1
|
Matyushenko AM, Nefedova VV, Kochurova AM, Kopylova GV, Koubassova NA, Shestak AG, Yampolskaya DS, Shchepkin DV, Kleymenov SY, Ryabkova NS, Katrukha IA, Bershitsky SY, Zaklyazminskaya EV, Tsaturyan AK, Levitsky DI. Novel Mutation Glu98Lys in Cardiac Tropomyosin Alters Its Structure and Impairs Myocardial Relaxation. Int J Mol Sci 2023; 24:12359. [PMID: 37569730 PMCID: PMC10419091 DOI: 10.3390/ijms241512359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
We characterized a novel genetic variant c.292G > A (p.E98K) in the TPM1 gene encoding cardiac tropomyosin 1.1 isoform (Tpm1.1), found in a proband with a phenotype of complex cardiomyopathy with conduction dysfunction and slow progressive neuromuscular involvement. To understand the molecular mechanism by which this mutation impairs cardiac function, we produced recombinant Tpm1.1 carrying an E98K substitution and studied how this substitution affects the structure of the Tpm1.1 molecule and its functional properties. The results showed that the E98K substitution in the N-terminal part of the Tpm molecule significantly destabilizes the C-terminal part of Tpm, thus indicating a long-distance destabilizing effect of the substitution on the Tpm coiled-coil structure. The E98K substitution did not noticeably affect Tpm's affinity for F-actin but significantly impaired Tpm's regulatory properties. It increased the Ca2+ sensitivity of the sliding velocity of regulated thin filaments over cardiac myosin in an in vitro motility assay and caused an incomplete block of the thin filament sliding at low Ca2+ concentrations. The incomplete motility block in the absence of Ca2+ can be explained by the loosening of the Tpm interaction with troponin I (TnI), thus increasing Tpm mobility on the surface of an actin filament that partially unlocks the myosin binding sites. This hypothesis is supported by the molecular dynamics (MD) simulation that showed that the E98 Tpm residue is involved in hydrogen bonding with the C-terminal part of TnI. Thus, the results allowed us to explain the mechanism by which the E98K Tpm mutation impairs sarcomeric function and myocardial relaxation.
Collapse
Affiliation(s)
- Alexander M. Matyushenko
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.M.M.); (V.V.N.); (D.S.Y.); (S.Y.K.)
| | - Victoria V. Nefedova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.M.M.); (V.V.N.); (D.S.Y.); (S.Y.K.)
| | - Anastasia M. Kochurova
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg 620049, Russia; (A.M.K.); (G.V.K.); (D.V.S.); (S.Y.B.)
| | - Galina V. Kopylova
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg 620049, Russia; (A.M.K.); (G.V.K.); (D.V.S.); (S.Y.B.)
| | - Natalia A. Koubassova
- Institute of Mechanics, Moscow State University, Moscow 119192, Russia; (N.A.K.); (A.K.T.)
| | - Anna G. Shestak
- Petrovsky National Research Centre of Surgery, Moscow 119991, Russia; (A.G.S.); (E.V.Z.)
| | - Daria S. Yampolskaya
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.M.M.); (V.V.N.); (D.S.Y.); (S.Y.K.)
| | - Daniil V. Shchepkin
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg 620049, Russia; (A.M.K.); (G.V.K.); (D.V.S.); (S.Y.B.)
| | - Sergey Y. Kleymenov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.M.M.); (V.V.N.); (D.S.Y.); (S.Y.K.)
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia S. Ryabkova
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (N.S.R.); (I.A.K.)
- HyTest Ltd., 20520 Turku, Finland
| | - Ivan A. Katrukha
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (N.S.R.); (I.A.K.)
- HyTest Ltd., 20520 Turku, Finland
| | - Sergey Y. Bershitsky
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg 620049, Russia; (A.M.K.); (G.V.K.); (D.V.S.); (S.Y.B.)
| | - Elena V. Zaklyazminskaya
- Petrovsky National Research Centre of Surgery, Moscow 119991, Russia; (A.G.S.); (E.V.Z.)
- N.P. Bochkov Research Centre for Medical Genetics, Moscow 20520, Russia
| | - Andrey K. Tsaturyan
- Institute of Mechanics, Moscow State University, Moscow 119192, Russia; (N.A.K.); (A.K.T.)
| | - Dmitrii I. Levitsky
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.M.M.); (V.V.N.); (D.S.Y.); (S.Y.K.)
| |
Collapse
|
2
|
Kopylova GV, Kochurova AM, Yampolskaya DS, Nefedova VV, Tsaturyan AK, Koubassova NA, Kleymenov SY, Levitsky DI, Bershitsky SY, Matyushenko AM, Shchepkin DV. Structural and Functional Properties of Kappa Tropomyosin. Int J Mol Sci 2023; 24:ijms24098340. [PMID: 37176047 PMCID: PMC10179609 DOI: 10.3390/ijms24098340] [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: 03/27/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In the myocardium, the TPM1 gene expresses two isoforms of tropomyosin (Tpm), alpha (αTpm; Tpm 1.1) and kappa (κTpm; Tpm 1.2). κTpm is the result of alternative splicing of the TPM1 gene. We studied the structural features of κTpm and its regulatory function in the atrial and ventricular myocardium using an in vitro motility assay. We tested the possibility of Tpm heterodimer formation from α- and κ-chains. Our result shows that the formation of ακTpm heterodimer is thermodynamically favorable, and in the myocardium, κTpm most likely exists as ακTpm heterodimer. Using circular dichroism, we compared the thermal unfolding of ααTpm, ακTpm, and κκTpm. κκTpm had the lowest stability, while the ακTpm was more stable than ααTpm. The differential scanning calorimetry results indicated that the thermal stability of the N-terminal part of κκTpm is much lower than that of ααTpm. The affinity of ααTpm and κκTpm to F-actin did not differ, and ακTpm interacted with F-actin significantly worse. The troponin T1 fragment enhanced the κκTpm and ακTpm affinity to F-actin. κκTpm differently affected the calcium regulation of the interaction of pig and rat ventricular myosin with the thin filament. With rat myosin, calcium sensitivity of thin filaments containing κκTpm was significantly lower than that with ααTpm and with pig myosin, and the sensitivity did not differ. Thin filaments containing κκTpm and ακTpm were better activated by pig atrial myosin than those containing ααTpm.
Collapse
Affiliation(s)
- Galina V Kopylova
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Anastasia M Kochurova
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Daria S Yampolskaya
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Victoria V Nefedova
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | | | | | - Sergey Y Kleymenov
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Dmitrii I Levitsky
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Sergey Y Bershitsky
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | | | - Daniil V Shchepkin
- Institute of Immunology and Physiology, Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| |
Collapse
|
3
|
Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023; 299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
Collapse
Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, United Kingdom; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, United Kingdom; BrisEngBio, School of Chemistry, University of Bristol, Bristol, United Kingdom; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, United Kingdom.
| |
Collapse
|
4
|
Molecular Dynamics Assessment of Mechanical Properties of the Thin Filaments in Cardiac Muscle. Int J Mol Sci 2023; 24:ijms24054792. [PMID: 36902223 PMCID: PMC10003134 DOI: 10.3390/ijms24054792] [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: 01/24/2023] [Revised: 02/19/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Contraction of cardiac muscle is regulated by Ca2+ ions via regulatory proteins, troponin (Tn), and tropomyosin (Tpm) associated with the thin (actin) filaments in myocardial sarcomeres. The binding of Ca2+ to a Tn subunit causes mechanical and structural changes in the multiprotein regulatory complex. Recent cryo-electron microscopy (cryo-EM) models of the complex allow one to study the dynamic and mechanical properties of the complex using molecular dynamics (MD). Here we describe two refined models of the thin filament in the calcium-free state that include protein fragments unresolved by cryo-EM and reconstructed using structure prediction software. The parameters of the actin helix and the bending, longitudinal, and torsional stiffness of the filaments estimated from the MD simulations performed with these models were close to those found experimentally. However, problems revealed from the MD simulation suggest that the models require further refinement by improving the protein-protein interaction in some regions of the complex. The use of relatively long refined models of the regulatory complex of the thin filament allows one to perform MD simulation of the molecular mechanism of Ca2+ regulation of contraction without additional constraints and study the effects of cardiomyopathy-associated mutation of the thin filament proteins of cardiac muscle.
Collapse
|
5
|
Deranek AE, Baldo AP, Lynn ML, Schwartz SD, Tardiff JC. Structure and Dynamics of the Flexible Cardiac Troponin T Linker Domain in a Fully Reconstituted Thin Filament. Biochemistry 2022; 61:1229-1242. [PMID: 35696530 DOI: 10.1021/acs.biochem.2c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural analysis of large protein complexes has been greatly enhanced through the application of electron microscopy techniques. One such multiprotein complex, the cardiac thin filament (cTF), has cyclic interactions with thick filament proteins to drive contraction of the heart that has recently been the subject of such studies. As important as these studies are, they provide limited or no information on highly flexible regions that in isolation would be characterized as inherently disordered. One such region is the extended cardiac troponin T (cTnT) linker between the regions of cTnT which have been labeled TNT1 and TNT2. It comprises a hinge region (residues 158-166) and a highly flexible region (residues 167-203). Critically, this region modulates the troponin/tropomyosin complex's position across the actin filament. Thus, the cTnT linker structure and dynamics are central to the regulation of the function of cardiac muscles, but up to now, it was ill-understood. To establish the cTnT linker structure, we coupled an atomistic computational cTF model with time-resolved fluorescence resonance energy transfer measurements in both ±Ca2+ conditions utilizing fully reconstituted cTFs. We mapped the cTnT linker's positioning across the actin filament, and by coupling the experimental results to computation, we found mean structures and ranges of motion of this part of the complex. With this new insight, we can now address cTnT linker structural dynamics in both myofilament activation and disease.
