Mechanical Engineering, Chonnam National University, Gwangju 61186, South Korea
| | - Kevin Gray
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- NanoSurface Biomedical, Inc. Seattle, WA 98195, USA
| | - Jesse Macadangdang
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- NanoSurface Biomedical, Inc. Seattle, WA 98195, USA
| | - Eun Hyun Ahn
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Elisa C. Clark
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Michael A. Laflamme
- Toronto General Hospital Research Institute, McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Charles E. Murry
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine/Cardiology, University of Washington, Seattle, WA 98195, USA
| | - Leslie Tung
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Deok-Ho Kim
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- To whom correspondence should be addressed: Dr. Deok-Ho Kim, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Ross Research Building, 715B, 720 Rutland Avenue, Baltimore, MD 21205,
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14
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Bowman JD, Coldren WH, Lindert S. Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations. J Chem Inf Model 2019; 59:2964-2972. [PMID: 31141358 DOI: 10.1021/acs.jcim.9b00256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cardiac troponin C (cTnC) binds intracellular calcium and subsequently cardiac troponin I (cTnI), initiating cardiac muscle contraction. Due to its role in contraction, cTnC has been a therapeutic target in the search for small molecules to treat conditions that interfere with normal muscle contraction like the heritable cardiomyopathies. Structural studies have shown the binding location of small molecules such as bepridil, dfbp-o, 3-methyldiphenylamine (DPA), and W7 to be a hydrophobic pocket in the regulatory domain of cTnC (cNTnC) but have not shown the influence of these small molecules on the energetics of opening this domain. Here we describe an application of an umbrella sampling method used to elucidate the impact these calcium sensitivity modulators have on the free energy of cNTnC hydrophobic patch opening. We found that all these molecules lowered the free energy of opening in the absence of the cTnI, with bepridil facilitating the least endergonic transformation. In the presence of cTnI, however, we saw a stabilization of the open configuration due to DPA and dfbp-o binding, and a destabilization of the open configuration imparted by bepridil and W7. Predicted poor binding molecule NSC34337 left the hydrophobic patch in under 3 ns in conventional MD simulations suggesting that only hydrophobic patch binders stabilized the open conformation. In conclusion, this study presents a novel approach to study the impact of small molecules on hydrophobic patch opening through umbrella sampling, and it proposes mechanisms for calcium sensitivity modulation.
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Affiliation(s)
- Jacob D Bowman
- Department of Chemistry and Biochemistry , Ohio State University , 2114 Newman & Wolfrom Laboratory, 100 West 18th Avenue , Columbus , Ohio 43210 , United States
| | - William H Coldren
- Department of Chemistry and Biochemistry , Ohio State University , 2114 Newman & Wolfrom Laboratory, 100 West 18th Avenue , Columbus , Ohio 43210 , United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , 2114 Newman & Wolfrom Laboratory, 100 West 18th Avenue , Columbus , Ohio 43210 , United States
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15
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Szatkowski L, Lynn ML, Holeman T, Williams MR, Baldo AP, Tardiff JC, Schwartz SD. Proof of Principle that Molecular Modeling Followed by a Biophysical Experiment Can Develop Small Molecules that Restore Function to the Cardiac Thin Filament in the Presence of Cardiomyopathic Mutations. ACS OMEGA 2019; 4:6492-6501. [PMID: 31342001 PMCID: PMC6649307 DOI: 10.1021/acsomega.8b03340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/28/2019] [Indexed: 06/10/2023]
Abstract
This article reports a coupled computational experimental approach to design small molecules aimed at targeting genetic cardiomyopathies. We begin with a fully atomistic model of the cardiac thin filament. To this we dock molecules using accepted computational drug binding methodologies. The candidates are screened for their ability to repair alterations in biophysical properties caused by mutation. Hypertrophic and dilated cardiomyopathies caused by mutation are initially biophysical in nature, and the approach we take is to correct the biophysical insult prior to irreversible cardiac damage. Candidate molecules are then tested experimentally for both binding and biophysical properties. This is a proof of concept study-eventually candidate molecules will be tested in transgenic animal models of genetic (sarcomeric) cardiomyopathies.
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Affiliation(s)
- Lukasz Szatkowski
- Department
of Chemistry and Biochemistry, University
of Arizona, Tucson, Arizona 85721, United States
| | - Melissa L. Lynn
- Department of Physiological
Sciences and Department of Medicine, University of Arizona, Tucson, Arizona 85724, United States
| | - Teryn Holeman
- Department of Physiological
Sciences and Department of Medicine, University of Arizona, Tucson, Arizona 85724, United States
| | - Michael R. Williams
- Department
of Chemistry and Biochemistry, University
of Arizona, Tucson, Arizona 85721, United States
| | - Anthony P. Baldo
- Department
of Chemistry and Biochemistry, University
of Arizona, Tucson, Arizona 85721, United States
| | - Jil C. Tardiff
- Department of Physiological
Sciences and Department of Medicine, University of Arizona, Tucson, Arizona 85724, United States
| | - Steven D. Schwartz
- Department
of Chemistry and Biochemistry, University
of Arizona, Tucson, Arizona 85721, United States
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16
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Tikunova SB, Cuesta A, Price M, Li MX, Belevych N, Biesiadecki BJ, Reiser PJ, Hwang PM, Davis JP. 3-Chlorodiphenylamine activates cardiac troponin by a mechanism distinct from bepridil or TFP. J Gen Physiol 2018; 151:9-17. [PMID: 30442775 PMCID: PMC6314390 DOI: 10.1085/jgp.201812131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/02/2018] [Indexed: 01/14/2023] Open
Abstract
Cardiac troponin activators could be beneficial in systolic heart failure. Tikunova et al. demonstrate that, unlike previously known calcium sensitizers, the small molecule 3-chlorodiphenylamine does not activate isolated cardiac troponin C but instead activates the intact troponin complex. Despite extensive efforts spanning multiple decades, the development of highly effective Ca2+ sensitizers for the heart remains an elusive goal. Existing Ca2+ sensitizers have other targets in addition to cardiac troponin (cTn), which can lead to adverse side effects, such as hypotension or arrhythmias. Thus, there is a need to design Ca2+-sensitizing drugs with higher affinity and selectivity for cTn. Previously, we determined that many compounds based on diphenylamine (DPA) were able to bind to a cTnC–cTnI chimera with moderate affinity (Kd ∼10–120 µM). Of these compounds, 3-chlorodiphenylamine (3-Cl-DPA) bound most tightly (Kd of 10 µM). Here, we investigate 3-Cl-DPA further and find that it increases the Ca2+ sensitivity of force development in skinned cardiac muscle. Using NMR, we show that, like the known Ca2+ sensitizers, trifluoperazine (TFP) and bepridil, 3-Cl-DPA is able to bind to the isolated N-terminal domain (N-domain) of cTnC (Kd of 6 µM). However, while the bulky molecules of TFP and bepridil stabilize the open state of the N-domain of cTnC, the small and flexible 3-Cl-DPA molecule is able to bind without stabilizing this open state. Thus, unlike TFP, which drastically slows the rate of Ca2+ dissociation from the N-domain of isolated cTnC in a dose-dependent manner, 3-Cl-DPA has no effect on the rate of Ca2+ dissociation. On the other hand, the affinity of 3-Cl-DPA for a cTnC–TnI chimera is at least an order of magnitude higher than that of TFP or bepridil, likely because 3-Cl-DPA is less disruptive of cTnI binding to cTnC. Therefore, 3-Cl-DPA has a bigger effect on the rate of Ca2+ dissociation from the entire cTn complex than TFP and bepridil. Our data suggest that 3-Cl-DPA activates the cTn complex via a unique mechanism and could be a suitable scaffold for the development of novel treatments for systolic heart failure.
