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Barry ME, Rynkiewicz MJ, Pavadai E, Viana A, Lehman W, Moore JR. Glutamate 139 of tropomyosin is critical for cardiac thin filament blocked-state stabilization. J Mol Cell Cardiol 2024; 188:30-37. [PMID: 38266978 DOI: 10.1016/j.yjmcc.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/14/2023] [Accepted: 01/20/2024] [Indexed: 01/26/2024]
Abstract
The cardiac thin filament proteins troponin and tropomyosin control actomyosin formation and thus cardiac contractility. Calcium binding to troponin changes tropomyosin position along the thin filament, allowing myosin head binding to actin required for heart muscle contraction. The thin filament regulatory proteins are hot spots for genetic mutations causing heart muscle dysfunction. While much of the thin filament structure has been characterized, critical regions of troponin and tropomyosin involved in triggering conformational changes remain unresolved. A poorly resolved region, helix-4 (H4) of troponin I, is thought to stabilize tropomyosin in a position on actin that blocks actomyosin interactions at low calcium concentrations during muscle relaxation. We have proposed that contact between glutamate 139 on tropomyosin and positively charged residues on H4 leads to blocking-state stabilization. In this study, we attempted to disrupt these interactions by replacing E139 with lysine (E139K) to define the importance of this residue in thin filament regulation. Comparison of mutant and wild-type tropomyosin was carried out using in-vitro motility assays, actin co-sedimentation, and molecular dynamics simulations to determine perturbations in troponin-tropomyosin function caused by the tropomyosin mutation. Motility assays revealed that mutant thin filaments moved at higher velocity at low calcium with increased calcium sensitivity demonstrating that tropomyosin residue 139 is vital for proper tropomyosin-mediated inhibition during relaxation. Similarly, molecular dynamic simulations revealed a mutation-induced decrease in interaction energy between tropomyosin-E139K and troponin I (R170 and K174). These results suggest that salt-bridge stabilization of tropomyosin position by troponin IH4 is essential to prevent actomyosin interactions during cardiac muscle relaxation.
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Affiliation(s)
- Meaghan E Barry
- Department of Biological Sciences, University of Massachusetts Lowell, One University Ave, Lowell, MA 01854, United States of America
| | - Michael J Rynkiewicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisan School of Medicine, 700 Albany Street, W-408E, Boston, MA 02118, United States of America
| | - Elumalai Pavadai
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisan School of Medicine, 700 Albany Street, W-408E, Boston, MA 02118, United States of America
| | - Alex Viana
- Department of Biological Sciences, University of Massachusetts Lowell, One University Ave, Lowell, MA 01854, United States of America
| | - William Lehman
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisan School of Medicine, 700 Albany Street, W-408E, Boston, MA 02118, United States of America
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts Lowell, One University Ave, Lowell, MA 01854, United States of America.
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Rynkiewicz MJ, Pavadai E, Sevrieva I, Irving M, Lehman W. Modeling the troponin core domain on thin filaments using data from cryoelectron microscopy and fluorescence approaches. Biophys J 2023; 122:169a. [PMID: 36782791 DOI: 10.1016/j.bpj.2022.11.1061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Michael J Rynkiewicz
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Elumalai Pavadai
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Ivanka Sevrieva
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Malcolm Irving
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
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3
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Doran M, Rynkiewicz MJ, Pavadai E, Bodt SML, Rasicci D, Moore JR, Bullitt E, Yengo CM, Lehman W. The role of myosin loop-4 in localizing tropomyosin on actin during muscle activation and relaxation. Biophys J 2023; 122:401a-402a. [PMID: 36784047 DOI: 10.1016/j.bpj.2022.11.2189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Matthew Doran
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Elumalai Pavadai
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Skylar M L Bodt
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Dave Rasicci
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Christopher M Yengo
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
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Doran MH, Rynkiewicz MJ, Pavadai E, Bodt SM, Rasicci D, Moore JR, Yengo CM, Bullitt E, Lehman W. Myosin loop-4 is critical for optimal tropomyosin repositioning on actin during muscle activation and relaxation. J Gen Physiol 2023; 155:e202213274. [PMID: 36459134 PMCID: PMC9723511 DOI: 10.1085/jgp.202213274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/28/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
During force-generating steps of the muscle crossbridge cycle, the tip of the myosin motor, specifically loop-4, contacts the tropomyosin cable of actin filaments. In the current study, we determined the corresponding effect of myosin loop-4 on the regulatory positioning of tropomyosin on actin. To accomplish this, we compared high-resolution cryo-EM structures of myosin S1-decorated thin filaments containing either wild-type or a loop-4 mutant construct, where the seven-residue portion of myosin loop-4 that contacts tropomyosin was replaced by glycine residues, thus removing polar side chains from residues 366-372. Cryo-EM analysis of fully decorated actin-tropomyosin filaments with wild-type and mutant S1, yielded 3.4-3.6 Å resolution reconstructions, with even higher definition at the actin-myosin interface. Loop-4 densities both in wild-type and mutant S1 were clearly identified, and side chains were resolved in the wild-type structure. Aside from loop-4, actin and myosin structural domains were indistinguishable from each other when filaments were decorated with either mutant or wild-type S1. In marked contrast, the position of tropomyosin on actin in the two reconstructions differed by 3 to 4 Å. In maps of filaments containing the mutant, tropomyosin was located closer to the myosin-head and thus moved in the direction of the C-state conformation adopted by myosin-free thin filaments. Complementary interaction energy measurements showed that tropomyosin in the mutant thin filaments sits on actin in a local energy minimum, whereas tropomyosin is positioned by wild-type S1 in an energetically unfavorable location. We propose that the high potential energy associated with tropomyosin positioning in wild-type filaments favors an effective transition to B- and C-states following release of myosin from the thin filaments during relaxation.