Collapse
Affiliation(s)
- Andrea E Deranek
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Anthony P Baldo
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Melissa L Lynn
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Jil C Tardiff
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85721, United States
| |
Collapse
|
6
|
The Mechanisms of Thin Filament Assembly and Length Regulation in Muscles. Int J Mol Sci 2022; 23:ijms23105306. [PMID: 35628117 PMCID: PMC9140763 DOI: 10.3390/ijms23105306] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
The actin containing tropomyosin and troponin decorated thin filaments form one of the crucial components of the contractile apparatus in muscles. The thin filaments are organized into densely packed lattices interdigitated with myosin-based thick filaments. The crossbridge interactions between these myofilaments drive muscle contraction, and the degree of myofilament overlap is a key factor of contractile force determination. As such, the optimal length of the thin filaments is critical for efficient activity, therefore, this parameter is precisely controlled according to the workload of a given muscle. Thin filament length is thought to be regulated by two major, but only partially understood mechanisms: it is set by (i) factors that mediate the assembly of filaments from monomers and catalyze their elongation, and (ii) by factors that specify their length and uniformity. Mutations affecting these factors can alter the length of thin filaments, and in human cases, many of them are linked to debilitating diseases such as nemaline myopathy and dilated cardiomyopathy.
Collapse
|
7
|
Torner JM, Arora PS. Conformational control in a photoswitchable coiled coil. Chem Commun (Camb) 2021; 57:1442-1445. [PMID: 33514971 DOI: 10.1039/d0cc08318f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The coiled coil is a common protein tertiary structure intimately involved in mediating protein recognition and function. Due to their structural simplicity, coiled coils have served as attractive scaffolds for the development of functional biomaterials. Herein we describe the design of conformationally-defined coiled coil photoswitches as potential environmentally-sensitive biomaterials.
Collapse
Affiliation(s)
- Justin M Torner
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
| |
Collapse
|
8
|
Ghosh P, Torner J, Arora PS, Maayan G. Dual Control of Peptide Conformation with Light and Metal Coordination. Chemistry 2021; 27:8956-8959. [PMID: 33909298 DOI: 10.1002/chem.202101006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 11/08/2022]
Abstract
The design of a stimuli-responsive peptide whose conformation is controlled by wavelength-specific light and metal coordination is described. The peptide adopts a defined tertiary structure and its conformation can be modulated between an α-helical coiled coil and β-sheet. The peptide is designed with a hydrophobic interface to induce coiled coil formation and is based on a recently described strategy to obtain switchable helix dimers. Herein, we endowed the helix dimer with 8-hydroxyquinoline (HQ) groups to achieve metal coordination and shift to a β-sheet structure. It was found that the conformational shift only occurs upon introduction of Zn2+ ; other metal ions (Cu2+ , Fe3+ , Co2+ , Mg2 , and Ni2+ ) do not offer switching likely due to non-specific metal-peptide coordination. A control peptide lacking the metal-coordinating residues does not show conformational switching with Zn2+ supporting the role of this metal in stabilizing the β-sheet conformation in a defined manner.
Collapse
Affiliation(s)
- Pritam Ghosh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa, 3200008, Israel
| | - Justin Torner
- Department of Chemistry, New York University, New York, New York, 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, New York, 10003, United States
| | - Galia Maayan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa, 3200008, Israel
| |
Collapse
|
9
|
Hornos F, Feng HZ, Rizzuti B, Palomino-Schätzlein M, Wieczorek D, Neira JL, Jin JP. The muscle-relaxing C-terminal peptide from troponin I populates a nascent helix, facilitating binding to tropomyosin with a potent therapeutic effect. J Biol Chem 2021; 296:100228. [PMID: 33814345 PMCID: PMC7948816 DOI: 10.1074/jbc.ra120.016012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 11/06/2022] Open
Abstract
The conserved C-terminal end segment of troponin I (TnI) plays a critical role in regulating muscle relaxation. This function is retained in the isolated C-terminal 27 amino acid peptide (residues 184-210) of human cardiac TnI (HcTnI-C27): When added to skinned muscle fibers, HcTnI-C27 reduces the Ca2+-sensitivity of activated myofibrils and facilitates relaxation without decreasing the maximum force production. However, the underlying mechanism of HcTnI-C27 function is unknown. We studied the conformational preferences of HcTnI-C27 and a myopathic mutant, Arg192His, (HcTnI-C27-H). Both peptides were mainly disordered in aqueous solution with a nascent helix involving residues from Trp191 to Ile195, as shown by NMR analysis and molecular dynamics simulations. The population of nascent helix was smaller in HcTnI-C27-H than in HcTnI-C27, as shown by circular dichroism (CD) titrations. Fluorescence and isothermal titration calorimetry (ITC) showed that both peptides bound tropomyosin (αTm), with a detectably higher affinity (∼10 μM) of HcTnI-C27 than that of HcTnI-C27-H (∼15 μM), consistent with an impaired Ca2+-desensitization effect of the mutant peptide on skinned muscle strips. Upon binding to αTm, HcTnI-C27 acquired a weakly stable helix-like conformation involving residues near Trp191, as shown by transferred nuclear Overhauser effect spectroscopy and hydrogen/deuterium exchange experiments. With the potent Ca2+-desensitization effect of HcTnI-C27 on skinned cardiac muscle from a mouse model of hypertrophic cardiomyopathy, the data support that the C-terminal end domain of TnI can function as an isolated peptide with the intrinsic capacity of binding tropomyosin, providing a promising therapeutic approach to selectively improve diastolic function of the heart.
Collapse
MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Binding Sites
- Calcium/metabolism
- Cardiomyopathy, Hypertrophic/genetics
- Cardiomyopathy, Hypertrophic/metabolism
- Cardiomyopathy, Hypertrophic/pathology
- Cardiomyopathy, Hypertrophic/prevention & control
- Disease Models, Animal
- Gene Expression
- Humans
- Kinetics
- Mice
- Molecular Docking Simulation
- Muscle Fibers, Skeletal/drug effects
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/pathology
- Muscle Relaxation
- Mutation
- Myofibrils/drug effects
- Myofibrils/metabolism
- Myofibrils/pathology
- Peptides/chemistry
- Peptides/genetics
- Peptides/metabolism
- Peptides/pharmacology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Interaction Domains and Motifs
- Sequence Alignment
- Sequence Homology, Amino Acid
- Substrate Specificity
- Tropomyosin/chemistry
- Tropomyosin/genetics
- Tropomyosin/metabolism
- Troponin I/chemistry
- Troponin I/genetics
- Troponin I/metabolism
Collapse
Affiliation(s)
- Felipe Hornos
- IDIBE, Universidad Miguel Hernández, Alicante, Spain
| | - Han-Zhong Feng
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Cosenza, Italy
| | | | - David Wieczorek
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cinncinnnati, Ohio, USA
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain.
| | - J-P Jin
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA.
| |
Collapse
|
10
|
Impact of A134 and E218 Amino Acid Residues of Tropomyosin on Its Flexibility and Function. Int J Mol Sci 2020; 21:ijms21228720. [PMID: 33218166 PMCID: PMC7698929 DOI: 10.3390/ijms21228720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022] Open
Abstract
Tropomyosin (Tpm) is one of the major actin-binding proteins that play a crucial role in the regulation of muscle contraction. The flexibility of the Tpm molecule is believed to be vital for its functioning, although its role and significance are under discussion. We choose two sites of the Tpm molecule that presumably have high flexibility and stabilized them with the A134L or E218L substitutions. Applying differential scanning calorimetry (DSC), molecular dynamics (MD), co-sedimentation, trypsin digestion, and in vitro motility assay, we characterized the properties of Tpm molecules with these substitutions. The A134L mutation prevented proteolysis of Tpm molecule by trypsin, and both substitutions increased the thermal stability of Tpm and its bending stiffness estimated from MD simulation. None of these mutations affected the primary binding of Tpm to F-actin; still, both of them increased the thermal stability of the actin-Tpm complex and maximal sliding velocity of regulated thin filaments in vitro at a saturating Ca2+ concentration. However, the mutations differently affected the Ca2+ sensitivity of the sliding velocity and pulling force produced by myosin heads. The data suggest that both regions of instability are essential for correct regulation and fine-tuning of Ca2+-dependent interaction of myosin heads with F-actin.