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Affiliation(s)
- Svetlana B Tikunova
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH
| | - Andres Cuesta
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH
| | - Morgan Price
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH
| | - Monica X Li
- Departments of Medicine and Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Natalya Belevych
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH
| | | | - Peter J Reiser
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH
| | - Peter M Hwang
- Departments of Medicine and Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH
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17
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Li MX, Gelozia S, Danmaliki GI, Wen Y, Liu PB, Lemieux MJ, West FG, Sykes BD, Hwang PM. The calcium sensitizer drug MCI-154 binds the structural C-terminal domain of cardiac troponin C. Biochem Biophys Rep 2018; 16:145-151. [PMID: 30417133 PMCID: PMC6218639 DOI: 10.1016/j.bbrep.2018.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 10/12/2018] [Accepted: 10/19/2018] [Indexed: 11/27/2022] Open
Abstract
The compound MCI-154 was previously shown to increase the calcium sensitivity of cardiac muscle contraction. Using solution NMR spectroscopy, we demonstrate that MCI-154 interacts with the calcium-sensing subunit of the cardiac troponin complex, cardiac troponin C (cTnC). Surprisingly, however, it binds only to the structural C-terminal domain of cTnC (cCTnC), and not to the regulatory N-terminal domain (cNTnC) that determines the calcium sensitivity of cardiac muscle. Physiologically, cTnC is always bound to cardiac troponin I (cTnI), so we examined its interaction with MCI-154 in the presence of two soluble constructs, cTnI1–77 and cTnI135–209, which contain all of the segments of cTnI known to interact with cTnC. Neither the cTnC-cTnI1–77 complex nor the cTnC-cTnI135–209 complex binds to MCI-154. Since residues 39–60 of cTnI are known to bind tightly to the cCTnC domain to form a structured core that is invariant throughout the cardiac cycle, we conclude that MCI-154 does not bind to cTnC when it is part of the intact cardiac troponin complex. Thus, MCI-154 likely exerts its calcium sensitizing effect by interacting with a target other than cardiac troponin. MCI-154 is a small molecule calcium sensitizer in cardiac muscle. The N-domain of cardiac troponin C controls calcium sensitivity in cardiac muscle. MCI-154 binds weakly to the promiscuous C-terminal domain of troponin C. Cardiac troponin C does not bind MCI-154 in the presence of troponin I. MCI-154 does not exert its calcium sensitizing effect directly through troponin C.
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Affiliation(s)
- Monica X Li
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Shorena Gelozia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Yurong Wen
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Philip B Liu
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Frederick G West
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Peter M Hwang
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2R3.,Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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18
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Cai F, Hwang PM, Sykes BD. Structural Changes Induced by the Binding of the Calcium Desensitizer W7 to Cardiac Troponin. Biochemistry 2018; 57:6461-6469. [DOI: 10.1021/acs.biochem.8b00882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Fangze Cai
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Peter M. Hwang
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Brian D. Sykes
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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19
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Gonzalez-Martinez D, Johnston JR, Landim-Vieira M, Ma W, Antipova O, Awan O, Irving TC, Bryant Chase P, Pinto JR. Structural and functional impact of troponin C-mediated Ca 2+ sensitization on myofilament lattice spacing and cross-bridge mechanics in mouse cardiac muscle. J Mol Cell Cardiol 2018; 123:26-37. [PMID: 30138628 DOI: 10.1016/j.yjmcc.2018.08.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/26/2018] [Accepted: 08/05/2018] [Indexed: 12/25/2022]
Abstract
Acto-myosin cross-bridge kinetics are important for beat-to-beat regulation of cardiac contractility; however, physiological and pathophysiological mechanisms for regulation of contractile kinetics are incompletely understood. Here we explored whether thin filament-mediated Ca2+ sensitization influences cross-bridge kinetics in permeabilized, osmotically compressed cardiac muscle preparations. We used a murine model of hypertrophic cardiomyopathy (HCM) harboring a cardiac troponin C (cTnC) Ca2+-sensitizing mutation, Ala8Val in the regulatory N-domain. We also treated wild-type murine muscle with bepridil, a cTnC-targeting Ca2+ sensitizer. Our findings suggest that both methods of increasing myofilament Ca2+ sensitivity increase cross-bridge cycling rate measured by the rate of tension redevelopment (kTR); force per cross-bridge was also enhanced as measured by sinusoidal stiffness and I1,1/I1,0 ratio from X-ray diffraction. Computational modeling suggests that Ca2+ sensitization through this cTnC mutation or bepridil accelerates kTR primarily by promoting faster cross-bridge detachment. To elucidate if myofilament structural rearrangements are associated with changes in kTR, we used small angle X-ray diffraction to simultaneously measure myofilament lattice spacing and isometric force during steady-state Ca2+ activations. Within in vivo lattice dimensions, lattice spacing and steady-state isometric force increased significantly at submaximal activation. We conclude that the cTnC N-domain controls force by modulating both the number and rate of cycling cross-bridges, and that the both methods of Ca2+ sensitization may act through stabilization of cTnC's D-helix. Furthermore, we propose that the transient expansion of the myofilament lattice during Ca2+ activation may be an additional factor that could increase the rate of cross-bridge cycling in cardiac muscle. These findings may have implications for the pathophysiology of HCM.
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Affiliation(s)
- David Gonzalez-Martinez
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Jamie R Johnston
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Weikang Ma
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Olga Antipova
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA; X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Omar Awan
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Thomas C Irving
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - J Renato Pinto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA.
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20
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Klein BA, Reiz B, Robertson IM, Irving M, Li L, Sun YB, Sykes BD. Reversible Covalent Reaction of Levosimendan with Cardiac Troponin C in Vitro and in Situ. Biochemistry 2018; 57:2256-2265. [DOI: 10.1021/acs.biochem.8b00109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Brittney A. Klein
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Béla Reiz
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta T6H 2H7, Canada
| | - Ian M. Robertson
- Pharmaceutical and Health Benefits Branch, Ministry of Health, Government of Alberta, Edmonton, Alberta T5J 3Z5, Canada
| | - Malcolm Irving
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, King’s College London, London SE1 1UL, U.K
| | - Liang Li
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta T6H 2H7, Canada
| | - Yin-Biao Sun
- Randall Centre for Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, King’s College London, London SE1 1UL, U.K
| | - Brian D. Sykes
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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21
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Aprahamian ML, Tikunova SB, Price MV, Cuesta AF, Davis JP, Lindert S. Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders. J Chem Inf Model 2017; 57:3056-3069. [PMID: 29144742 DOI: 10.1021/acs.jcim.7b00536] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Calcium-dependent cardiac muscle contraction is regulated by the protein complex troponin. Calcium binds to the N-terminal domain of troponin C (cNTnC) which initiates the process of contraction. Heart failure is a consequence of a disruption of this process. With the prevalence of this condition, a strong need exists to find novel compounds to increase the calcium sensitivity of cNTnC. Desirable are small chemical molecules that bind to the interface between cTnC and the cTnI switch peptide and exhibit calcium sensitizing properties by possibly stabilizing cTnC in an open conformation. To identify novel drug candidates, we employed a structure-based drug discovery protocol that incorporated the use of a relaxed complex scheme (RCS). In preparation for the virtual screening, cNTnC conformations were identified based on their ability to correctly predict known cNTnC binders using a receiver operating characteristics analysis. Following a virtual screen of the National Cancer Institute's Developmental Therapeutic Program database, a small number of molecules were experimentally tested using stopped-flow kinetics and steady-state fluorescence titrations. We identified two novel compounds, 3-(4-methoxyphenyl)-6,7-chromanediol (NSC600285) and 3-(4-methylphenyl)-7,8-chromanediol (NSC611817), that show increased calcium sensitivity of cTnC in the presence of the regulatory domain of cTnI. The effects of NSC600285 and NSC611817 on the calcium dissociation rate was stronger than that of the known calcium sensitizer bepridil. Thus, we identified a 3-phenylchromane group as a possible key pharmacophore in the sensitization of cardiac muscle contraction. Building on this finding is of interest to researchers working on development of drugs for calcium sensitization.