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Affiliation(s)
- Matthew H. Doran
- Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Michael J. Rynkiewicz
- Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Elumalai Pavadai
- Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Skylar M.L. Bodt
- Department of Cellular and Molecular Physiology, Pennsylvania State College of Medicine, Hershey, PA
| | - David Rasicci
- Department of Cellular and Molecular Physiology, Pennsylvania State College of Medicine, Hershey, PA
| | - Jeffrey R. Moore
- Department of Biological Science, University of Massachusetts Lowell, Lowell, MA
| | - Christopher M. Yengo
- Department of Cellular and Molecular Physiology, Pennsylvania State College of Medicine, Hershey, PA
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - William Lehman
- Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
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Pavadai E, Rynkiewicz MJ, Yang Z, Gould IR, Marston SB, Lehman W. Modulation of cardiac thin filament structure by phosphorylated troponin-I analyzed by protein-protein docking and molecular dynamics simulation. Arch Biochem Biophys 2022; 725:109282. [PMID: 35577070 PMCID: PMC10680062 DOI: 10.1016/j.abb.2022.109282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 12/16/2022]
Abstract
Tropomyosin, controlled by troponin-linked Ca2+-binding, regulates muscle contraction by a macromolecular scale steric-mechanism that governs myosin-crossbridge-actin interactions. At low-Ca2+, C-terminal domains of troponin-I (TnI) trap tropomyosin in a position on thin filaments that interferes with myosin-binding, thus causing muscle relaxation. Steric inhibition is reversed at high-Ca2+ when TnI releases from F-actin-tropomyosin as Ca2+ and the TnI switch-peptide bind to the N-lobe of troponin-C (TnC). The opposite end of cardiac TnI contains a phosphorylation-sensitive ∼30 residue-long N-terminal peptide that is absent in skeletal muscle, and likely modifies these interactions in hearts. Here, PKA-dependent phosphorylation of serine 23 and 24 modulates Ca2+ and possibly switch-peptide binding to TnC, causing faster relaxation during the cardiac-cycle (lusitropy). The cardiac-specific N-terminal TnI domain is not captured in crystal structures of troponin or in cryo-EM reconstructions of thin filaments; thus, its global impact on thin filament structure and function is uncertain. Here, we used protein-protein docking and molecular dynamics simulation-based protocols to build a troponin model that was guided by and hence consistent with the recent seminal Yamada structure of Ca2+-activated thin filaments. We find that when present on thin filaments, phosphorylated Ser23/24 along with adjacent polar TnI residues interact closely with both tropomyosin and the N-lobe of TnC during our simulations. These interactions would likely bias tropomyosin to an off-state positioning on actin. In situ, such enhanced relaxation kinetics would promote cardiac lusitropy.
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Affiliation(s)
- Elumalai Pavadai
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Zeyu Yang
- Department of Chemistry and Institute of Chemical Biology, Imperial College London, Shepard's Bush, London, W12 0BZ, UK
| | - Ian R Gould
- Department of Chemistry and Institute of Chemical Biology, Imperial College London, Shepard's Bush, London, W12 0BZ, UK
| | - Steven B Marston
- National Heart & Lung Institute, Imperial College London, Dovehouse Street, W12 0NN, UK
| | - William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.
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6
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Baral P, Pavadai E, Zhou Z, Xu Y, Tison CK, Pokhrel R, Gerstman BS, Chapagain PP. Immunoinformatic screening of Marburgvirus epitopes and computational investigations of epitope-allele complexes. Int Immunopharmacol 2022; 111:109109. [PMID: 35926269 DOI: 10.1016/j.intimp.2022.109109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/14/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022]
Abstract
Marburgvirus (MARV), a member of the Filovirus family, causes severe hemorrhagic fever in humans. Currently, there are no approved vaccines or post exposure treatment methods available against MARV. With the aim of identifying vaccine candidates against MARV, we employ different sequence-based computational methods to predict the MHC-I and MHC-II T-cell epitopes as well as B-cell epitopes for the complete MARV genome. We analyzed the variations in the predicted epitopes among four MARV variants, the Lake Victoria, Angola, Musoke, and Ravn. We used a consensus approach to identify several epitopes, including novel epitopes, and narrowed down the selection based on different parameters such as antigenicity and IC50 values. The selected epitopes can be used in various vaccine constructs that give effective antibody responses. The MHC-I epitope-allele complexes for GP and NP with favorably low IC50 values were investigated using molecular dynamics computations to determine the molecular details of the epitope-allele complexes. This study provides information for further experimental validation of the potential epitopes and the design and development of MARV vaccines.