Collapse
|
11
|
Nefedova VV, Koubassova NA, Borzova VA, Kleymenov SY, Tsaturyan AK, Matyushenko AM, Levitsky DI. Tropomyosin pseudo-phosphorylation can rescue the effects of cardiomyopathy-associated mutations. Int J Biol Macromol 2020; 166:424-434. [PMID: 33129908 DOI: 10.1016/j.ijbiomac.2020.10.201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/28/2022]
Abstract
We applied various methods to investigate how mutations S283D and S61D that mimic phosphorylation of tropomyosin (Tpm) affect structural and functional properties of cardiac Tpm carrying cardiomyopathy-associated mutations in different parts of its molecule. Using differential scanning calorimetry and molecular dynamics, we have shown that the S61D mutation (but not the S283 mutation) causes significant destabilization of the N-terminal part of the Tpm molecule independently of the absence or presence of cardiomyopathy-associated mutations. Our results obtained by cosedimentation of Tpm with F-actin demonstrated that both S283D and S61D mutations can reduce or even eliminate undesirable changes in Tpm affinity for F-actin caused by some cardiomyopathy-associated mutations. The results indicate that Tpm pseudo-phosphorylation by mutations S283D or S61D can rescue the effects of mutations in the TPM1 gene encoding a cardiac isoform of Tpm that lead to the development of such severe inherited heart diseases as hypertrophic or dilated cardiomyopathies.
Collapse
Affiliation(s)
- Victoria V Nefedova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, 119071 Moscow, Russia
| | - Natalia A Koubassova
- Institute of Mechanics, Moscow State University, Mitchurinsky prosp. 1, 119192 Moscow, Russia
| | - Vera A Borzova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, 119071 Moscow, Russia
| | - Sergey Y Kleymenov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, 119071 Moscow, Russia; Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 119334 Moscow, Russia
| | - Andrey K Tsaturyan
- Institute of Mechanics, Moscow State University, Mitchurinsky prosp. 1, 119192 Moscow, Russia
| | - Alexander M Matyushenko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, 119071 Moscow, Russia
| | - Dmitrii I Levitsky
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33, 119071 Moscow, Russia.
| |
Collapse
|
12
|
Silva AMM, Ige T, Goonasekara CL, Heeley DH. Threonine-77 Is a Determinant of the Low-Temperature Conditioning of the Most Abundant Isoform of Tropomyosin in Atlantic Salmon. Biochemistry 2020; 59:2859-2869. [PMID: 32686411 DOI: 10.1021/acs.biochem.0c00416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Atlantic salmon Salmo salar survives below 10 °C. The main skeletal muscle is composed of a single isoform of tropomyosin (classified as Tpm1 α-fast) that is >92% identical to the mammalian homologue. How salmon Tpm1 maintains flexibility is investigated by reversing the only full charge substitution; threonine-77(g) in salmon and lysine in other vertebrates. The mutation (Thr-77 to Lys), which falls within a known destabilizing alanine cluster, (i) yields a useful electrophoretic shift in the absence and presence of an anionic detergent, (ii) increases the Tms of both cooperative transitions (calorimetry, 0.1 M salt, pH 7) [35 °C (minor) and 44 °C (major); ΔTm1 = 5 °C, ΔTm2 = 3.5 °C], (iii) increases the Tm of CN1A (residues 11-127) to 53 °C (ΔTm = 13 °C), a value similar to that of mammalian CN1A, (iv) markedly reduces the rate of proteolysis at Leu-169, and (v) weakens the affinity of salmon Tpm1 for troponin-Sepharose. Glu-82(e), the interstrand ionic partner of Lys-77(g), is conserved. The change in ionic interactions at this locus is postulated to be "sensed" in actin period 5 (residues 166-207) and likely beyond. Wild type (acetylated) salmon Tmp1 binds more tightly to F-actin at 4 °C than at 22 °C, which is the opposite of the long-known relationship displayed by the mammalian homologue. All of the evidence indicates that the presence of a neutral 77th amino acid destabilizes a sizable portion of salmon Tpm1 that includes the midregion. Threonine-77 is a key factor in rescuing the thin filament from the peril of cold-induced rigidity.
Collapse
Affiliation(s)
| | - Tolulope Ige
- Department of Biochemistry, Memorial University, St. John's, NL, Canada A1B 3X9
| | - Charitha L Goonasekara
- Department of Biochemistry, Faculty of Medicine, Kotelawala University, Colombo 10390, Sri Lanka
| | - David H Heeley
- Department of Biochemistry, Memorial University, St. John's, NL, Canada A1B 3X9
| |
Collapse
|
13
|
Sano KI, Yuki T, Nomata Y, Nakayama N, Iida R, Mitomo H, Ijiro K, Osada Y. Intrahelical Interactions in an α-Helical Coiled Coil Determine the Structural Stability of Tropomyosin. Biochemistry 2020; 59:2194-2202. [DOI: 10.1021/acs.biochem.0c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ken-Ichi Sano
- Department of Applied Chemistry, Faculty of Fundamental Engineering, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Tsubasa Yuki
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Yuta Nomata
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Norihisa Nakayama
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Ryo Iida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Hideyuki Mitomo
- Research Institute for Electronic Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0021, Japan
| | - Kuniharu Ijiro
- Research Institute for Electronic Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0021, Japan
| | - Yoshihito Osada
- Nano Medical Engineering Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| |
Collapse
|
14
|
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] [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.
Collapse
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
| |
Collapse
|
15
|
Park WM. Coiled-Coils: the Molecular Zippers that Self-Assemble Protein Nanostructures. Int J Mol Sci 2020; 21:E3584. [PMID: 32438665 PMCID: PMC7278914 DOI: 10.3390/ijms21103584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.
Collapse
Affiliation(s)
- Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
16
|
Cryo-EM structures of cardiac thin filaments reveal the 3D architecture of troponin. J Struct Biol 2020; 209:107450. [PMID: 31954841 DOI: 10.1016/j.jsb.2020.107450] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/06/2020] [Accepted: 01/12/2020] [Indexed: 02/06/2023]
Abstract
Troponin is an essential component of striated muscle and it regulates the sliding of actomyosin system in a calcium-dependent manner. Despite its importance, the structure of troponin has been elusive due to its high structural heterogeneity. In this study, we analyzed the 3D structures of murine cardiac thin filaments using a cryo-electron microscope equipped with a Volta phase plate (VPP). Contrast enhancement by a VPP enabled us to reconstruct the entire repeat of the thin filament. We determined the orientation of troponin relative to F-actin and tropomyosin, and characterized the interactions between troponin and tropomyosin. This study provides a structural basis for understanding the molecular mechanism of actomyosin system.
Collapse
|
17
|
Yamada Y, Namba K, Fujii T. Cardiac muscle thin filament structures reveal calcium regulatory mechanism. Nat Commun 2020; 11:153. [PMID: 31919429 PMCID: PMC6952405 DOI: 10.1038/s41467-019-14008-1] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/12/2019] [Indexed: 01/04/2023] Open
Abstract
Contraction of striated muscles is driven by cyclic interactions of myosin head projecting from the thick filament with actin filament and is regulated by Ca2+ released from sarcoplasmic reticulum. Muscle thin filament consists of actin, tropomyosin and troponin, and Ca2+ binding to troponin triggers conformational changes of troponin and tropomyosin to allow actin-myosin interactions. However, the structural changes involved in this regulatory mechanism remain unknown. Here we report the structures of human cardiac muscle thin filament in the absence and presence of Ca2+ by electron cryomicroscopy. Molecular models in the two states built based on available crystal structures reveal the structures of a C-terminal region of troponin I and an N-terminal region of troponin T in complex with the head-to-tail junction of tropomyosin together with the troponin core on actin filament. Structural changes of the thin filament upon Ca2+ binding now reveal the mechanism of Ca2+ regulation of muscle contraction.
Collapse
Affiliation(s)
- Yurika Yamada
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Takashi Fujii
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
18
|
Kopylova GV, Matyushenko AM, Koubassova NA, Shchepkin DV, Bershitsky SY, Levitsky DI, Tsaturyan AK. Functional outcomes of structural peculiarities of striated muscle tropomyosin. J Muscle Res Cell Motil 2019; 41:55-70. [DOI: 10.1007/s10974-019-09552-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/17/2019] [Indexed: 12/27/2022]
|
19
|
James JK, Nanda V. Comparative dynamics of tropomyosin in vertebrates and invertebrates. Proteins 2019; 88:265-273. [PMID: 31390486 DOI: 10.1002/prot.25797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/21/2022]
Abstract
Tropomyosin (Tpm) is an extended α-helical coiled-coil homodimer that regulates actinomyosin interactions in muscle. Molecular simulations of four Tpms, two from the vertebrate class Mammalia (rat and pig), and two from the invertebrate class Malacostraca (shrimp and lobster), showed that despite extensive sequence and structural homology across metazoans, dynamic behavior-particularly long-range structural fluctuations-were clearly distinct. Vertebrate Tpms were more flexible and sampled complex, multi-state conformational landscapes. Invertebrate Tpms were more rigid, sampling a highly constrained harmonic landscape. Filtering of trajectories by principle component analysis into essential subspaces showed significant overlap within but not between phyla. In vertebrate Tpms, hinge-regions decoupled long-range interhelical motions and suggested distinct domains. In contrast, crustacean Tpms did not exhibit long-range dynamic correlations-behaving more like a single rigid rod on the nanosecond time scale. These observations suggest there may be divergent mechanisms for Tpm binding to actin filaments, where conformational flexibility in mammalian Tpm allows a preorganized shape complementary to the filament surface, and where rigidity in the crustacean Tpm requires concerted bending and binding.