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Affiliation(s)
- Melanie L Aprahamian
- Department of Chemistry and Biochemistry, Ohio State University , Columbus, Ohio 43210, United States
| | - Svetlana B Tikunova
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, Ohio State University , Columbus, Ohio 43210, United States
| | - Morgan V Price
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, Ohio State University , Columbus, Ohio 43210, United States
| | - Andres F Cuesta
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, Ohio State University , Columbus, Ohio 43210, United States
| | - Jonathan P Davis
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, 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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22
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Schlecht W, Dong WJ. Dynamic Equilibrium of Cardiac Troponin C's Hydrophobic Cleft and Its Modulation by Ca 2+ Sensitizers and a Ca 2+ Sensitivity Blunting Phosphomimic, cTnT(T204E). Bioconjug Chem 2017; 28:2581-2590. [PMID: 28876897 DOI: 10.1021/acs.bioconjchem.7b00418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several studies have suggested that conformational dynamics are important in the regulation of thin filament activation in cardiac troponin C (cTnC); however, little direct evidence has been offered to support these claims. In this study, a dye homodimerization approach is developed and implemented that allows the determination of the dynamic equilibrium between open and closed conformations in cTnC's hydrophobic cleft. Modulation of this equilibrium by Ca2+, cardiac troponin I (cTnI), cardiac troponin T (cTnT), Ca2+-sensitizers, and a Ca2+-desensitizing phosphomimic of cTnT (cTnT(T204E) is characterized. Isolated cTnC contained a small open conformation population in the absence of Ca2+ that increased significantly upon the addition of saturating levels of Ca2+. This suggests that the Ca2+-induced activation of thin filament arises from an increase in the probability of hydrophobic cleft opening. The inclusion of cTnI increased the population of open cTnC, and the inclusion of cTnT had the opposite effect. Samples containing Ca2+-desensitizing cTnT(T204E) showed a slight but insignificant decrease in open conformation probability compared to samples with cardiac troponin T, wild type [cTnT(wt)], while Ca2+ sensitizer treated samples generally increased open conformation probability. These findings show that an equilibrium between the open and closed conformations of cTnC's hydrophobic cleft play a significant role in tuning the Ca2+ sensitivity of the heart.
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Affiliation(s)
- William Schlecht
- The Voiland School of Chemical Engineering and Bioengineering and ‡The Department of Integrated Neuroscience and Physiology, Washington State University , Pullman, Washington 99164, United States
| | - Wen-Ji Dong
- The Voiland School of Chemical Engineering and Bioengineering and ‡The Department of Integrated Neuroscience and Physiology, Washington State University , Pullman, Washington 99164, United States
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23
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Veltri T, de Oliveira GAP, Bienkiewicz EA, Palhano FL, Marques MDA, Moraes AH, Silva JL, Sorenson MM, Pinto JR. Amide hydrogens reveal a temperature-dependent structural transition that enhances site-II Ca 2+-binding affinity in a C-domain mutant of cardiac troponin C. Sci Rep 2017; 7:691. [PMID: 28386062 PMCID: PMC5429600 DOI: 10.1038/s41598-017-00777-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/14/2017] [Indexed: 01/07/2023] Open
Abstract
The hypertrophic cardiomyopathy-associated mutant D145E, in cardiac troponin C (cTnC) C-domain, causes generalised instability at multiple sites in the isolated protein. As a result, structure and function of the mutant are more susceptible to higher temperatures. Above 25 °C there are large, progressive increases in N-domain Ca2+-binding affinity for D145E but only small changes for the wild-type protein. NMR-derived backbone amide temperature coefficients for many residues show a sharp transition above 30–40 °C, indicating a temperature-dependent conformational change that is most prominent around the mutated EF-hand IV, as well as throughout the C-domain. Smaller, isolated changes occur in the N-domain. Cardiac skinned fibres reconstituted with D145E are more sensitive to Ca2+ than fibres reconstituted with wild-type, and this defect is amplified near body-temperature. We speculate that the D145E mutation destabilises the native conformation of EF-hand IV, leading to a transient unfolding and dissociation of helix H that becomes more prominent at higher temperatures. This creates exposed hydrophobic surfaces that may be capable of binding unnaturally to a variety of targets, possibly including the N-domain of cTnC when it is in its open Ca2+-saturated state. This would constitute a potential route for propagating signals from one end of TnC to the other.
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Affiliation(s)
- Tiago Veltri
- Department of Biomedical Sciences, Florida State University College of Medicine, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA.,Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas F° 373, Cidade Universitária, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ewa A Bienkiewicz
- Department of Biomedical Sciences, Florida State University College of Medicine, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA
| | - Fernando L Palhano
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas F° 373, Cidade Universitária, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Mayra de A Marques
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adolfo H Moraes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Martha M Sorenson
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas F° 373, Cidade Universitária, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Jose R Pinto
- Department of Biomedical Sciences, Florida State University College of Medicine, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA.
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24
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Cai F, Li MX, Pineda-Sanabria SE, Gelozia S, Lindert S, West F, Sykes BD, Hwang PM. Structures reveal details of small molecule binding to cardiac troponin. J Mol Cell Cardiol 2016; 101:134-144. [PMID: 27825981 DOI: 10.1016/j.yjmcc.2016.10.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 11/27/2022]
Abstract
In cardiac and skeletal muscle, the troponin complex turns muscle contraction on and off in a calcium-dependent manner. Many small molecules are known to bind to the troponin complex to modulate its calcium binding affinity, and this may be useful in a broad range of conditions in which striated muscle function is compromised, such as congestive heart failure. As a tool for developing drugs specific for the cardiac isoform of troponin, we have designed a chimeric construct (cChimera) consisting of the regulatory N-terminal domain of cardiac troponin C (cNTnC) fused to the switch region of cardiac troponin I (cTnI), mimicking the key binding event that turns on muscle contraction. We demonstrate by solution NMR spectroscopy that cChimera faithfully reproduces the native interface between cTnI and cNTnC. We determined that small molecules based on diphenylamine can bind to cChimera with a KD as low as 10μM. Solution NMR structures show that minimal structural perturbations in cChimera are needed to accommodate 3-methyldiphenylamine (3-mDPA), which is probably why it binds with higher affinity than previously studied compounds like bepridil, despite its significantly smaller size. The unsubstituted aromatic ring of 3-mDPA binds to an inner hydrophobic pocket adjacent to the central beta sheet of cNTnC. However, the methyl-substituted ring is able to bind in two different orientations, either inserting into the cNTnC-cTnI interface or "flipping out" to form contacts primarily with helix C of cNTnC. Our work suggests that preservation of the native interaction between cNTnC and cTnI is key to the development of a high affinity cardiac troponin-specific drug.
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Affiliation(s)
- Fangze Cai
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Monica X Li
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | | | - Shorena Gelozia
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Frederick West
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada; Department of Medicine, University of Alberta, Edmonton, AB, Canada.
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25
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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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26
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Dewan S, McCabe KJ, Regnier M, McCulloch AD, Lindert S. Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation-An Integrated Multiscale Modeling Study. J Phys Chem B 2016; 120:8264-75. [PMID: 27133568 PMCID: PMC5001916 DOI: 10.1021/acs.jpcb.6b01950] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in cardiac troponin C (D75Y, E59D, and G159D), a key regulatory protein of myofilament contraction, have been associated with dilated cardiomyopathy (DCM). Despite reports of altered myofilament function in these mutants, the underlying molecular alterations caused by these mutations remain elusive. Here we investigate in silico the intramolecular mechanisms by which these mutations affect myofilament contraction. On the basis of the location of cardiac troponin C (cTnC) mutations, we tested the hypothesis that intramolecular effects can explain the altered myofilament calcium sensitivity of force development for D75Y and E59D cTnC, whereas altered cardiac troponin C-troponin I (cTnC-cTnI) interaction contributes to the reported contractile effects of the G159D mutation. We employed a multiscale approach combining molecular dynamics (MD) and Brownian dynamics (BD) simulations to estimate cTnC calcium association and hydrophobic patch opening. We then integrated these parameters into a Markov model of myofilament activation to compute the steady-state force-pCa relationship. The analysis showed that myofilament calcium sensitivity with D75Y and E59D can be explained by changes in calcium binding affinity of cTnC and the rate of hydrophobic patch opening, if a partial cTnC interhelical opening angle (110°) is sufficient for cTnI switch peptide association to cTnC. In contrast, interactions between cTnC and cTnI within the cardiac troponin complex must also be accounted for to explain contractile alterations due to G159D. In conclusion, this is the first multiscale in silico study to elucidate how direct molecular effects of genetic mutations in cTnC translate to altered myofilament contractile function.