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Affiliation(s)
- Prabin Baral
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Elumalai Pavadai
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Ziyou Zhou
- Biotech Group, Luna Labs USA, Charlottesville, VA 22903, USA
| | - Yang Xu
- Biotech Group, Luna Labs USA, Charlottesville, VA 22903, USA
| | | | - Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
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Rynkiewicz MJ, Pavadai E, Lehman W. Modeling Human Cardiac Thin Filament Structures. Front Physiol 2022; 13:932333. [PMID: 35812320 PMCID: PMC9257132 DOI: 10.3389/fphys.2022.932333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022] Open
Abstract
Striated muscle contraction is regulated in a calcium-dependent manner through dynamic motions of the tropomyosin/troponin polymer, a multicomponent complex wrapped around actin-containing thin filaments. Tropomyosin/troponin sterically blocks myosin-binding at low-calcium concentrations but moves to expose myosin-binding sites at high-calcium concentrations leading to force development. Understanding the key intermolecular interactions that define these dynamic motions will promote our understanding of mutation-induced contractile dysfunction that eventually leads to hypertrophic cardiomyopathy, dilated cardiomyopathy, and skeletal myopathies. Advancements in cryoelectron microscopy (cryoEM) have resulted in a partial elucidation of structures of the thin filament, revealing many atomic-level interactions between the component proteins and critical calcium-dependent conformational alterations. However, building models at the resolutions achieved can be challenging since landmarks in the maps are often missing or ambiguous. Therefore, current computational analyses including de novo structure prediction, protein-protein docking, molecular dynamics flexible fitting, and molecular dynamics simulations are needed to ensure good quality models. We review here our efforts to model the troponin T domain spanning the head-to-tail overlap domain of tropomyosin, improving previous models. Next, we refined the published cryoEM modeled structures, which had mistakenly compressed alpha helices, with a model that has expected helical parameters while matching densities in the cryoEM volume. Lastly, we used this model to reinterpret the interactions between tropomyosin and troponin I showing key features that hold the tropomyosin cable in its low-calcium, sterically blocking position. These revised thin filament models show improved intermolecular interactions in the key low- and high-calcium regulatory states, providing novel insights into function.
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Bhattarai N, Pavadai E, Pokhrel R, Baral P, Hossen L, Stahelin RV, Chapagain PP, Gerstman BS. Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane. Proteins 2022; 90:340-350. [PMID: 34431571 PMCID: PMC8738135 DOI: 10.1002/prot.26221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/01/2021] [Accepted: 08/16/2021] [Indexed: 02/03/2023]
Abstract
Outbreaks of the Ebola virus (EBOV) continue to occur and while a vaccine and treatment are now available, there remains a dearth of options for those who become sick with EBOV disease. An understanding at the atomic and molecular level of the various steps in the EBOV replication cycle can provide molecular targets for disrupting the virus. An important step in the EBOV replication cycle is the transport of EBOV structural matrix VP40 protein molecules to the plasma membrane inner leaflet, which involves VP40 binding to the host cell's Sec24c protein. Though some VP40 residues involved in the binding are known, the molecular details of VP40-Sec24c binding are not known. We use various molecular computational techniques to investigate the molecular details of how EBOV VP40 binds with the Sec24c complex of the ESCRT-I pathway. We employed different docking programs to identify the VP40-binding site on Sec24c and then performed molecular dynamics simulations to determine the atomic details and binding interactions of the complex. We also investigated how the inter-protein interactions of the complex are affected upon mutations of VP40 amino acids in the Sec24c-binding region. Our results provide a molecular basis for understanding previous coimmunoprecipitation experimental studies. In addition, we found that VP40 can bind to a site on Sec24c that can also bind Sec23 and suggests that VP40 may use the COPII transport mechanism in a manner that may not need the Sec23 protein in order for VP40 to be transported to the plasma membrane.
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Affiliation(s)
- Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Elumalai Pavadai
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Prabin Baral
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Lokman Hossen
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry & Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette IN 47906
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Bernard S. Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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Pavadai E, Rynkiewicz MJ, Yang Z, Gould I, Marston SB, Lehman W. N-Terminal domains of cardiac troponin-I modulate thin filament structure. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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10
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Sundar S, Ghosh A, Bojan SJ, Rynkiewicz MJ, Brown LE, Lehman W, Moore JR, Pavadai E. Using novel small molecules to alter cardiac thin filament function. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Lehman W, Pavadai E, Rynkiewicz MJ. C-terminal troponin-I residues trap tropomyosin in the muscle thin filament blocked-state. Biochem Biophys Res Commun 2021; 551:27-32. [PMID: 33714756 DOI: 10.1016/j.bbrc.2021.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022]
Abstract
Tropomyosin and troponin regulate muscle contraction by participating in a macromolecular scale steric-mechanism to control myosin-crossbridge - actin interactions and consequently contraction. At low-Ca2+, the C-terminal 30% of troponin subunit-I (TnI) is proposed to trap tropomyosin in a position on thin filaments that sterically interferes with myosin-binding, thus causing muscle relaxation. In contrast, at high-Ca2+, inhibition is released after the C-terminal domains dissociate from F-actin-tropomyosin as its component switch-peptide domain binds to the N-lobe of troponin-C (TnC). Recent, paradigm-shifting, cryo-EM reconstructions by the Namba group have revealed density attributed to TnI along cardiac muscle thin filaments at both low- and high-Ca2+ concentration. Modeling the reconstructions showed expected high-Ca2+ hydrophobic interactions of the TnI switch-peptide and TnC. However, under low-Ca2+ conditions, sparse interactions of TnI and tropomyosin, and in particular juxtaposition of non-polar switch-peptide residues and charged tropomyosin amino acids in the published model seem difficult to reconcile with an expected steric-blocking conformation. This anomaly is likely due to inaccurate fitting of tropomyosin into the cryo-EM volume. In the current study, the low-Ca2+ cryo-EM volume was fitted with a more accurate tropomyosin model and representation of cardiac TnI. Our results show that at low-Ca2+ a cluster of hydrophobic residues at the TnI switch-peptide and adjacent H4 helix (Ala149, Ala151, Met 154, Leu159, Gly160, Ala161, Ala163, Leu167, Leu169, Ala171, Leu173) draw-in tropomyosin surface residues (Ile143, Ile146, Ala151, Ile154), presumably attracting the entire tropomyosin cable to its myosin-blocking position on actin. The modeling confirms that neighboring TnI "inhibitory domain" residues (Arg145, Arg148) bind to thin filaments at actin residue Asp25, as previously suggested. ClusPro docking of TnI residues 137-184 to actin-tropomyosin, including the TnI inhibitory-domain, switch-peptide and Helix H4, verified the modeled configuration. Our residue-to-residue contact-mapping of the TnI-tropomyosin association lends itself to experimental validation and functional localization of disease-bearing mutations.