Collapse
Affiliation(s)
- Jose K James
- Center for Advanced Biotechnology and Medicine, and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
| |
Collapse
|
20
|
Machek ML, Sonnenschein HA, Graham SI, Shikwana F, Kim SL, Garcia DuBar S, Minzer ID, Wey R, Bell JK. Predicting and validating a model of suppressor of IKKepsilon through biophysical characterization. Protein Sci 2019; 28:1423-1436. [PMID: 31074891 PMCID: PMC6635840 DOI: 10.1002/pro.3640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/03/2019] [Accepted: 05/01/2019] [Indexed: 12/23/2022]
Abstract
Suppressor of IKKepsilon (SIKE) is a 207 residue protein that is implicated in the TLR3-TANK-binding kinase-1-mediated response to viral infection. SIKE's function in this pathway is unknown, but SIKE forms interactions with two distinct cytoskeletal proteins, α-actinin and tubulin, and SIKE knockout reduces cell migration. As structure informs function and in the absence of solved structural homologs, our studies were directed toward creating a structural model of SIKE through biochemical and biophysical characterization to probe and interrogate SIKE function. Circular dichroism revealed a primarily (73%) helical structure of minimal stability ( =32°C) but reversibly denatured. Limited proteolysis (LP) and chemical modification identified the N-terminal 2/3 of the protein as dynamic and accessible, whereas size exclusion chromatography (SEC) confirmed three homo-oligomeric species. SEC coupled to chemical crosslinking characterized the primary species as dimeric, a secondary hexameric species, and a higher order aggregate/polymer. Fluorescence polarization using intrinsic tryptophan fluorescence contextualized the anisotropy value for the SIKE dimer (molecular weight 51.8 kDa) among proteins of known structure, bovine serum albumin (BSA; 66 kDa), and glutamate dehydrogenase (GDH; 332 kDa). Radii of gyration for BSA and GDH provided exclusionary values for SIKE tertiary and dimeric quaternary models that otherwise conformed to secondary structure, LP, and modification data. Dimeric quaternary models were further culled using acrylamide quenching data of SIKE's single tryptophan that showed a single, protected environment. The low cooperativity of folding and regions of dynamic and potentially disordered structure advance the hypothesis that SIKE forms a conformational ensemble of native states that accommodate SIKE's interactions with multiple, distinct protein-binding partners.
Collapse
Affiliation(s)
- Megan L. Machek
- Department of Chemistry & BiochemistryUniversity of San DiegoSan DiegoCalifornia92110
| | - Halie A. Sonnenschein
- Department of Chemistry & BiochemistryUniversity of San DiegoSan DiegoCalifornia92110
| | - Sasha‐Kaye I. Graham
- Department of Chemistry & BiochemistryUniversity of San DiegoSan DiegoCalifornia92110
| | - Flowreen Shikwana
- Department of Chemistry & BiochemistryUniversity of San DiegoSan DiegoCalifornia92110
| | | | | | - Ian D. Minzer
- Department of Chemistry & BiochemistryUniversity of San DiegoSan DiegoCalifornia92110
| | - Ryan Wey
- ACS SEED ScholarsUniversity of San DiegoSan DiegoCalifornia92110
| | - Jessica K. Bell
- Department of Chemistry & BiochemistryUniversity of San DiegoSan DiegoCalifornia92110
| |
Collapse
|
21
|
Deacon DC, Happe CL, Chen C, Tedeschi N, Manso AM, Li T, Dalton ND, Peng Q, Farah EN, Gu Y, Tenerelli KP, Tran VD, Chen J, Peterson KL, Schork NJ, Adler ED, Engler AJ, Ross RS, Chi NC. Combinatorial interactions of genetic variants in human cardiomyopathy. Nat Biomed Eng 2019; 3:147-157. [PMID: 30923642 PMCID: PMC6433174 DOI: 10.1038/s41551-019-0348-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Abstract
Dilated cardiomyopathy (DCM) is a leading cause of morbidity and mortality worldwide; yet how genetic variation and environmental factors impact DCM heritability remains unclear. Here, we report that compound genetic interactions between DNA sequence variants contribute to the complex heritability of DCM. By using genetic data from a large family with a history of DCM, we discovered that heterozygous sequence variants in the TROPOMYOSIN 1 (TPM1) and VINCULIN (VCL) genes cose-gregate in individuals affected by DCM. In vitro studies of patient-derived and isogenic human-pluripotent-stem-cell-derived cardio-myocytes that were genome-edited via CRISPR to create an allelic series of TPM1 and VCL variants revealed that cardiomyocytes with both TPM1 and VCL variants display reduced contractility and sarcomeres that are less organized. Analyses of mice genetically engineered to harbour these human TPM1 and VCL variants show that stress on the heart may also influence the variable penetrance and expressivity of DCM-associated genetic variants in vivo. We conclude that compound genetic variants can interact combinatorially to induce DCM, particularly when influenced by other disease-provoking stressors.
Collapse
Affiliation(s)
- Dekker C Deacon
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra L Happe
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Chao Chen
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Neil Tedeschi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ana Maria Manso
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Veterans Administration Healthcare San Diego, San Diego, CA, USA
| | - Ting Li
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nancy D Dalton
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qian Peng
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA
| | - Elie N Farah
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yusu Gu
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kevin P Tenerelli
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Vivien D Tran
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ju Chen
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kirk L Peterson
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas J Schork
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA
| | - Eric D Adler
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
| | - Robert S Ross
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Veterans Administration Healthcare San Diego, San Diego, CA, USA.
| | - Neil C Chi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
22
|
Nakayama N, Takaoka S, Ota M, Takagaki K, Sano KI. Effect of the Aspect Ratio of Coiled-Coil Protein Carriers on Cellular Uptake. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14286-14293. [PMID: 30384613 DOI: 10.1021/acs.langmuir.8b02616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We showed previously that a rigid and fibrous-structured cationic coiled-coil artificial protein had cell-penetrating activity that was significantly greater when compared with a less-structured cell-penetrating peptide. Nanomaterials with anisotropic structures often show aspect-ratio-dependent unique physicochemical properties, as well as cell-penetrating activities. In this report, we have designed and demonstrated the cell-penetrating activity of a shorter cationic coiled-coil protein. An aspect ratio at 4.5:1 was found to be critical for ensuring that the cationic coiled-coil protein showed strong cell-penetrating activity. At an aspect ratio of 3.5:1, the cationic coiled-coil protein showed cell-penetrating activity that was similar to a less-structured short cationic cell-penetrating peptide. Interestingly, at an aspect ratio of 4:1, the cationic coiled-coil protein exhibited intermediate cell-penetrating activity. These findings should aid in the principle design of intracellular drug delivery carriers including coiled-coil artificial proteins, their derivatives, and α-helical cell-penetrating peptides as well as provide a framework for developing synthetic nanomaterials, such as metal nanorods and synthetic polymers.
Collapse
Affiliation(s)
- Norihisa Nakayama
- Graduate School of Environmental Symbiotic System Major , Nippon Institute of Technology , Miyashiro , Saitama 345-8501 , Japan
| | - Sho Takaoka
- BioMimetics Sympathies Inc. , Aomi, Koto-Ku, Tokyo 135-0064 , Japan
| | - Megumi Ota
- BioMimetics Sympathies Inc. , Aomi, Koto-Ku, Tokyo 135-0064 , Japan
| | - Kentaro Takagaki
- BioMimetics Sympathies Inc. , Aomi, Koto-Ku, Tokyo 135-0064 , Japan
| | - Ken-Ichi Sano
- Graduate School of Environmental Symbiotic System Major , Nippon Institute of Technology , Miyashiro , Saitama 345-8501 , Japan
- Department of Applied Chemistry, Faculty of Fundamental Engineering , Nippon Institute of Technology , Miyashiro , Saitama 345-8501 , Japan
| |
Collapse
|
23
|
Zhou Q, An T, Pham KTM, Hu H, Li Z. The CIF1 protein is a master orchestrator of trypanosome cytokinesis that recruits several cytokinesis regulators to the cytokinesis initiation site. J Biol Chem 2018; 293:16177-16192. [PMID: 30171070 DOI: 10.1074/jbc.ra118.004888] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/28/2018] [Indexed: 12/13/2022] Open
Abstract
To proliferate, the parasitic protozoan Trypanosoma brucei undergoes binary fission in a unidirectional manner along the cell's longitudinal axis from the cell anterior toward the cell posterior. This unusual mode of cell division is controlled by a regulatory pathway composed of two evolutionarily conserved protein kinases, Polo-like kinase and Aurora B kinase, and three trypanosome-specific proteins, CIF1, CIF2, and CIF3, which act in concert at the cytokinesis initiation site located at the distal tip of the newly assembled flagellum attachment zone (FAZ). However, additional regulators that function in this cytokinesis signaling cascade remain to be identified and characterized. Using proximity biotinylation, co-immunofluorescence microscopy, and co-immunoprecipitation, we identified 52 CIF1-associated proteins and validated six CIF1-interacting proteins, including the putative protein phosphatase KPP1, the katanin p80 subunit KAT80, the cleavage furrow-localized proteins KLIF and FRW1, and the FAZ tip-localized proteins FAZ20 and FPRC. Further analyses of the functional interplay between CIF1 and its associated proteins revealed a requirement of CIF1 for localization of a set of CIF1-associated proteins, an interdependence between KPP1 and CIF1, and an essential role of katanin in the completion of cleavage furrow ingression. Together, these results suggest that CIF1 acts as a master regulator of cytokinesis in T. brucei by recruiting a cohort of cytokinesis regulatory proteins to the cytokinesis initiation site.