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Affiliation(s)
- Sukriti Dewan
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, 92093
| | - Kimberly J. McCabe
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, 92093
| | - Michael Regnier
- Dept. of Bioengineering, University of Washington, Seattle, WA 98195
- Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109
| | - Andrew D. McCulloch
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, 92093
| | - Steffen Lindert
- Department of Chemistry & Biochemistry, Ohio State University, Columbus, OH, 43210
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27
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Pineda-Sanabria SE, Robertson IM, Sun YB, Irving M, Sykes BD. Probing the mechanism of cardiovascular drugs using a covalent levosimendan analog. J Mol Cell Cardiol 2016; 92:174-84. [PMID: 26853943 PMCID: PMC4831045 DOI: 10.1016/j.yjmcc.2016.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/24/2016] [Accepted: 02/02/2016] [Indexed: 01/16/2023]
Abstract
One approach to improve contraction in the failing heart is the administration of calcium (Ca2 +) sensitizers. Although it is known that levosimendan and other sensitizers bind to troponin C (cTnC), their in vivo mechanism is not fully understood. Based on levosimendan, we designed a covalent Ca2 + sensitizer (i9) that targets C84 of cTnC and exchanged this complex into cardiac muscle. The NMR structure of the covalent complex showed that i9 binds deep in the hydrophobic pocket of cTnC. Despite slightly reducing troponin I affinity, i9 enhanced the Ca2 + sensitivity of cardiac muscle. We conclude that i9 enhances Ca2 + sensitivity by stabilizing the open conformation of cTnC. These findings provide new insights into the in vivo mechanism of Ca2 + sensitization and demonstrate that directly targeting cTnC has significant potential in cardiovascular therapy. A Ca2 + sensitizer, i9 was designed that forms a covalent bond with C84 of cTnC. i9 stabilized the open state of the N-domain of cTnC. The structure of the covalent cTnC-cTnI-i9 complex was solved by NMR. The structure showed that i9 binds deep in the hydrophobic pocket of cTnC. Despite slightly reducing cTnI affinity, i9 enhanced the Ca2 + sensitivity of cardiac muscle.
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Affiliation(s)
- Sandra E Pineda-Sanabria
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ian M Robertson
- Randall Division of Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Yin-Biao Sun
- Randall Division of Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Malcolm Irving
- Randall Division of Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Brian D Sykes
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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28
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Schlecht W, Li KL, Hu D, Dong W. Fluorescence Based Characterization of Calcium Sensitizer Action on the Troponin Complex. Chem Biol Drug Des 2015; 87:171-81. [PMID: 26375298 DOI: 10.1111/cbdd.12651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/15/2015] [Accepted: 08/05/2015] [Indexed: 11/29/2022]
Abstract
Calcium sensitizers enhance the transduction of the Ca(2+) signal into force within the heart and have found use in treating heart failure. However the mechanisms of action for most Ca(2+) sensitizers remain unclear. To address this issue an efficient fluorescence based approach to Ca(2+) sensitizer screening was developed which monitors cardiac troponin C's (cTnC's) hydrophobic cleft. This approach was tested on four common Ca(2+) -sensitizers, EMD 57033, levosimendan, bepridil and pimobendan with the aim of elucidating the mechanisms of action for each as well as proving the efficacy of the new screening method. Ca(2+) -titration experiments were employed to determine the effect on Ca(2+) sensitivity and cooperativity of cTnC opening, while stopped flow experiments were used to investigate the impact on cTnC relaxation kinetics. Bepridil was shown to increase the sensitivity of cTnC for Ca(2+) under all reconstitution conditions, sensitization by the other drugs was context dependent. Levosimendan and pimobendan reduced the rate of cTnC closing consistent with a stabilization of cTnC's open conformation while bepridil increased the rate of relaxation. Experiments were also run on samples containing cTnT(T204E), a known Ca(2+) -desensitizing phosphorylation mimic. Levosimendan, bepridil, and pimobendan were found to elevate the Ca(2+) -sensitivity of cTnT(T204E) containing samples in this context.
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Affiliation(s)
- William Schlecht
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, PO Box 646515, Washington State University, Pullman, WA 99164-6515, USA
| | - King-Lun Li
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, PO Box 646515, Washington State University, Pullman, WA 99164-6515, USA
| | - Dehong Hu
- The Environmental and Molecular Science Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard Richland, WA 99354, USA
| | - Wenji Dong
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, PO Box 646515, Washington State University, Pullman, WA 99164-6515, USA
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29
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Li MX, Hwang PM. Structure and function of cardiac troponin C (TNNC1): Implications for heart failure, cardiomyopathies, and troponin modulating drugs. Gene 2015; 571:153-66. [PMID: 26232335 DOI: 10.1016/j.gene.2015.07.074] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/24/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
Abstract
In striated muscle, the protein troponin complex turns contraction on and off in a calcium-dependent manner. The calcium-sensing component of the complex is troponin C, which is expressed from the TNNC1 gene in both cardiac muscle and slow-twitch skeletal muscle (identical transcript in both tissues) and the TNNC2 gene in fast-twitch skeletal muscle. Cardiac troponin C (cTnC) is made up of two globular EF-hand domains connected by a flexible linker. The structural C-domain (cCTnC) contains two high affinity calcium-binding sites that are always occupied by Ca(2+) or Mg(2+) under physiologic conditions, stabilizing an open conformation that remains anchored to the rest of the troponin complex. In contrast, the regulatory N-domain (cNTnC) contains a single low affinity site that is largely unoccupied at resting calcium concentrations. During muscle activation, calcium binding to cNTnC favors an open conformation that binds to the switch region of troponin I, removing adjacent inhibitory regions of troponin I from actin and allowing muscle contraction to proceed. Regulation of the calcium binding affinity of cNTnC is physiologically important, because it directly impacts the calcium sensitivity of muscle contraction. Calcium sensitivity can be modified by drugs that stabilize the open form of cNTnC, post-translational modifications like phosphorylation of troponin I, or downstream thin filament protein interactions that impact the availability of the troponin I switch region. Recently, mutations in cTnC have been associated with hypertrophic or dilated cardiomyopathy. A detailed understanding of how calcium sensitivity is regulated through the troponin complex is necessary for explaining how mutations perturb its function to promote cardiomyopathy and how post-translational modifications in the thin filament affect heart function and heart failure. Troponin modulating drugs are being developed for the treatment of cardiomyopathies and heart failure.
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Affiliation(s)
- Monica X Li
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Peter M Hwang
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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30
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Abstract
Various human diseases can disrupt the balance between muscle contraction and relaxation. Sarcomeric modulators can be used to readjust this balance either indirectly by intervening in signalling pathways or directly through interaction with the muscle proteins that control contraction. Such agents represent a novel approach to treating any condition in which striated muscle function is compromised, including heart failure, cardiomyopathies, skeletal myopathies and a wide range of neuromuscular conditions. Here, we review agents that modulate the mechanical function of the sarcomere, focusing on emerging compounds that target myosin or the troponin complex.
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31
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Denessiouk K, Permyakov S, Denesyuk A, Permyakov E, Johnson MS. Two structural motifs within canonical EF-hand calcium-binding domains identify five different classes of calcium buffers and sensors. PLoS One 2014; 9:e109287. [PMID: 25313560 PMCID: PMC4196763 DOI: 10.1371/journal.pone.0109287] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/29/2014] [Indexed: 11/18/2022] Open
Abstract
Proteins with EF-hand calcium-binding motifs are essential for many cellular processes, but are also associated with cancer, autism, cardiac arrhythmias, and Alzheimer's, skeletal muscle and neuronal diseases. Functionally, all EF-hand proteins are divided into two groups: (1) calcium sensors, which function to translate the signal to various responses; and (2) calcium buffers, which control the level of free Ca2+ ions in the cytoplasm. The borderline between the two groups is not clear, and many proteins cannot be described as definitive buffers or sensors. Here, we describe two highly-conserved structural motifs found in all known different families of the EF-hand proteins. The two motifs provide a supporting scaffold for the DxDxDG calcium binding loop and contribute to the hydrophobic core of the EF hand domain. The motifs allow more precise identification of calcium buffers and calcium sensors. Based on the characteristics of the two motifs, we could classify individual EF-hand domains into five groups: (1) Open static; (2) Closed static; (3) Local dynamic; (4) Dynamic; and (5) Local static EF-hand domains.