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Affiliation(s)
- William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Elumalai Pavadai
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, USA.
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Doran M, Lehman W, Bullitt E, Rynkiewicz M, Pavadai E, Regnier M, Geeves M, Moore J, Walklate J. Cryo-EM and protein–protein docking reveal myosin loop 4 contacts actin and tropomyosin on thin filaments. Acta Crystallogr A Found Adv 2020. [DOI: 10.1107/s0108767320099006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Doran MH, Pavadai E, Rynkiewicz MJ, Walklate J, Bullitt E, Moore JR, Regnier M, Geeves MA, Lehman W. Cryo-EM and Molecular Docking Shows Myosin Loop 4 Contacts Actin and Tropomyosin on Thin Filaments. Biophys J 2020; 119:821-830. [PMID: 32730789 DOI: 10.1016/j.bpj.2020.07.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/07/2020] [Indexed: 12/29/2022] Open
Abstract
The motor protein myosin drives muscle and nonmuscle motility by binding to and moving along actin of thin filaments. Myosin binding to actin also modulates interactions of the regulatory protein, tropomyosin, on thin filaments, and conversely tropomyosin affects myosin binding to actin. Insight into this reciprocity will facilitate a molecular level elucidation of tropomyosin regulation of myosin interaction with actin in muscle contraction, and in turn, promote better understanding of nonmuscle cell motility. Indeed, experimental approaches such as fiber diffraction, cryoelectron microscopy, and three-dimensional reconstruction have long been used to define regulatory interaction of tropomyosin and myosin on actin at a structural level. However, their limited resolution has not proven sufficient to determine tropomyosin and myosin contacts at an atomic-level and thus to fully substantiate possible functional contributions. To overcome this deficiency, we have followed a hybrid approach by performing new cryogenic electron microscopy reconstruction of myosin-S1-decorated F-actin-tropomyosin together with atomic scale protein-protein docking of tropomyosin to the EM models. Here, cryo-EM data were derived from filaments reconstituted with α1-actin, cardiac αα-tropomyosin, and masseter muscle β-myosin complexes; masseter myosin, which shares sequence identity with β-cardiac myosin-heavy chain, was used because of its stability in vitro. The data were used to build an atomic model of the tropomyosin cable that fits onto the actin filament between the tip of the myosin head and a cleft on the innermost edge of actin subunits. The docking and atomic scale fitting showed multiple discrete interactions of myosin loop 4 and acidic residues on successive 39-42 residue-long tropomyosin pseudorepeats. The contacts between S1 and tropomyosin on actin appear to compete with and displace ones normally found between actin and tropomyosin on myosin-free thin filaments in relaxed muscle, thus restructuring the filament during myosin-induced activation.
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Affiliation(s)
- Matthew H Doran
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Elumalai Pavadai
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Jonathan Walklate
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Michael A Geeves
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts.
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Pavadai E, Lehman W, Rynkiewicz MJ. Protein-Protein Docking Reveals Dynamic Interactions of Tropomyosin on Actin Filaments. Biophys J 2020; 119:75-86. [PMID: 32521240 DOI: 10.1016/j.bpj.2020.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 01/01/2023] Open
Abstract
Experimental approaches such as fiber diffraction and cryo-electron microscopy reconstruction have defined regulatory positions of tropomyosin on actin but have not, as yet, succeeded at determining key atomic-level contacts between these proteins or fully substantiated the dynamics of their interactions at a structural level. To overcome this deficiency, we have previously employed computational approaches to deduce global dynamics of thin filament components by energy landscape determination and molecular dynamics simulations. Still, these approaches remain computationally challenging for any complex and large macromolecular assembly like the thin filament. For example, tropomyosin cable wrapping around actin of thin filaments features both head-to-tail polymeric interactions and local twisting, both of which depart from strict superhelical symmetry. This produces a complex energy surface that is difficult to model and thus to evaluate globally. Therefore, at this stage of our understanding, assessing global molecular dynamics can prove to be inherently impractical. As an alternative, we adopted a "divide and conquer" protocol to investigate actin-tropomyosin interactions at an atomistic level. Here, we first employed unbiased protein-protein docking tools to identify binding specificity of individual tropomyosin pseudorepeat segments over the actin surface. Accordingly, tropomyosin "ligand" segments were rotated and translated over potential "target" binding sites on F-actin where the corresponding interaction energetics of billions of conformational poses were ranked by the programs PIPER and ClusPro. These data were used to assess favorable interactions and then to rebuild models of seamless and continuous tropomyosin cables over the F-actin substrate, which were optimized further by flexible fitting routines and molecular dynamics. The models generated azimuthally distinct regulatory positions for tropomyosin cables along thin filaments on actin dominated by stereo-specific head-to-tail overlap linkage. The outcomes are in good agreement with current cryo-electron microscopy topology and consistent with long-thought residue-to-residue interactions between actin and tropomyosin.