Collapse
Affiliation(s)
- Qing Zhou
- From the Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Tai An
- From the Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Kieu T M Pham
- From the Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Huiqing Hu
- From the Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Ziyin Li
- From the Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
| |
Collapse
|
24
|
James JK, Pike DH, Khan IJ, Nanda V. Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin. Structure 2018; 26:997-1006.e5. [PMID: 29887498 PMCID: PMC6697176 DOI: 10.1016/j.str.2018.05.002] [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] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/28/2018] [Accepted: 05/08/2018] [Indexed: 11/26/2022]
Abstract
To what extent do structural and biophysical features of food allergen proteins distinguish them from other proteins in our diet? Invertebrate tropomyosins (Tpms) as a class are considered "pan-allergens," inducing food allergy to shellfish and respiratory allergy to dust mites. Vertebrate Tpms are not known to elicit allergy or cross-reactivity, despite their high structural similarity and sequence identity to invertebrate homologs. We expect allergens are sufficiently stable against gastrointestinal proteases to survive for immune sensitization in the intestines, and that proteolytic stability will correlate with thermodynamic stability. Thermal denaturation of shrimp Tpm shows that it is more stable than non-allergen vertebrate Tpm. Shrimp Tpm is also more resistant to digestion. Molecular dynamics uncover local dynamics that select epitopes and global differences in flexibility between shrimp and pig Tpm that discriminate allergens from non-allergens. Molecular determinants of allergenicity depend not only on sequence but on contributions of protein structure and dynamics.
Collapse
Affiliation(s)
- Jose K James
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Douglas H Pike
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - I John Khan
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
25
|
Zhao Y, Chwastyk M, Cieplak M. Structural entanglements in protein complexes. J Chem Phys 2018; 146:225102. [PMID: 29166058 DOI: 10.1063/1.4985221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both termini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK, and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.
Collapse
Affiliation(s)
- Yani Zhao
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, PL-02668 Warsaw, Poland
| | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, PL-02668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, PL-02668 Warsaw, Poland
| |
Collapse
|
26
|
Seafood allergy: A comprehensive review of fish and shellfish allergens. Mol Immunol 2018; 100:28-57. [PMID: 29858102 DOI: 10.1016/j.molimm.2018.04.008] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 11/23/2022]
Abstract
Seafood refers to several distinct groups of edible aquatic animals including fish, crustacean, and mollusc. The two invertebrate groups of crustacean and mollusc are, for culinary reasons, often combined as shellfish but belong to two very different phyla. The evolutionary and taxonomic diversity of the various consumed seafood species poses a challenge in the identification and characterisation of the major and minor allergens critical for reliable diagnostics and therapeutic treatments. Many allergenic proteins are very different between these groups; however, some pan-allergens, including parvalbumin, tropomyosin and arginine kinase, seem to induce immunological and clinical cross-reactivity. This extensive review details the advances in the bio-molecular characterisation of 20 allergenic proteins within the three distinct seafood groups; fish, crustacean and molluscs. Furthermore, the structural and biochemical properties of the major allergens are described to highlight the immunological and subsequent clinical cross-reactivities. A comprehensive list of purified and recombinant allergens is provided, and the applications of component-resolved diagnostics and current therapeutic developments are discussed.
Collapse
|
27
|
Simonyan AO, Sirenko VV, Karpicheva OE, Robaszkiewicz K, Śliwinska M, Moraczewska J, Krutetskaya ZI, Borovikov YS. The primary cause of muscle disfunction associated with substitutions E240K and R244G in tropomyosin is aberrant behavior of tropomyosin and response of actin and myosin during ATPase cycle. Arch Biochem Biophys 2018; 644:17-28. [PMID: 29510086 DOI: 10.1016/j.abb.2018.03.002] [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: 06/26/2017] [Revised: 02/16/2018] [Accepted: 03/02/2018] [Indexed: 10/17/2022]
Abstract
Using the polarized photometry technique we have studied the effects of two amino acid replacements, E240K and R244G, in tropomyosin (Tpm1.1) on the position of Tpm1.1 on troponin-free actin filaments and the spatial arrangement of actin monomers and myosin heads at various mimicked stages of the ATPase cycle in the ghost muscle fibres. E240 and R244 are located in the C-terminal, seventh actin-binding period, in f and b positions of the coiled-coil heptapeptide repeat. Actin, Tpm1.1, and myosin subfragment-1 (S1) were fluorescently labeled: 1.5-IAEDANS was attached to actin and S1, 5-IAF was bound to Tpm1.1. The labeled proteins were incorporated in the ghost muscle fibres and changes in polarized fluorescence during the ATPase cycle have been measured. It was found that during the ATPase cycle both mutant tropomyosins occupied a position close to the inner domain of actin. The relative amount of the myosin heads in the strongly-bound conformations and of the switched on actin monomers increased at mimicking different stages of the ATPase cycle. This might be one of the reasons for muscle dysfunction in congenital fibre type disproportion caused by the substitutions E240K and R244G in tropomyosin.
Collapse
Affiliation(s)
- Armen O Simonyan
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Basis of Cell Motility, 4 Tikhoretsky Ave., 194064, Saint Petersburg, Russia; Saint Petersburg State University, Faculty of Biology, Department of Biophysics, 7/9 Universitetskaya Emb., 199034, Saint Petersburg, Russia
| | - Vladimir V Sirenko
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Basis of Cell Motility, 4 Tikhoretsky Ave., 194064, Saint Petersburg, Russia
| | - Olga E Karpicheva
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Basis of Cell Motility, 4 Tikhoretsky Ave., 194064, Saint Petersburg, Russia
| | - Katarzyna Robaszkiewicz
- Kazimierz Wielki University in Bydgoszcz, Institute of Experimental Biology, Department of Biochemistry and Cell Biology, Ks. J. Poniatowski 12 Str., 85-671, Bydgoszcz, Poland
| | - Małgorzata Śliwinska
- Kazimierz Wielki University in Bydgoszcz, Institute of Experimental Biology, Department of Biochemistry and Cell Biology, Ks. J. Poniatowski 12 Str., 85-671, Bydgoszcz, Poland
| | - Joanna Moraczewska
- Kazimierz Wielki University in Bydgoszcz, Institute of Experimental Biology, Department of Biochemistry and Cell Biology, Ks. J. Poniatowski 12 Str., 85-671, Bydgoszcz, Poland
| | - Zoya I Krutetskaya
- Saint Petersburg State University, Faculty of Biology, Department of Biophysics, 7/9 Universitetskaya Emb., 199034, Saint Petersburg, Russia
| | - Yurii S Borovikov
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Basis of Cell Motility, 4 Tikhoretsky Ave., 194064, Saint Petersburg, Russia.
| |
Collapse
|
28
|
Zhang Z, Zhang X, Chen W, Zhou P. Conformation stability, in vitro digestibility and allergenicity of tropomyosin from shrimp (Exopalaemon modestus) as affected by high intensity ultrasound. Food Chem 2018; 245:997-1009. [DOI: 10.1016/j.foodchem.2017.11.072] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
|
29
|
Barua B, Sckolnick M, White HD, Trybus KM, Hitchcock-DeGregori SE. Distinct sites in tropomyosin specify shared and isoform-specific regulation of myosins II and V. Cytoskeleton (Hoboken) 2018; 75:150-163. [PMID: 29500902 PMCID: PMC5899941 DOI: 10.1002/cm.21440] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/07/2018] [Accepted: 02/19/2018] [Indexed: 12/25/2022]
Abstract
Muscle contraction, cytokinesis, cellular movement, and intracellular transport depend on regulated actin-myosin interaction. Most actin filaments bind one or more isoform of tropomyosin, a coiled-coil protein that stabilizes the filaments and regulates interactions with other actin-binding proteins, including myosin. Isoform-specific allosteric regulation of muscle myosin II by actin-tropomyosin is well-established while that of processive myosins, such as myosin V, which transport organelles and macromolecules in the cell periphery, is less certain. Is the regulation by tropomyosin a universal mechanism, the consequence of the conserved periodic structures of tropomyosin, or is it the result of specialized interactions between particular isoforms of myosin and tropomyosin? Here, we show that striated muscle tropomyosin, Tpm1.1, inhibits fast skeletal muscle myosin II but not myosin Va. The non-muscle tropomyosin, Tpm3.1, in contrast, activates both myosins. To decipher the molecular basis of these opposing regulatory effects, we introduced mutations at conserved surface residues within the six periodic repeats (periods) of Tpm3.1, in positions homologous or analogous to those important for regulation of skeletal muscle myosin by Tpm1.1. We identified conserved residues in the internal periods of both tropomyosin isoforms that are important for the function of myosin Va and striated myosin II. Conserved residues in the internal and C-terminal periods that correspond to Tpm3.1-specific exons inhibit myosin Va but not myosin II function. These results suggest that tropomyosins may directly impact myosin function through both general and isoform-specific mechanisms that identify actin tracks for the recruitment and function of particular myosins.