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Affiliation(s)
- Konstantin Denessiouk
- Biochemistry, Department of Biosciences, Åbo Akademi University, Turku, Finland
- * E-mail:
| | - Sergei Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
| | - Alexander Denesyuk
- Biochemistry, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Eugene Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
| | - Mark S. Johnson
- Biochemistry, Department of Biosciences, Åbo Akademi University, Turku, Finland
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32
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Pineda-Sanabria SE, Julien O, Sykes BD. Versatile cardiac troponin chimera for muscle protein structural biology and drug discovery. ACS Chem Biol 2014; 9:2121-30. [PMID: 25010113 DOI: 10.1021/cb500249j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Investigation of the molecular interactions within and between subunits of the heterotrimeric troponin complex, and with other proteins in the sarcomere, has revealed salient structural elements involved in regulation of muscle contraction. The discovery of new cardiotonic drugs and structural studies utilizing intact troponin, or regulatory complexes formed between the key regions identified in troponin C and troponin I, face intrinsic and technical difficulties associated with weak protein-protein interactions and with solubility, aggregation, stability of the overall architecture, isotope labeling, and size, respectively. We have designed and characterized a chimeric troponin C-troponin I hybrid protein with a cleavable linker that is useful for producing isotopically labeled troponin peptides, stabilizes their interaction, and has proven to be a faithful representation of the original complex in the systolic state, but lacking its disadvantages, making it particularly suitable for drug screening and structural studies.
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Affiliation(s)
- Sandra E. Pineda-Sanabria
- Department of Biochemistry, University of Alberta, 4-19 Medical
Sciences Building, Edmonton, Alberta Canada, T6G 2H7
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, 4-19 Medical
Sciences Building, Edmonton, Alberta Canada, T6G 2H7
| | - Brian D. Sykes
- Department of Biochemistry, University of Alberta, 4-19 Medical
Sciences Building, Edmonton, Alberta Canada, T6G 2H7
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33
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Robertson IM, Pineda-Sanabria SE, Holmes PC, Sykes BD. Conformation of the critical pH sensitive region of troponin depends upon a single residue in troponin I. Arch Biochem Biophys 2014; 552-553:40-9. [DOI: 10.1016/j.abb.2013.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/18/2013] [Accepted: 12/05/2013] [Indexed: 12/20/2022]
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34
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Katrukha IA. Human cardiac troponin complex. Structure and functions. BIOCHEMISTRY (MOSCOW) 2014; 78:1447-65. [DOI: 10.1134/s0006297913130063] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Zhang XL, Tibbits GF, Paetzel M. The structure of cardiac troponin C regulatory domain with bound Cd2+ reveals a closed conformation and unique ion coordination. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:722-34. [PMID: 23633581 DOI: 10.1107/s0907444913001182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/11/2013] [Indexed: 12/22/2022]
Abstract
The amino-terminal domain of cardiac troponin C (cNTnC) is an essential Ca(2+) sensor found in cardiomyocytes. It undergoes a conformational change upon Ca(2+) binding and transduces the signal to the rest of the troponin complex to initiate cardiac muscle contraction. Two classical EF-hand motifs (EF1 and EF2) are present in cNTnC. Under physiological conditions, only EF2 binds Ca(2+); EF1 is a vestigial site that has lost its function in binding Ca(2+) owing to amino-acid sequence changes during evolution. Proteins with EF-hand motifs are capable of binding divalent cations other than calcium. Here, the crystal structure of wild-type (WT) human cNTnC in complex with Cd(2+) is presented. The structure of Cd(2+)-bound cNTnC with the disease-related mutation L29Q, as well as a structure with the residue differences D2N, V28I, L29Q and G30D (NIQD), which have been shown to have functional importance in Ca(2+) sensing at lower temperatures in ectothermic species, have also been determined. The structures resemble the overall conformation of NMR structures of Ca(2+)-bound cNTnC, but differ significantly from a previous crystal structure of Cd(2+)-bound cNTnC in complex with deoxycholic acid. The subtle structural changes observed in the region near the mutations may play a role in the increased Ca(2+) affinity. The 1.4 Å resolution WT cNTnC structure, which is the highest resolution structure yet obtained for cardiac troponin C, reveals a Cd(2+) ion coordinated in the canonical pentagonal bipyramidal geometry in EF2 despite three residues in the loop being disordered. A Cd(2+) ion found in the vestigial ion-binding site of EF1 is coordinated in a noncanonical `distorted' octahedral geometry. A comparison of the ion coordination observed within EF-hand-containing proteins for which structures have been solved in the presence of Cd(2+) is presented. A refolded WT cNTnC structure is also presented.
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Affiliation(s)
- Xiaolu Linda Zhang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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36
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Lindert S, Kekenes-Huskey PM, McCammon JA. Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C. Biophys J 2012; 103:1784-9. [PMID: 23083722 DOI: 10.1016/j.bpj.2012.08.058] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 01/06/2023] Open
Abstract
Troponin (Tn) is an important regulatory protein in the thin-filament complex of cardiomyocytes. Calcium binding to the troponin C (TnC) subunit causes a change in its dynamics that leads to the transient opening of a hydrophobic patch on TnC's surface, to which a helix of another subunit, troponin I (TnI), binds. This process initiates contraction, making it an important target for studies investigating the detailed molecular processes that underlie contraction. Here we use microsecond-timescale Anton molecular dynamics simulations to investigate the dynamics and kinetics of the opening transition of the TnC hydrophobic patch. Free-energy differences for opening are calculated for wild-type Ca(2+)-bound TnC (∼8 kcal/mol), V44Q Ca(2+)-bound TnC (3.2 kcal/mol), E40A Ca(2+)-bound TnC (∼12 kcal/mol), and wild-type apo TnC (∼20 kcal/mol). These results suggest that the mutations have a profound impact on the frequency with which the hydrophobic patch presents to TnI. In addition, these simulations corroborate that cardiac wild-type TnC does not open on timescales relevant to contraction without calcium being bound.
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Affiliation(s)
- Steffen Lindert
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA.
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37
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Lindert S, Kekenes-Huskey PM, Huber G, Pierce L, McCammon JA. Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. J Phys Chem B 2012; 116:8449-59. [PMID: 22329450 PMCID: PMC3405770 DOI: 10.1021/jp212173f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/26/2012] [Indexed: 11/28/2022]
Abstract
Troponin C (TnC) is an important regulatory molecule in cardiomyocytes. Calcium binding to site II in TnC initiates a series of molecular events that result in muscle contraction. The most direct change upon Ca(2+) binding is an opening motion of the molecule that exposes a hydrophobic patch on the surface allowing for Troponin I to bind. Molecular dynamics simulations were used to elucidate the dynamics of this crucial protein in three different states: apo, Ca(2+)-bound, and Ca(2+)-TnI-bound. Dynamics between the states are compared, and the Ca(2+)-bound system is investigated for opening motions. On the basis of the simulations, NMR chemical shifts and order parameters are calculated and compared with experimental observables. Agreement indicates that the simulations sample the relevant dynamics of the system. Brownian dynamics simulations are used to investigate the calcium association of TnC. We find that calcium binding gives rise to correlative motions involving the EF hand and collective motions conducive of formation of the TnI-binding interface. We furthermore indicate the essential role of electrostatic steering in facilitating diffusion-limited binding of Ca(2+).
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Affiliation(s)
- Steffen Lindert
- Department of Pharmacology, NSF Center for Theoretical Biological Physics, National Biomedical Computation Resource, University of California San Diego, La Jolla, California 92093, United States.