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Affiliation(s)
- Elumalai Pavadai
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts.
| | - Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
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Pavadai E, Rynkiewicz MJ, Ghosh A, Lehman W. Docking Troponin-T onto the Tropomyosin Overlapping Domain of Thin-Filaments. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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16
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Pavadai E, Rynkiewicz MJ, Lehman W. A Tropomyosin Cable Model on Thin-Filaments Deduced by Protein-Protein Docking. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Pokhrel R, Pavadai E, Gerstman B, Chapagain PP. Ion Selective Pentameric Pore Formation by Ebola Virus Delta Peptide. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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18
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Baral P, Pavadai E, Gerstman B, Chapagain PP. Lassa Virus Epitope-Allele Complexes Identified through Computational Modeling. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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19
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Pavadai E, Rynkiewicz MJ, Ghosh A, Lehman W. Docking Troponin T onto the Tropomyosin Overlapping Domain of Thin Filaments. Biophys J 2019; 118:325-336. [PMID: 31864661 DOI: 10.1016/j.bpj.2019.11.3393] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/14/2019] [Accepted: 11/26/2019] [Indexed: 01/02/2023] Open
Abstract
Complete description of thin filament conformational transitions accompanying muscle regulation requires ready access to atomic structures of actin-bound tropomyosin-troponin. To date, several molecular-docking protocols have been employed to identify troponin interactions on actin-tropomyosin because high-resolution experimentally determined structures of filament-associated troponin are not available. However, previously published all-atom models of the thin filament show chain separation and corruption of components during our molecular dynamics simulations of the models, implying artifactual subunit organization, possibly due to incorporation of unorthodox tropomyosin-TnT crystal structures and complex FRET measurements during model construction. For example, the recent Williams et al. (2016) atomistic model of the thin filament displays a paucity of salt bridges and hydrophobic complementarity between the TnT tail (TnT1) and tropomyosin, which is difficult to reconcile with the high, 20 nM Kd binding of TnT onto tropomyosin. Indeed, our molecular dynamics simulations show the TnT1 component in their model partially dissociates from tropomyosin in under 100 ns, whereas actin-tropomyosin and TnT1 models themselves remain intact. We therefore revisited computational work aiming to improve TnT1-thin filament models by employing unbiased docking methodologies, which test billions of trial rotations and translations of TnT1 over three-dimensional grids covering end-to-end bonded tropomyosin alone or tropomyosin on F-actin. We limited conformational searches to the association of well-characterized TnT1 helical domains and either isolated tropomyosin or actin-tropomyosin yet avoided docking TnT domains that lack known or predicted structure. The docking programs PIPER and ClusPro were used, followed by interaction energy optimization and extensive molecular dynamics. TnT1 docked to either side of isolated tropomyosin but uniquely onto one location of actin-bound tropomyosin. The antiparallel interaction with tropomyosin contained abundant salt bridges and intimately integrated hydrophobic networks joining TnT1 and the tropomyosin N-/C-terminal overlapping domain. The TnT1-tropomyosin linkage yields well-defined molecular crevices. Interaction energy measurements strongly favor this TnT1-tropomyosin design over previously proposed models.
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Affiliation(s)
- Elumalai Pavadai
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Michael J Rynkiewicz
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Anita Ghosh
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts.
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20
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Pavadai E, Bhattarai N, Baral P, Stahelin RV, Chapagain PP, Gerstman BS. Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. J Phys Chem B 2019; 123:9045-9053. [PMID: 31576755 DOI: 10.1021/acs.jpcb.9b04674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Ebola virus (EBOV) is a virulent pathogen that causes severe hemorrhagic fever with a high fatality rate in humans. The EBOV transformer protein VP40 plays crucial roles in viral assembly and budding at the plasma membrane of infected cells. One of VP40's roles is to form the long, flexible, pleomorphic filamentous structural matrix for the virus. Each filament contains three unique interfaces: monomer NTD-NTD to form a dimer, dimer-to-dimer NTD-NTD oligomerization to form a hexamer, and end-to-end hexamer CTD-CTD to build the filament. However, the atomic-level details of conformational flexibility of the VP40 filament are still elusive. In this study, we have performed explicit-solvent, all-atom molecular dynamic simulations to explore the conformational flexibility of the three different interface structures of the filament. Using dynamic network analysis and other calculational methods, we find that the CTD-CTD hexamer interface with weak interdomain amino acid communities is the most flexible, and the NTD-NTD oligomer interface with strong interdomain communities is the least flexible. Our study suggests that the high flexibility of the CTD-CTD interface may be essential for the supple bending of the Ebola filovirus, and such flexibility may present a target for molecular interventions to disrupt the Ebola virus functioning.