Collapse
Affiliation(s)
- Bipasha Barua
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854
| | - Maria Sckolnick
- Department of Molecular Physiology & Biophysics University of Vermont, Burlington, VT 05405
| | - Howard D. White
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507
| | - Kathleen M. Trybus
- Department of Molecular Physiology & Biophysics University of Vermont, Burlington, VT 05405
| | - Sarah E. Hitchcock-DeGregori
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854
| |
Collapse
|
30
|
Ozawa H, Umezawa K, Takano M, Ishizaki S, Watabe S, Ochiai Y. Structural and dynamical characteristics of tropomyosin epitopes as the major allergens in shrimp. Biochem Biophys Res Commun 2018; 498:119-124. [DOI: 10.1016/j.bbrc.2018.02.172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 12/16/2022]
|
31
|
Matyushenko AM, Shchepkin DV, Kopylova GV, Bershitsky SY, Koubassova NA, Tsaturyan AK, Levitsky DI. Functional role of the core gap in the middle part of tropomyosin. FEBS J 2018; 285:871-886. [PMID: 29278453 DOI: 10.1111/febs.14369] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 11/27/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022]
Abstract
Tropomyosin (Tpm) is an α-helical coiled-coil actin-binding protein playing an essential role in the regulation of muscle contraction. The middle part of the Tpm molecule has some specific features, such as the presence of noncanonical residues as well as a substantial gap at the interhelical interface, which are believed to destabilize a coiled-coil and impart structural flexibility to this part of the molecule. To study how the gap affects structural and functional properties of α-striated Tpm (the Tpm1.1 isoform that is expressed in cardiac and skeletal muscles) we replaced large conserved apolar core residues located at both sides of the gap with smaller ones by mutations M127A/I130A and M141A/Q144A. We found that in contrast with the stabilizing substitutions D137L and G126R studied earlier, these substitutions have no appreciable influence on thermal unfolding and domain structure of the Tpm molecule. They also do not affect actin-binding properties of Tpm. However, they strongly increase sliding velocity of regulated actin filaments in an in vitro motility assay and cause an oversensitivity of the velocity to Ca2+ similar to the stabilizing substitutions D137L and G126R. Molecular dynamics shows that the substitutions studied here increase bending stiffness of the coiled-coil structure of Tpm, like that of G126R/D137L, probably due to closure of the interhelical gap in the area of the substitutions. Our results clearly indicate that the conserved middle part of Tpm is important for the fine tuning of the Ca2+ regulation of actin-myosin interaction in muscle.
Collapse
Affiliation(s)
- Alexander M Matyushenko
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daniil V Shchepkin
- Institute of Immunology and Physiology, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Galina V Kopylova
- Institute of Immunology and Physiology, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Sergey Y Bershitsky
- Institute of Immunology and Physiology, Russian Academy of Sciences, Yekaterinburg, Russia
| | | | | | - Dmitrii I Levitsky
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| |
Collapse
|
32
|
Negahdaripour M, Golkar N, Hajighahramani N, Kianpour S, Nezafat N, Ghasemi Y. Harnessing self-assembled peptide nanoparticles in epitope vaccine design. Biotechnol Adv 2017; 35:575-596. [PMID: 28522213 PMCID: PMC7127164 DOI: 10.1016/j.biotechadv.2017.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/23/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
Abstract
Vaccination has been one of the most successful breakthroughs in medical history. In recent years, epitope-based subunit vaccines have been introduced as a safer alternative to traditional vaccines. However, they suffer from limited immunogenicity. Nanotechnology has shown value in solving this issue. Different kinds of nanovaccines have been employed, among which virus-like nanoparticles (VLPs) and self-assembled peptide nanoparticles (SAPNs) seem very promising. Recently, SAPNs have attracted special interest due to their unique properties, including molecular specificity, biodegradability, and biocompatibility. They also resemble pathogens in terms of their size. Their multivalency allows an orderly repetitive display of antigens on their surface, which induces a stronger immune response than single immunogens. In vaccine design, SAPN self-adjuvanticity is regarded an outstanding advantage, since the use of toxic adjuvants is no longer required. SAPNs are usually composed of helical or β-sheet secondary structures and are tailored from natural peptides or de novo structures. Flexibility in subunit selection opens the door to a wide variety of molecules with different characteristics. SAPN engineering is an emerging area, and more novel structures are expected to be generated in the future, particularly with the rapid progress in related computational tools. The aim of this review is to provide a state-of-the-art overview of self-assembled peptide nanoparticles and their use in vaccine design in recent studies. Additionally, principles for their design and the application of computational approaches to vaccine design are summarized.
Collapse
Affiliation(s)
- Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Golkar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutics Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sedigheh Kianpour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
33
|
England J, Granados-Riveron J, Polo-Parada L, Kuriakose D, Moore C, Brook JD, Rutland CS, Setchfield K, Gell C, Ghosh TK, Bu'Lock F, Thornborough C, Ehler E, Loughna S. Tropomyosin 1: Multiple roles in the developing heart and in the formation of congenital heart defects. J Mol Cell Cardiol 2017; 106:1-13. [PMID: 28359939 PMCID: PMC5441184 DOI: 10.1016/j.yjmcc.2017.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 12/03/2022]
Abstract
Tropomyosin 1 (TPM1) is an essential sarcomeric component, stabilising the thin filament and facilitating actin's interaction with myosin. A number of sarcomeric proteins, such as alpha myosin heavy chain, play crucial roles in cardiac development. Mutations in these genes have been linked to congenital heart defects (CHDs), occurring in approximately 1 in 145 live births. To date, TPM1 has not been associated with isolated CHDs. Analysis of 380 CHD cases revealed three novel mutations in the TPM1 gene; IVS1 + 2T > C, I130V, S229F and a polyadenylation signal site variant GATAAA/AATAAA. Analysis of IVS1 + 2T > C revealed aberrant pre-mRNA splicing. In addition, abnormal structural properties were found in hearts transfected with TPM1 carrying I130V and S229F mutations. Phenotypic analysis of TPM1 morpholino-treated embryos revealed roles for TPM1 in cardiac looping, atrial septation and ventricular trabeculae formation and increased apoptosis was seen within the heart. In addition, sarcomere assembly was affected and altered action potentials were exhibited. This study demonstrated that sarcomeric TPM1 plays vital roles in cardiogenesis and is a suitable candidate gene for screening individuals with isolated CHDs. Four mutations identified in the TPM1 gene; IVS1 + 2T > C, I130V, S229F and GATAAA/AATAAA. In vitro analysis of IVS1 + 2T > C revealed aberrant pre-mRNA splicing. I130V and S229F mutations caused abnormal structural properties in the sarcomere. Reduced TPM1 expression during early cardiogenesis causes aberrant gross morphology. Apoptosis, sarcomere assembly and cardiac conduction were also affected.
Collapse
Affiliation(s)
| | - Javier Granados-Riveron
- Laboratory of Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico
| | - Luis Polo-Parada
- Department of Medical Pharmacology and Physiology, School of Medicine, University of Missouri, USA
| | | | | | - J David Brook
- School of Life Sciences, University of Nottingham, UK
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, University of Nottingham, UK
| | | | | | | | - Frances Bu'Lock
- East Midlands Congenital Heart Centre, Glenfield Hospital, Leicester, UK
| | | | - Elisabeth Ehler
- Randall Division of Cell and Molecular Biophysics, The Cardiovascular Division, King's College London, UK
| | | |
Collapse
|
34
|
Abstract
α-Helical coiled coils constitute one of the most diverse folds yet described. They range in length over two orders of magnitude; they form rods, segmented ropes, barrels, funnels, sheets, spirals, and rings, which encompass anywhere from two to more than 20 helices in parallel or antiparallel orientation; they assume different helix crossing angles, degrees of supercoiling, and packing geometries. This structural diversity supports a wide range of biological functions, allowing them to form mechanically rigid structures, provide levers for molecular motors, project domains across large distances, mediate oligomerization, transduce conformational changes and facilitate the transport of other molecules. Unlike almost any other protein fold known to us, their structure can be computed from parametric equations, making them an ideal model system for rational protein design. Here we outline the principles by which coiled coils are structured, review the determinants of their folding and stability, and present an overview of their diverse architectures.
Collapse
|
35
|
Abstract
Tropomyosin is the archetypal-coiled coil, yet studies of its structure and function have proven it to be a dynamic regulator of actin filament function in muscle and non-muscle cells. Here we review aspects of its structure that deviate from canonical leucine zipper coiled coils that allow tropomyosin to bind to actin, regulate myosin, and interact directly and indirectly with actin-binding proteins. Four genes encode tropomyosins in vertebrates, with additional diversity that results from alternate promoters and alternatively spliced exons. At the same time that periodic motifs for binding actin and regulating myosin are conserved, isoform-specific domains allow for specific interaction with myosins and actin filament regulatory proteins, including troponin. Tropomyosin can be viewed as a universal regulator of the actin cytoskeleton that specifies actin filaments for cellular and intracellular functions.