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38
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Abstract
Cardiac troponin C (cTnC) is the Ca²⁺ dependent switch for contraction in heart muscle making it a potential target for drug research in the therapy of heart failure. Calcium binding on Troponin C (TnC) triggers a series of conformational changes exposing a hydrophobic pocket in the N-domain of TnC (cNTnC), which leads to force generation. Mutations and acidic pH have been related to altering the sensitivity of TnC affecting the efficiency of the heart. Bepridil, identified as a calcium sensitizer to TnC, has been experimentally found to bind to the N-domain pocket of TnC but with negative cooperativity. Screening and de novo design were carried out using LUDI and AUTOLUDI programs in this work to identify and design potential ligands that can bind to the hydrophobic pocket of TnC. Two docking centers and multiple searching radii including 5 Å, 5.5 Å, 6 Å, 6.5 Å, 7.0 Å and 7.5 Å were used in LUDI to screen the ZINC database. Based on the LUDI docking results, 8 molecules were identified from the database with good potential to bind into the binding pocket and they were used as template molecules to generate a series of new molecules by AUTOLUDI design. Out of all the newly-designed molecules, 14 new ligands were recognized to be potential ligands that can bind and fit well into the binding pocket. These molecules can be used as starting molecules to develop TnC ligands. The binding stability and binding affinity of these molecules to the protein was further analyzed by molecular dynamics simulations. The results show that the binding energies, interactions and complex stabilities of 6 ligands are comparable to or better than bepridil.
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Affiliation(s)
- Jayson F Varguhese
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
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Li AY, Lee J, Borek D, Otwinowski Z, Tibbits GF, Paetzel M. Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid reveals novel conformation. J Mol Biol 2011; 413:699-711. [PMID: 21920370 PMCID: PMC4068330 DOI: 10.1016/j.jmb.2011.08.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 01/07/2023]
Abstract
The amino-terminal regulatory domain of cardiac troponin C (cNTnC) plays an important role as the calcium sensor for the troponin complex. Calcium binding to cNTnC results in conformational changes that trigger a cascade of events that lead to cardiac muscle contraction. The cardiac N-terminal domain of TnC consists of two EF-hand calcium binding motifs, one of which is dysfunctional in binding calcium. Nevertheless, the defunct EF-hand still maintains a role in cNTnC function. For its structural analysis by X-ray crystallography, human cNTnC with the wild-type primary sequence was crystallized under a novel crystallization condition. The crystal structure was solved by the single-wavelength anomalous dispersion method and refined to 2.2 Å resolution. The structure displays several novel features. Firstly, both EF-hand motifs coordinate cadmium ions derived from the crystallization milieu. Secondly, the ion coordination in the defunct EF-hand motif accompanies unusual changes in the protein conformation. Thirdly, deoxycholic acid, also derived from the crystallization milieu, is bound in the central hydrophobic cavity. This is reminiscent of the interactions observed for cardiac calcium sensitizer drugs that bind to the same core region and maintain the "open" conformational state of calcium-bound cNTnC. The cadmium ion coordination in the defunct EF-hand indicates that this vestigial calcium binding site retains the structural and functional elements that allow it to coordinate a cadmium ion. However, it is a result of, or concomitant with, large and unusual structural changes in cNTnC.
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Affiliation(s)
- Alison Yueh Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
- Department of Biomedical Physiology and Kinesiology, Molecular Cardiac Physiology Group, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
| | - Jaeyong Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
| | - Dominika Borek
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Zbyszek Otwinowski
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Glen F. Tibbits
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
- Department of Biomedical Physiology and Kinesiology, Molecular Cardiac Physiology Group, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
- Cardiovascular Sciences, Child and Family Research Institute, 950 West 28 Ave, Vancouver, BC, Canada V5Z 4H4
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
- Department of Biomedical Physiology and Kinesiology, Molecular Cardiac Physiology Group, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada, V5A 1S6
- Address correspondence to: Dr. Mark Paetzel, Simon Fraser University, Department of Molecular Biology and Biochemistry, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6, Tel.: 778-782-4230, Fax.: 778-782-5583,
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40
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Robertson IM, Boyko RF, Sykes BD. Visualizing the principal component of ¹H, ¹⁵N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C. JOURNAL OF BIOMOLECULAR NMR 2011; 51:115-122. [PMID: 21947920 DOI: 10.1007/s10858-011-9546-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/13/2011] [Indexed: 05/31/2023]
Abstract
Laboratories often repeatedly determine the structure of a given protein under a variety of conditions, mutations, modifications, or in a number of states. This approach can be cumbersome and tedious. Given then a database of structures, identifiers, and corresponding (1)H,(15)N-HSQC NMR spectra for homologous proteins, we investigated whether structural information could be ascertained for a new homolog solely from its (1)H,(15)N-HSQC NMR spectrum. We addressed this question with two different approaches. First, we used a semi-automated approach with the program, ORBplus. ORBplus looks for patterns in the chemical shifts and correlates these commonalities to the explicit property of interest. ORBplus ranks resonances based on consistency of the magnitude and direction of the chemical shifts within the database, and the chemical shift correlation of the unknown protein with the database. ORBplus visualizes the results by a histogram and a vector diagram, and provides residue specific predictions on structural similarities with the database. The second method we used was partial least squares (PLS), which is a multivariate statistical technique used to correlate response and predictor variables. We investigated the ability of these methods to predict the tertiary structure of the contractile regulatory protein troponin C. Troponin C undergoes a closed-to-open conformational change, which is coupled to its function in muscle. We found that both ORBplus and PLS were able to identify patterns in the (1)H,(15)N-HSQC NMR data from different states of troponin C that correlated to its conformation.
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Affiliation(s)
- Ian M Robertson
- Department of Biochemistry, University of Alberta, Edmonton, AB T5K 2W7, Canada
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41
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Park S, Li C, Ames JB. Nuclear magnetic resonance structure of calcium-binding protein 1 in a Ca(2+) -bound closed state: implications for target recognition. Protein Sci 2011; 20:1356-66. [PMID: 21608059 DOI: 10.1002/pro.662] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/10/2011] [Indexed: 11/10/2022]
Abstract
Calcium-binding protein 1 (CaBP1), a neuron-specific member of the calmodulin (CaM) superfamily, regulates the Ca(2+) -dependent activity of inositol 1,4,5-triphosphate receptors (InsP3Rs) and various voltage-gated Ca(2+) channels. Here, we present the NMR structure of full-length CaBP1 with Ca(2+) bound at the first, third, and fourth EF-hands. A total of 1250 nuclear Overhauser effect distance measurements and 70 residual dipolar coupling restraints define the overall main chain structure with a root-mean-squared deviation of 0.54 Å (N-domain) and 0.48 Å (C-domain). The first 18 residues from the N-terminus in CaBP1 (located upstream of the first EF-hand) are structurally disordered and solvent exposed. The Ca(2+) -saturated CaBP1 structure contains two independent domains separated by a flexible central linker similar to that in calmodulin and troponin C. The N-domain structure of CaBP1 contains two EF-hands (EF1 and EF2), both in a closed conformation [interhelical angles = 129° (EF1) and 142° (EF2)]. The C-domain contains EF3 and EF4 in the familiar Ca(2+) -bound open conformation [interhelical angles = 105° (EF3) and 91° (EF4)]. Surprisingly, the N-domain adopts the same closed conformation in the presence or absence of Ca(2+) bound at EF1. The Ca(2+) -bound closed conformation of EF1 is reminiscent of Ca(2+) -bound EF-hands in a closed conformation found in cardiac troponin C and calpain. We propose that the Ca(2+) -bound closed conformation of EF1 in CaBP1 might undergo an induced-fit opening only in the presence of a specific target protein, and thus may help explain the highly specialized target binding by CaBP1.