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Affiliation(s)
| | | | | | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue University Cancer Center , Purdue University , West Lafayette , Indiana 47907 , United States
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21
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Jackson GE, Pavadai E, Gäde G, Andersen NH. The adipokinetic hormones and their cognate receptor from the desert locust, Schistocerca gregaria: solution structure of endogenous peptides and models of their binding to the receptor. PeerJ 2019; 7:e7514. [PMID: 31531269 PMCID: PMC6718158 DOI: 10.7717/peerj.7514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022] Open
Abstract
Background Neuropeptides exert their activity through binding to G protein-coupled receptors (GPCRs). GPCRs are well-known drug targets in the pharmaceutical industry and are currently discussed as targets to control pest insects. Here, we investigate the neuropeptide adipokinetic hormone (AKH) system of the desert locust Schistocerca gregaria. The desert locust is known for its high reproduction, and for forming devastating swarms consisting of billions of individual insects. It is also known that S. gregaria produces three different AKHs as ligands but has only one AKH receptor (AKHR). The AKH system is known to be essential for metabolic regulation, which is necessary for reproduction and flight activity. Methods Nuclear magnetic resonance techniques (NMR) in a dodecylphosphocholin (DPC) micelle solution were used to determine the structure of the three AKHs. The primary sequence of the S. gregaria AKHR was used to construct a 3D molecular model. Next, the three AKHs were individually docked to the receptor, and dynamic simulation of the whole ligand–receptor complex in a model membrane was performed. Results Although the three endogenous AKHs of S. gregaria have quite different amino acids sequences and chain length (two octa- and one decapeptide), NMR experiments assigned a turn structure in DPC micelle solution for all. The GPCR-ModSim program identified human kappa opioid receptor to be the best template after which the S. gregaria AKHR was modeled. All three AKHs were found to have the same binding site on this receptor, interact with similar residues of the receptor and have comparable binding constants. Molecular switches were also identified; the movement of the receptor could be visually shown when ligands (AKHs) were docked and the receptor was activated. Conclusions The study proposes a model of binding of the three endogenous ligands to the one existing AKHR in the desert locust and paves the way to use such a model for the design of peptide analogs and finally, peptide mimetics, in the search for novel species-specific insecticides based on receptor–ligand interaction.
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Affiliation(s)
- Graham E Jackson
- Department of Chemistry, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Elumalai Pavadai
- Department of Chemistry, University of Cape Town, Cape Town, Western Cape, South Africa.,Department of Physiology and Biophysics, Boston University, Boston, MA, USA
| | - Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA, USA
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22
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Pokhrel R, Pavadai E, Gerstman BS, Chapagain PP. Membrane pore formation and ion selectivity of the Ebola virus delta peptide. Phys Chem Chem Phys 2019; 21:5578-5585. [DOI: 10.1039/c8cp07323f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Ebola virus delta peptide homo-oligomerizes in the host cell membrane to form amphipathic pores that alter the membrane properties.
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Affiliation(s)
| | | | - Bernard S. Gerstman
- Department of Physics
- Miami
- USA
- Biomolecular Sciences Institute Florida International University
- Miami
| | - Prem P. Chapagain
- Department of Physics
- Miami
- USA
- Biomolecular Sciences Institute Florida International University
- Miami
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23
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Kaur G, Pavadai E, Wittlin S, Chibale K. 3D-QSAR Modeling and Synthesis of New Fusidic Acid Derivatives as Antiplasmodial Agents. J Chem Inf Model 2018; 58:1553-1560. [DOI: 10.1021/acs.jcim.8b00105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gurminder Kaur
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Elumalai Pavadai
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
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24
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Pavadai E, Gerstman BS, Chapagain PP. A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrix. Sci Rep 2018; 8:9776. [PMID: 29950600 PMCID: PMC6021417 DOI: 10.1038/s41598-018-28077-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/14/2018] [Indexed: 12/01/2022] Open
Abstract
The Ebola filovirus causes severe hemorrhagic fever with a high fatality rate in humans. The primary structural matrix protein VP40 displays transformer-protein characteristics and exists in different conformational and oligomeric states. VP40 plays crucial roles in viral assembly and budding at the plasma membrane of the infected cells and is capable of forming virus-like particles without the need for other Ebola proteins. However, no experimental three-dimensional structure for any filovirus VP40 cylindrical assembly matrix is currently available. Here, we use a protein-protein docking approach to develop cylindrical assembly models for an Ebola virion and also for a smaller structural matrix that does not contain genetic material. These models match well with the 2D averages of cryo-electron tomograms of the authentic virion. We also used all-atom molecular dynamics simulations to investigate the stability and dynamics of the cylindrical models and the interactions between the side-by-side hexamers to determine the amino acid residues that are especially important for stabilizing the hexamers in the cylindrical ring configuration matrix assembly. Our models provide helpful information to better understand the assembly processes of filoviruses and such structural studies may also lead to the design and development of antiviral drugs.
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Affiliation(s)
- Elumalai Pavadai
- Department of Physics, Florida International University, Miami, Florida, 33199, USA.