Collapse
|
36
|
Chang JB, Kim YH, Thompson E, No YH, Kim NH, Arrieta J, Manfrinato VR, Keating AE, Berggren KK. The Orientations of Large Aspect-Ratio Coiled-Coil Proteins Attached to Gold Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:1498-1505. [PMID: 26799936 DOI: 10.1002/smll.201502419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/30/2015] [Indexed: 06/05/2023]
Abstract
Methods for patterning biomolecules on a substrate at the single molecule level have been studied as a route to sensors with single-molecular sensitivity or as a way to probe biological phenomena at the single-molecule level. However, the arrangement and orientation of single biomolecules on substrates has been less investigated. Here, the arrangement and orientation of two rod-like coiled-coil proteins, cortexillin and tropomyosin, around patterned gold nanostructures is examined. The high aspect ratio of the coiled coils makes it possible to study their orientations and to pursue a strategy of protein orientation via two-point attachment. The proteins are anchored to the surfaces using thiol groups, and the number of cysteine residues in tropomyosin is varied to test how this variation affects the structure and arrangement of the surface-attached proteins. Molecular dynamics studies are used to interpret the observed positional distributions. Based on initial studies of protein attachment to gold post structures, two 31-nm-long tropomyosin molecules are aligned between the two sidewalls of a trench with a width of 68 nm. Because the approach presented in this study uses one of twenty natural amino acids, this method provides a convenient way to pattern biomolecules on substrates using standard chemistry.
Collapse
Affiliation(s)
- Jae-Byum Chang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yong Ho Kim
- Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 440-746, South Korea
- Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Evan Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Young Hyun No
- Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Nam Hyeong Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Jose Arrieta
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vitor R Manfrinato
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Karl K Berggren
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| |
Collapse
|
37
|
Fischer S, Rynkiewicz MJ, Moore JR, Lehman W. Tropomyosin diffusion over actin subunits facilitates thin filament assembly. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:012002. [PMID: 26798831 PMCID: PMC4714992 DOI: 10.1063/1.4940223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
Coiled-coil tropomyosin binds to consecutive actin-subunits along actin-containing thin filaments. Tropomyosin molecules then polymerize head-to-tail to form cables that wrap helically around the filaments. Little is known about the assembly process that leads to continuous, gap-free tropomyosin cable formation. We propose that tropomyosin molecules diffuse over the actin-filament surface to connect head-to-tail to partners. This possibility is likely because (1) tropomyosin hovers loosely over the actin-filament, thus binding weakly to F-actin and (2) low energy-barriers provide tropomyosin freedom for 1D axial translation on F-actin. We consider that these unique features of the actin-tropomyosin interaction are the basis of tropomyosin cable formation.
Collapse
Affiliation(s)
- Stefan Fischer
- Computational Biochemistry Group, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg , Im Neuenheimer Feld 368, D69120 Heidelberg, Germany
| | - Michael J Rynkiewicz
- Department of Physiology and Biophysics, Boston University School of Medicine , 72 East Concord Street, Boston, Massachusetts 02118, USA
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts Lowell , One University Avenue, Lowell, Massachusetts 01854, USA
| | - William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine , 72 East Concord Street, Boston, Massachusetts 02118, USA
| |
Collapse
|
38
|
Rynkiewicz MJ, Schott V, Orzechowski M, Lehman W, Fischer S. Electrostatic interaction map reveals a new binding position for tropomyosin on F-actin. J Muscle Res Cell Motil 2015; 36:525-33. [PMID: 26286845 DOI: 10.1007/s10974-015-9419-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/07/2015] [Indexed: 12/15/2022]
Abstract
Azimuthal movement of tropomyosin around the F-actin thin filament is responsible for muscle activation and relaxation. Recently a model of αα-tropomyosin, derived from molecular-mechanics and electron microscopy of different contractile states, showed that tropomyosin is rather stiff and pre-bent to present one specific face to F-actin during azimuthal transitions. However, a new model based on cryo-EM of troponin- and myosin-free filaments proposes that the interacting-face of tropomyosin can differ significantly from that in the original model. Because resolution was insufficient to assign tropomyosin side-chains, the interacting-face could not be unambiguously determined. Here, we use structural analysis and energy landscapes to further examine the proposed models. The observed bend in seven crystal structures of tropomyosin is much closer in direction and extent to the original model than to the new model. Additionally, we computed the interaction map for repositioning tropomyosin over the F-actin surface, but now extended over a much larger surface than previously (using the original interacting-face). This map shows two energy minima-one corresponding to the "blocked-state" as in the original model, and the other related by a simple 24 Å translation of tropomyosin parallel to the F-actin axis. The tropomyosin-actin complex defined by the second minimum fits perfectly into the recent cryo-EM density, without requiring any change in the interacting-face. Together, these data suggest that movement of tropomyosin between regulatory states does not require interacting-face rotation. Further, they imply that thin filament assembly may involve an interplay between initially seeded tropomyosin molecules growing from distinct binding-site regions on actin.
Collapse
Affiliation(s)
- Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Veronika Schott
- Department of Physiology & Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Computational Biochemistry Group, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, 69120, Heidelberg, Germany
| | - Marek Orzechowski
- Department of Physiology & Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Computational Biochemistry Group, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, 69120, Heidelberg, Germany
| | - William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
| | - Stefan Fischer
- Computational Biochemistry Group, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, 69120, Heidelberg, Germany.
| |
Collapse
|
39
|
Fudge KR, Heeley DH. Biochemical Characterization of the Roles of Glycines 24 and 27 and Threonine 179 in Tropomyosin from the Fast Skeletal Trunk Muscle of the Atlantic Salmon. Biochemistry 2015; 54:2769-76. [DOI: 10.1021/acs.biochem.5b00156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Korrina R. Fudge
- Department
of Biochemistry, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X9, Canada
| | - David H. Heeley
- Department
of Biochemistry, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X9, Canada
| |
Collapse
|
40
|
Nakayama N, Hagiwara K, Ito Y, Ijiro K, Osada Y, Sano KI. Superior cell penetration by a rigid and anisotropic synthetic protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2826-2832. [PMID: 25710086 DOI: 10.1021/la504494x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecules with structural anisotropy and rigidity, such as asbestos, demonstrate high cell-penetrating activity but also high toxicity. Here we synthesize a biodegradable, rigid, and fibrous artificial protein, CCPC 140, as a potential vehicle for cellular delivery. CCPC 140 penetrated 100% of cells tested in vitro, even at a concentration of 3.1 nM-superior to previously reported cell-penetrating peptides. The effects of cell-strain-dependency and aspect ratio on the cell-penetrating activity of CCPC 140 were also investigated.
Collapse
Affiliation(s)
- Norihisa Nakayama
- Graduate School of Environmental Symbiotic System Major and ‡Department of Innovative Systems Engineering, Nippon Institute of Technology , Miyashiro, Saitama 345-8501, Japan
| | | | | | | | | | | |
Collapse
|
41
|
Sevrieva I, Knowles AC, Kampourakis T, Sun YB. Regulatory domain of troponin moves dynamically during activation of cardiac muscle. J Mol Cell Cardiol 2014; 75:181-7. [PMID: 25101951 PMCID: PMC4169182 DOI: 10.1016/j.yjmcc.2014.07.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/09/2014] [Accepted: 07/26/2014] [Indexed: 11/24/2022]
Abstract
Heart muscle is activated by Ca2+ to generate force and shortening, and the signaling pathway involves allosteric mechanisms in the thin filament. Knowledge about the structure-function relationship among proteins in the thin filament is critical in understanding the physiology and pathology of the cardiac function, but remains obscure. We investigate the conformation of the cardiac troponin (Tn) on the thin filament and its response to Ca2+ activation and propose a molecular mechanism for the regulation of cardiac muscle contraction by Tn based uniquely on information from in situ protein domain orientation. Polarized fluorescence from bifunctional rhodamine is used to determine the orientation of the major component of Tn core domain on the thin filaments of cardiac muscle. We show that the C-terminal lobe of TnC (CTnC) does not move during activation, suggesting that CTnC, together with the coiled coil formed by the TnI and TnT chains (IT arm), acts as a scaffold that holds N-terminal lobe of TnC (NTnC) and the actin binding regions of troponin I. The NTnC, on the other hand, exhibits multiple orientations during both diastole and systole. By combining the in situ orientation data with published in vitro measurements of intermolecular distances, we construct a model for the in situ structure of the thin filament. The conformational dynamics of NTnC plays an important role in the regulation of cardiac muscle contraction by moving the C-terminal region of TnI from its actin-binding inhibitory location and enhancing the movement of tropomyosin away from its inhibitory position. In situ conformational changes of troponin in myocardium were investigated. A model for the cardiac thin filament was constructed based on the in situ data. The IT arm of cardiac troponin acts as a scaffold that holds the regulatory domain. The regulatory domain of cardiac troponin moves dynamically during activation. The dynamics of regulatory domain is important in cardiac muscle regulation.