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Affiliation(s)
- Saebomi Park
- Department of Chemistry, University of California, Davis, California 95616, USA
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42
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Varughese JF, Baxley T, Chalovich JM, Li Y. A computational and experimental approach to investigate bepridil binding with cardiac troponin. J Phys Chem B 2011; 115:2392-400. [PMID: 21332124 DOI: 10.1021/jp1094504] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cardiac troponin is a Ca(2+)-dependent switch for the contraction in heart muscle and a potential target for drugs in the therapy of heart failure. Bepridil is a drug that binds to troponin and increases calcium sensitivity of muscle contraction. Because bepridil has been well studied, it is a good model for analysis by computational and experimental methods. Molecular dynamics (MD) simulations were performed on troponin complexes of different sizes in the presence and absence of bepridil bound within the hydrophobic pocket at the N-terminal domain of troponin C. About 100 ns of simulation trajectory data were generated, which were analyzed using cross-correlation analyses and MMPBSA and MMGBSA techniques. The results indicated that bepridil binding within the hydrophobic pocket of cardiac TnC decreases the interaction of TnC with TnI at both the N-domain of TnC and the C-domain of TnC, and decreases the correlations of motions among the segments of the troponin subunits. The estimated calcium-binding affinities using MMPBSA showed that bepridil has a sensitizing effect for the isolated system of TnC, but loses this effect for the complex. Our experimental measurements of calcium dissociation rates were consistent with that prediction. We also observed that while bepridil enhanced the troponin-tropomyosin-actin-activated ATPase activity of myosin S1 at low calcium concentrations it was slightly inhibitory at high calcium concentrations. Bepridil increases the ATPase activity and force generation in muscle fibers, but its effects appear to depend on the concentration of calcium.
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Affiliation(s)
- Jayson F Varughese
- Department of Chemistry, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27858, USA
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43
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Li Y, Liu Z, Wang R. Test MM-PB/SA on true conformational ensembles of protein-ligand complexes. J Chem Inf Model 2011; 50:1682-92. [PMID: 20695488 DOI: 10.1021/ci100036a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular mechanics Poisson-Boltzmann surface area (MM-PB/SA) method has been popular for computing protein-ligand binding free energies in recent years. All previous evaluations of the MM-PB/SA method are based upon computer-generated conformational ensembles, which may be affected by the defective computational methods used for preparing these conformational ensembles. In an attempt to reach more convincing conclusions, we have evaluated the MM-PB/SA method on a set of 24 diverse protein-ligand complexes, each of which has a set of conformations derived from NMR spectroscopy. Our results indicate that both MM-PB/SA and molecular mechanics generalized Born surface area (MM-GB/SA) are able to produce a modest correlation between their results and the experimentally measured binding free energies on our test set. In particular, both MM-PB/SA and MM-GB/SA produced better results by using a representative structure (R = 0.72-0.79) rather than averaging over the conformational ensemble of each given complex (R = 0.61-0.74). A head-to-head comparison with four selected scoring functions (X-Score, PLP, ChemScore, and DrugScore) on the same test set reveals that MM-PB/SA and MM-GB/SA results are marginally better than those produced by scoring funcitons, supporting the value of the MM-PB/SA method. Nevertheless, scoring functions are still more cost-effective options, especially for high-throughput tasks.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, Shanghai 200032, People's Republic of China
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44
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Park S, Li C, Ames JB. 1H, 15N, and 13C chemical shift assignments of calcium-binding protein 1 with Ca2+ bound at EF1, EF3 and EF4. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:159-161. [PMID: 20503119 PMCID: PMC2947014 DOI: 10.1007/s12104-010-9235-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 05/17/2010] [Indexed: 05/29/2023]
Abstract
Calcium-binding protein 1 (CaBP1) regulates inositol 1,4,5-trisphosphate receptors (InsP(3)Rs) and a variety of voltage-gated Ca(2+) channels in the brain. We report complete NMR chemical shift assignments of the Ca(2+)-saturated form of CaBP1 with Ca(2+) bound at EF1, EF3 and EF4 (residues 1-167, BMRB no. 16862).
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Affiliation(s)
- Saebomi Park
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Congmin Li
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - James B. Ames
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616 USA
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45
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Robertson IM, Sun YB, Li MX, Sykes BD. A structural and functional perspective into the mechanism of Ca2+-sensitizers that target the cardiac troponin complex. J Mol Cell Cardiol 2010; 49:1031-41. [PMID: 20801130 DOI: 10.1016/j.yjmcc.2010.08.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/17/2010] [Accepted: 08/19/2010] [Indexed: 11/25/2022]
Abstract
The Ca(2+) dependent interaction between troponin I (cTnI) and troponin C (cTnC) triggers contraction in heart muscle. Heart failure is characterized by a decrease in cardiac output, and compounds that increase the sensitivity of cardiac muscle to Ca(2+) have therapeutic potential. The Ca(2+)-sensitizer, levosimendan, targets cTnC; however, detailed understanding of its mechanism has been obscured by its instability. In order to understand how this class of positive inotropes function, we investigated the mode of action of two fluorine containing novel analogs of levosimendan; 2',4'-difluoro(1,1'-biphenyl)-4-yloxy acetic acid (dfbp-o) and 2',4'-difluoro(1,1'-biphenyl)-4-yl acetic acid (dfbp). The affinities of dfbp and dfbp-o for the regulatory domain of cTnC were measured in the absence and presence of cTnI by NMR spectroscopy, and dfbp-o was found to bind more strongly than dfbp. Dfbp-o also increased the affinity of cTnI for cTnC. Dfbp-o increased the Ca(2+)-sensitivity of demembranated cardiac trabeculae in a manner similar to levosimendan. The high resolution NMR solution structure of the cTnC-cTnI-dfbp-o ternary complex showed that dfbp-o bound at the hydrophobic interface formed by cTnC and cTnI making critical interactions with residues such as Arg147 of cTnI. In the absence of cTnI, docking localized dfbp-o to the same position in the hydrophobic groove of cTnC. The structural and functional data reveal that the levosimendan class of Ca(2+)-sensitizers work by binding to the regulatory domain of cTnC and stabilizing the pivotal cTnC-cTnI regulatory unit via a network of hydrophobic and electrostatic interactions, in contrast to the destabilizing effects of antagonists such as W7 at the same interface.
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Affiliation(s)
- Ian M Robertson
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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46
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Davis FP, Sali A. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol 2010; 6:e1000668. [PMID: 20140189 PMCID: PMC2816688 DOI: 10.1371/journal.pcbi.1000668] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 12/31/2009] [Indexed: 02/03/2023] Open
Abstract
Protein–protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions. Specifically, we identify ligand and protein binding sites that overlap upon alignment of homologous proteins. Of the 2,619 protein structure families observed to bind proteins, 1,028 also bind small molecules (250–1000 Da), and 197 exhibit a statistically significant (p<0.01) overlap between ligand and protein binding positions. These “bi-functional positions”, which bind both ligands and proteins, are particularly enriched in tyrosine and tryptophan residues, similar to “energetic hotspots” described previously, and are significantly less conserved than mono-functional and solvent exposed positions. Homology transfer identifies ligands whose binding sites overlap at least 20% of the protein interface for 35% of domain–domain and 45% of domain–peptide mediated interactions. The analysis recovered known small-molecule modulators of protein interactions as well as predicted new interaction targets based on the sequence similarity of ligand binding sites. We illustrate the predictive utility of the method by suggesting structural mechanisms for the effects of sanglifehrin A on HIV virion production, bepridil on the cellular entry of anthrax edema factor, and fusicoccin on vertebrate developmental pathways. The results, available at http://pibase.janelia.org, represent a comprehensive collection of structurally characterized modulators of protein interactions, and suggest that homologous structures are a useful resource for the rational design of interaction modulators. Proteins function through their interactions with other biological molecules, including other proteins. Often times, these interactions underlie cellular processes that go awry in disease. Therefore, modulating these interactions with small molecules is an active area of research for new drugs to treat diseases and new chemical tools to dissect cellular interaction networks. However, targeting protein–protein interactions has proven to be more challenging than the typical drug targets found on individual proteins. Here, we present a computational approach that aims to help in this challenge by identifying regions of protein–protein interfaces that may be amenable to targeting by small molecules. Through a comprehensive analysis of all known protein structures, we identify closely related proteins that in one case bind a protein and in another case bind a small molecule. We find that a significant number of protein–protein interactions occur through surface regions that bind small molecules in related proteins. These “bi-functional” positions, which can bind both proteins and ligands, will serve as an additional piece of structural information that can aid experimentalists in developing small molecules that modulate protein interactions.