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, Florida, 33199, USA.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida, 33199, USA.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, USA
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25
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Pavadai E, Gerstman BS, Chapagain PP. A Cylindrical Assembly Model and Dynamics of the Ebola Virus VP40. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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26
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Jackson GE, Pavadai E, Gäde G, Timol Z, Andersen NH. Data for the homology modelling of the red pigment-concentrating hormone receptor (Dappu-RPCHR) of the crustacean Daphnia pulex, and docking of its cognate agonist (Dappu-RPCH). Data Brief 2017; 15:941-947. [PMID: 29159233 PMCID: PMC5683752 DOI: 10.1016/j.dib.2017.10.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/13/2017] [Accepted: 10/19/2017] [Indexed: 11/23/2022] Open
Abstract
The data presented in this article are related to the publication “Interaction of the red pigment-concentrating hormone of the crustacean Daphnia pulex, with its cognate receptor, Dappu-RPCHR: A nuclear magnetic resonance and modeling study” (Jackson et al., 2017) [1]. This article contains the data for homology modeling of the red pigment-concentrating hormone (RPCH) receptor of the water flea, Daphnia pulex (Dappu-RPCHR), which was constructed from its primary sequence. This is the first 3D model of a crustacean G-protein coupled receptor. Docking of the agonist, pGlu-Val-Asn-Phe-Ser-Thr-Ser-Trp amide (Dappu-RPCH), was used to find a binding pocket on the receptor and compared to the binding pocket of the adipokinetic hormone (AKH) receptor from the malaria mosquito. Data for the receptor, with and without loop refinement, together with the docked agonist, are presented.
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Affiliation(s)
- Graham E Jackson
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Elumalai Pavadai
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Gerd Gäde
- Biological Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Zaheer Timol
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Niels H Andersen
- Chemistry Department, University of Washington, Seattle, WA 98195, United States
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27
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Jackson GE, Pavadai E, Gäde G, Timol Z, Andersen NH. Interaction of the red pigment-concentrating hormone of the crustacean Daphnia pulex, with its cognate receptor, Dappu-RPCHR: A nuclear magnetic resonance and modeling study. Int J Biol Macromol 2017; 106:969-978. [PMID: 28837848 DOI: 10.1016/j.ijbiomac.2017.08.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 11/17/2022]
Abstract
The primary sequence of the red pigment-concentrating hormone (RPCH) receptor of the water flea, Daphnia pulex, was used in homology modeling to construct the first 3D model of a crustacean G-protein coupled receptor, Dappu-RPCHR. This receptor was found to belong to the class A subfamily of GPCRs with a disulfide bridge between Cys72 and Cys150 and an ionic lock between Arg97 and Thr224 and Thr220. NMR restrained molecular dynamics was used to determine the structure of an agonist, Dappu-RPCH, in a membrane-mimicking environment. The agonist was found to be flexible but has two main conformations in solution, both having β-turns. Docking of the predominant structure was used to find a binding pocket on the receptor. The pocket's spatial location was similar to that of the AKH receptor of Anopheles gambiae. The binding affinity was -69kcalmol-1 with the N-terminus of Dappu-RPCH inserted between helices 4 and 6, and the C-terminus interacting with extra-cellular loop, ECL2. Upon binding, H-bonding to the peptide may activate the receptor. This development of the first Dappu-RPCH/Dappu-RPCHR model could be useful for understanding ligand-receptor interactions in crustaceans.
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Affiliation(s)
- Graham E Jackson
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
| | - Elumalai Pavadai
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa; Current address, Department of Physics, Florida International University, Miami, 33199, FL, United States
| | - Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Zaheer Timol
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Niels H Andersen
- Chemistry Department, University of Washington, Seattle, WA, 98195, United States
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Pavadai E, Kaur G, Wittlin S, Chibale K. Identification of steroid-like natural products as antiplasmodial agents by 2D and 3D similarity-based virtual screening. Medchemcomm 2017; 8:1152-1157. [PMID: 30108825 DOI: 10.1039/c7md00063d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/17/2017] [Indexed: 11/21/2022]
Abstract
The emergence of drug resistance in Plasmodium falciparum to available antimalarial drugs has challenged current antimalarial treatments. New antimalarials, particularly those with novel mechanisms of action and no cross resistance to current drugs, are therefore urgently needed. To identify new growth inhibitors of Plasmodium falciparum, 2D and 3D similarity-based virtual screening methods were employed in parallel with an in-house database of steroid-type natural products using fusidic acid as a search query. The resulting hit compounds were further filtered based on the predicted partition coefficient, log P. The virtual screening strategy resulted in the identification of nine new compounds that inhibited parasite growth with IC50 values of <20 μM. Four compounds exhibited IC50 values in the range of 1.39-3.45 μM and three of which showed a promising selectivity index. Further, the predicted ADME properties of the four most active compounds were found to be comparable to fusidic acid. These compounds can be further explored using structural modifications in the identification and development of more potent parasite growth inhibitors with improved selectivity.