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Affiliation(s)
- Fred P. Davis
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America
- * E-mail: (FPD); (AS)
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (FPD); (AS)
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47
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Oleszczuk M, Robertson IM, Li MX, Sykes BD. Solution structure of the regulatory domain of human cardiac troponin C in complex with the switch region of cardiac troponin I and W7: the basis of W7 as an inhibitor of cardiac muscle contraction. J Mol Cell Cardiol 2010; 48:925-33. [PMID: 20116385 DOI: 10.1016/j.yjmcc.2010.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 01/19/2010] [Accepted: 01/20/2010] [Indexed: 10/19/2022]
Abstract
The solution structure of Ca(2+)-bound regulatory domain of cardiac troponin C (cNTnC) in complex with the switch region of troponin I (cTnI(147-163)) and the calmodulin antagonist, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfinamide (W7), has been determined by NMR spectroscopy. The structure reveals that the W7 naphthalene ring interacts with the terminal methyl groups of M47, M60, and M81 as well as aliphatic and aromatic side chains of several other residues in the hydrophobic pocket of cNTnC. The H3 ring proton of W7 also contacts the methyl groups of I148 and M153 of cTnI(147-163). The N-(6-aminohexyl) tail interacts primarily with the methyl groups of V64 and M81, which are located on the C- and D-helices of cNTnC. Compared to the structure of the cNTnC*Ca(2+)*W7 complex (Hoffman, R. M. B. and Sykes, B. D. (2009) Biochemistry 48, 5541-5552), the tail of W7 reorients slightly toward the surface of cNTnC while the ring remains in the hydrophobic pocket. The positively charged -NH(3)(+) group from the tail of W7 repels the positively charged R147 of cTnI(147-163). As a result, the N-terminus of the peptide moves away from cNTnC and the helical content of cTnI(147-163) is diminished, when compared to the structure of cNTnC*Ca(2+)*cTnI(147-163) (Li, M. X., Spyracopoulos, L., and Sykes B. D. (1999) Biochemistry 38, 8289-8298). Thus the ternary structure cNTnC*Ca(2+)*W7*cTnI(147-163) reported in this study offers an explanation for the approximately 13-fold affinity reduction of cTnI(147-163) for cNTnC*Ca(2+) in the presence of W7 and provides a structural basis for the inhibitory effect of W7 in cardiac muscle contraction. This generates molecular insight into structural features that are useful for the design of cTnC-specific Ca(2+)-desensitizing drugs.
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Affiliation(s)
- Marta Oleszczuk
- Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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48
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Hoffman RMB, Sykes BD. Structure of the inhibitor W7 bound to the regulatory domain of cardiac troponin C. Biochemistry 2009; 48:5541-52. [PMID: 19419198 PMCID: PMC2697600 DOI: 10.1021/bi9001826] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The calmodulin antagonist W7 binds to troponin C in the presence of Ca(2+) and inhibits striated muscle contraction. This study integrates multiple data into the structure of the regulatory domain of human cardiac troponin C (cNTnC) bound to Ca(2+) and W7. The protein-W7 interface is defined through a three-dimensional {(1)H,(13)C}-edited-{(1)H,(12)C}-detected NOESY NMR experiment, and other aspects of the structure are modeled as perturbations to previously known coordinates and restraints. The structure determination protocol optimizes the protein-W7 contacts prior to the introduction of protein-W7 steric interactions or conformational changes in the protein. The structure determination protocol gives families of conformers that all have an optimal docking as assessed by satisfaction of the target function. The structure supports the previously proposed troponin I blocking mechanism for the activity of W7 in striated muscle and suggests a role for the flexible tail of W7 in stabilization of the bound state. This clarifies the structure-activity relationships of W7 and implicates an electrostatically mediated component of activity in common analogues of W7, including the antipsychotic trifluoroperazine and the cardiotonic levosimendan.
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Affiliation(s)
- Ryan M B Hoffman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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49
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Robertson IM, Baryshnikova OK, Li MX, Sykes BD. Defining the binding site of levosimendan and its analogues in a regulatory cardiac troponin C-troponin I complex. Biochemistry 2008; 47:7485-95. [PMID: 18570382 PMCID: PMC2652250 DOI: 10.1021/bi800438k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction of Cardiac Troponin C (cTnC) and Cardiac Troponin I (cTnI) plays a critical role in transmitting the Ca (2+) signal to the other myofilament proteins in the activation of cardiac muscle contraction. As such, the cTnC-cTnI interface is a logical target for cardiotonic agents such as levosimendan that can modulate the Ca (2+) sensitivity of the myofilaments. Evidence indicates that drug candidates may exert their effects by targeting a site formed by binding of the switch region of cTnI to the regulatory N domain of cTnC (cNTnC). In this study, we utilized two-dimensional (1)H- (15)N HSQC NMR spectroscopy to monitor the binding of levosimendan and its analogues, CMDP, AMDP, CI-930, imazodan, and MPDP, to cNTnC.Ca (2+) in complex with two versions of the switch region of cTnI (cTnI 147-163 and cTnI 144-163). Levosimendan, CMDP, AMDP, and CI-930 were found to bind to both cNTnC.Ca (2+).cTnI 147-163 and cNTnC.Ca (2+).cTnI 144-163 complexes. These compounds contain a methyl group that is absent in MPDP or imazodan. Thus, the methyl group is one of the pharmacophores responsible for the action of these pyridazinone drugs on cTnC. Furthermore, the results showed that the cNTnC.Ca (2+).cTnI 144-163 complex presents a higher-affinity binding site for these compounds than the cNTnC.Ca (2+).cTnI 147-163 complex. This is consistent with our observation that the affinity of cTnI 144-163 for cNTnC.Ca (2+) is approximately 10-fold stronger than that of cTnI 147-163, likely a result of electrostatic forces between the N-terminal RRV extension in cTnI 144-163 and the acidic residues in the C and D helices of cNTnC. These results will help in the delineation of the mode of action of levosimendan on the important functional unit of cardiac troponin that constitutes the regulatory domain of cTnC and the switch region of cTnI.
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Affiliation(s)
- Ian M Robertson
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Kreutziger KL, Piroddi N, Scellini B, Tesi C, Poggesi C, Regnier M. Thin filament Ca2+ binding properties and regulatory unit interactions alter kinetics of tension development and relaxation in rabbit skeletal muscle. J Physiol 2008; 586:3683-700. [PMID: 18535094 DOI: 10.1113/jphysiol.2008.152181] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The influence of Ca(2+) binding properties of individual troponin versus cooperative regulatory unit interactions along thin filaments on the rate tension develops and declines was examined in demembranated rabbit psoas fibres and isolated myofibrils. Native skeletal troponin C (sTnC) was replaced with sTnC mutants having altered Ca(2+) dissociation rates (k(off)) or with mixtures of sTnC and D28A, D64A sTnC, that does not bind Ca(2+) at sites I and II (xxsTnC), to reduce near-neighbour regulatory unit (RU) interactions. At saturating Ca(2+), the rate of tension redevelopment (k(TR)) was not altered for fibres containing sTnC mutants with decreased k(off) or mixtures of sTnC:xxsTnC. We examined the influence of k(off) on maximal activation and relaxation in myofibrils because they allow rapid and large changes in [Ca(2+)]. In myofibrils with M80Q sTnC(F27W) (decreased k(off)), maximal tension, activation rate (k(ACT)), k(TR) and rates of relaxation were not altered. With I60Q sTnC(F27W) (increased k(off)), maximal tension, k(ACT) and k(TR) decreased, with no change in relaxation rates. Surprisingly, the duration of the slow phase of relaxation increased or decreased with decreased or increased k(off), respectively. For all sTnC reconstitution conditions, Ca(2+) dependence of k(TR) in fibres showed Ca(2+) sensitivity of k(TR) (pCa(50)) shifted parallel to tension and low-Ca(2+) k(TR) was elevated. Together the data suggest the Ca(2+)-dependent rate of tension development and the duration (but not rate) of relaxation can be greatly influenced by k(off) of sTnC. This influence of sTnC binding kinetics occurs primarily within individual RUs, with only minor contributions of RU interactions at low Ca(2+).
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Affiliation(s)
- Kareen L Kreutziger
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195, USA
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