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Affiliation(s)
- Elumalai Pavadai
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; ; ; Tel: +1 (305) 348 6661 ; Tel: +27 21 650 2553
| | - Gurminder Kaur
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; ; ; Tel: +1 (305) 348 6661 ; Tel: +27 21 650 2553
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4051 Basel , Switzerland.,University of Basel , 4002 Basel , Switzerland
| | - Kelly Chibale
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; ; ; Tel: +1 (305) 348 6661 ; Tel: +27 21 650 2553.,Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Rondebosch 7701 , South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit , University of Cape Town , Rondebosch 7701 , South Africa
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Pavadai E, El Mazouni F, Wittlin S, de Kock C, Phillips MA, Chibale K. Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening. J Chem Inf Model 2016; 56:548-62. [PMID: 26915022 DOI: 10.1021/acs.jcim.5b00680] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH), a key enzyme in the de novo pyrimidine biosynthesis pathway, which the Plasmodium falciparum relies on exclusively for survival, has emerged as a promising target for antimalarial drugs. In an effort to discover new and potent PfDHODH inhibitors, 3D-QSAR pharmacophore models were developed based on the structures of known PfDHODH inhibitors and the validated Hypo1 model was used as a 3D search query for virtual screening of the National Cancer Institute database. The virtual hit compounds were further filtered based on molecular docking and Molecular Mechanics/Generalized Born Surface Area binding energy calculations. The combination of the pharmacophore and structure-based virtual screening resulted in the identification of nine new compounds that showed >25% inhibition of PfDHODH at a concentration of 10 μM, three of which exhibited IC50 values in the range of 0.38-20 μM. The most active compound, NSC336047, displayed species-selectivity for PfDHODH over human DHODH and inhibited parasite growth with an IC50 of 26 μM. In addition to this, 13 compounds inhibited parasite growth with IC50 values of ≤ 50 μM, 4 of which showed IC50 values in the range of 5-12 μM. These compounds could be further explored in the identification and development of more potent PfDHODH and parasite growth inhibitors.
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Affiliation(s)
| | - Farah El Mazouni
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute , Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel , 4002 Basel, Switzerland
| | - Carmen de Kock
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town , Observatory 7925, South Africa
| | - Margaret A Phillips
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
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30
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Njogu PM, Guantai EM, Pavadai E, Chibale K. Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis. ACS Infect Dis 2016; 2:8-31. [PMID: 27622945 DOI: 10.1021/acsinfecdis.5b00093] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).
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Affiliation(s)
- Peter M. Njogu
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Eric M. Guantai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Elumalai Pavadai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
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31
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Mutai P, Pavadai E, Wiid I, Ngwane A, Baker B, Chibale K. Synthesis, antimycobacterial evaluation and pharmacophore modeling of analogues of the natural product formononetin. Bioorg Med Chem Lett 2015; 25:2510-3. [DOI: 10.1016/j.bmcl.2015.04.064] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 11/30/2022]
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Kaur G, Singh K, Pavadai E, Njoroge M, Espinoza-Moraga M, De Kock C, Smith PJ, Wittlin S, Chibale K. Synthesis of fusidic acid bioisosteres as antiplasmodial agents and molecular docking studies in the binding site of elongation factor-G. Med Chem Commun 2015. [DOI: 10.1039/c5md00343a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural modifications through bioisosteric approach yielded fusidic acid analogues with 2–35 folds increase in antiplasmodial activity as compared to fusidic acid.
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Affiliation(s)
- Gurminder Kaur
- Department of Chemistry
- University of Cape Town
- Rondebosch 7701
- South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit
| | - Kawaljit Singh
- Department of Chemistry
- University of Cape Town
- Rondebosch 7701
- South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit
| | - Elumalai Pavadai
- Department of Chemistry
- University of Cape Town
- Rondebosch 7701
- South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit
| | - Mathew Njoroge
- Department of Chemistry
- University of Cape Town
- Rondebosch 7701
- South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit
| | - Marlene Espinoza-Moraga
- Department of Chemistry
- University of Cape Town
- Rondebosch 7701
- South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit
| | - Carmen De Kock
- Division of Clinical Pharmacology
- Department of Medicine
- University of Cape Town
- Groote Schuur Hospital
- Observatory
| | - Peter J. Smith
- Division of Clinical Pharmacology
- Department of Medicine
- University of Cape Town
- Groote Schuur Hospital
- Observatory
| | - Sergio Wittlin
- University of Basel
- 4002 Basel
- Switzerland
- Swiss Tropical and Public Health Institute
- Socinstrasse 57
| | - Kelly Chibale
- Department of Chemistry
- University of Cape Town
- Rondebosch 7701
- South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit
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33
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Singh K, Kumar M, Pavadai E, Naran K, Warner DF, Ruminski PG, Chibale K. Synthesis of new verapamil analogues and their evaluation in combination with rifampicin against Mycobacterium tuberculosis and molecular docking studies in the binding site of efflux protein Rv1258c. Bioorg Med Chem Lett 2014; 24:2985-90. [PMID: 24894561 DOI: 10.1016/j.bmcl.2014.05.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 11/19/2022]
Abstract
New verapamil analogues were synthesized and their inhibitory activities against Mycobacterium tuberculosis H37Rv determined in vitro alone and in combination with rifampicin (RIF). Some analogues showed comparable activity to verapamil and exhibited better synergies with RIF. Molecular docking studies of the binding sites of Rv1258c, a M. tuberculosis efflux protein previously implicated in intrinsic resistance to RIF, suggested a potential rationale for the superior synergistic interactions observed with some analogues.
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Affiliation(s)
- Kawaljit Singh
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Malkeet Kumar
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Elumalai Pavadai
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Krupa Naran
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Division of Medical Microbiology, University of Cape Town, Rondebosch 7701, South Africa
| | - Digby F Warner
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Division of Medical Microbiology, University of Cape Town, Rondebosch 7701, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Peter G Ruminski
- Centre for World Health and Medicine, Saint Louis University, USA
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa.
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