Collapse
Affiliation(s)
- Ivanka Sevrieva
- Randall Division of Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK
| | - Andrea C Knowles
- Randall Division of Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK
| | - Thomas Kampourakis
- Randall Division of Cell and Molecular Biophysics and British Heart Foundation Centre of Research Excellence, 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, King's College London, London, SE1 1UL, UK.
| |
Collapse
|
42
|
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]
|
43
|
Yar S, Monasky MM, Solaro RJ. Maladaptive modifications in myofilament proteins and triggers in the progression to heart failure and sudden death. Pflugers Arch 2014; 466:1189-97. [PMID: 24488009 DOI: 10.1007/s00424-014-1457-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 01/16/2014] [Accepted: 01/19/2014] [Indexed: 12/25/2022]
Abstract
In this review, we address the following question: Are modifications at the level of sarcomeric proteins in acquired heart failure early inducers of altered cardiac dynamics and signaling leading to remodeling and progression to decompensation? There is no doubt that most inherited cardiomyopathies are caused by mutations in proteins of the sarcomere. We think this linkage indicates that early changes at the level of the sarcomeres in acquired cardiac disorders may be significant in triggering the progression to failure. We consider evidence that there are rate-limiting mechanisms downstream of the trigger event of Ca(2+) binding to troponin C, which control cardiac dynamics. We discuss new perspectives on how modifications in these mechanisms may be of relevance to redox signaling in diastolic heart failure, to angiotensin II signaling via β-arrestin, and to remodeling related to altered structural rigidity of tropomyosin. We think that these new perspectives provide a rationale for future studies directed at a more thorough understanding of the question driving our review.
Collapse
Affiliation(s)
- Sumeyye Yar
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, M/C 901, Chicago, IL, 60612, USA
| | | | | |
Collapse
|
44
|
Bhardwaj A, Casjens SR, Cingolani G. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:342-53. [PMID: 24531468 PMCID: PMC3940195 DOI: 10.1107/s1399004713027685] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/09/2013] [Indexed: 11/10/2022]
Abstract
Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.
Collapse
Affiliation(s)
- Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Sherwood R. Casjens
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| |
Collapse
|
45
|
Lai CC, Yeh YH, Hsieh WP, Kuo CT, Wang WC, Chu CH, Hung CL, Cheng CY, Tsai HY, Lee JL, Tang CY, Hsu LA. Whole-exome sequencing to identify a novel LMNA gene mutation associated with inherited cardiac conduction disease. PLoS One 2013; 8:e83322. [PMID: 24349489 PMCID: PMC3861486 DOI: 10.1371/journal.pone.0083322] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/01/2013] [Indexed: 01/10/2023] Open
Abstract
Background Inherited cardiac conduction diseases (CCD) are rare but are caused by mutations in a myriad of genes. Recently, whole-exome sequencing has successfully led to the identification of causal mutations for rare monogenic Mendelian diseases. Objective To investigate the genetic background of a family affected by inherited CCD. Methods and Results We used whole-exome sequencing to study a Chinese family with multiple family members affected by CCD. Using the pedigree information, we proposed a heterozygous missense mutation (c.G695T, Gly232Val) in the lamin A/C (LMNA) gene as a candidate mutation for susceptibility to CCD in this family. The mutation is novel and is expected to affect the conformation of the coiled-coil rod domain of LMNA according to a structural model prediction. Its pathogenicity in lamina instability was further verified by expressing the mutation in a cellular model. Conclusions Our results suggest that whole-exome sequencing is a feasible approach to identifying the candidate genes underlying inherited conduction diseases.
Collapse
Affiliation(s)
- Chun-Chi Lai
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Yung-Hsin Yeh
- First Cardiovascular Division, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Tao-Yuan, Taiwan
| | - Wen-Ping Hsieh
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Tai Kuo
- First Cardiovascular Division, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Tao-Yuan, Taiwan
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing-Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Han Chu
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Chiu-Lien Hung
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing-Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Yang Cheng
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsin-Yi Tsai
- First Cardiovascular Division, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Tao-Yuan, Taiwan
| | - Jia-Lin Lee
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing-Hua University, Hsinchu, Taiwan
| | - Chuan-Yi Tang
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Lung-An Hsu
- First Cardiovascular Division, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Tao-Yuan, Taiwan
- * E-mail:
| |
Collapse
|
46
|
Parry DAD. Fifty years of fibrous protein research: a personal retrospective. J Struct Biol 2013; 186:320-34. [PMID: 24148884 DOI: 10.1016/j.jsb.2013.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 02/02/2023]
Abstract
As a result of X-ray fiber diffraction studies on fibrous proteins and crystallographic data on fragments derived from them, new experimental techniques across the biophysical and biochemical spectra, sophisticated computer modeling and refinement procedures, widespread use of bioinformatics and improved specimen preparative procedures the structures of many fibrous proteins have now been determined to at least low resolution. In so doing these structures have yielded insight into the relationship that exists between sequence and conformation and this, in turn, has led to improved methodologies for predicting structure from sequence data alone. In this personal retrospective a selection of progress made during the past 50years is discussed in terms of events to which the author has made some contribution.
Collapse
Affiliation(s)
- David A D Parry
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.
| |
Collapse
|
47
|
Lehman W, Li XE, Orzechowski M, Fischer S. The structural dynamics of α-tropomyosin on F-actin shape the overlap complex between adjacent tropomyosin molecules. Arch Biochem Biophys 2013; 552-553:68-73. [PMID: 24071513 DOI: 10.1016/j.abb.2013.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/31/2013] [Accepted: 09/13/2013] [Indexed: 12/15/2022]
Abstract
Coiled-coil tropomyosin, localized on actin filaments in virtually all eukaryotic cells, serves as a gatekeeper regulating access of the motor protein myosin and other actin-binding proteins onto the thin filament surface. Tropomyosin's modular pseudo-repeating pattern of approximately 39 amino acid residues is designed to allow binding of the coiled-coil to successive actin subunits along thin filaments. Even though different tropomyosin isoforms contain varying numbers of repeat modules, the pseudo-repeat length, in all cases, matches that of a single actin subunit. Thus, the seven pseudo-repeats of 42nm long muscle tropomyosin bind to seven successive actin subunits along thin filaments, while simultaneously bending into a super-helical conformation that is preshaped to the actin filament helix. In order to form a continuous cable on thin filaments that is free of gaps, adjacent tropomyosin molecules polymerize head-to-tail by means of a short (∼9 residue) overlap. Several laboratories have engineered peptides to mimic the N- and C-terminal tropomyosin association and to characterize the overlap structure. All overlapping domains examined show a compact N-terminal coiled-coil inserting into a partially opened C-terminal partner, where the opposing coiled-coils at the overlap junction face each other at up to ∼90° twist angles. Here, Molecular Dynamics (MD) simulations were carried out to determine constraints on the formation of the tropomyosin overlap complex and to assess the amount of twisting exhibited by full-length tropomyosin when bound to actin. With the exception of the last 20-40 C- and N-terminal residues, we find that the average tropomyosin structure closely resembles a "canonical" model proposed in the classic work of McLachlan and Stewart, displaying perfectly symmetrical supercoil geometry matching the F-actin helix with an integral number of coiled-coil turns, a coiled-coil helical pitch of 137Å, a superhelical pitch of 770Å, and no localized pseudo-rotation. Over the middle 70% of tropomyosin, the average twisting of the coiled-coil deviates only by 10° from the canonical model and the torsional freedom is very small (std. dev. of 7°). This small degree of twisting cannot yield the orthogonal N- and C-termini configuration observed experimentally. In marked contrast, considerable coiled-coil unfolding, splaying and twisting at N- and C-terminal ends is observed, providing the conformational plasticity needed for head-to-tail nexus formation.
Collapse
Affiliation(s)
- William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA.
| | - Xiaochuan Edward Li
- Department of Physiology and Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA; Computational Biochemistry Group, IWR, University of Heidelberg, Im Neuenheimer Feld 368, Heidelberg D69120, Germany
| | - Marek Orzechowski
- Department of Physiology and Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA; Computational Biochemistry Group, IWR, University of Heidelberg, Im Neuenheimer Feld 368, Heidelberg D69120, Germany
| | - Stefan Fischer
- Computational Biochemistry Group, IWR, University of Heidelberg, Im Neuenheimer Feld 368, Heidelberg D69120, Germany.
| |
Collapse
|
48
|
Liu R, Holck AL, Yang E, Liu C, Xue W. Tropomyosin from tilapia (Oreochromis mossambicus) as an allergen. Clin Exp Allergy 2013; 43:365-77. [PMID: 23414545 DOI: 10.1111/cea.12056] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 09/24/2012] [Accepted: 10/24/2012] [Indexed: 01/01/2023]
Abstract
BACKGROUND Tilapia is among the most common fresh water fish species raised by fish farms and can cause allergic reactions upon ingestion. OBJECTIVE To investigate important allergens in Tilapia (Oreochromis mossambicus). METHODS Allergens were detected using immunoblotting. An important allergen was purified to homogeneity by reversed-phase High Pressure Liquid Chromatography and characterized by enzyme linked immunosorbent assay (ELISA), competitive ELISA, Mass spectrometry (MS), circular dichroism measurements and differential scanning calorimetry. RESULTS By immunoblotting using sera from 10 patients with confirmed tilapia allergy, we identified a number of allergens with apparent molecular weights 114 to 17 kD. All patients produced IgE against a 32 kD allergen, Ore m 4, which was identified by MS as tropomyosin (TM). IgE binding of the pure protein was confirmed by immunoblotting, ELISA and ELISA inhibition. cDNA from tilapia tropomyosin (TM) was sequenced and compared with TMs from other species. The tilapia TM showed 53.5% homology to TM from shrimp. Homology was much higher to human TM isoform 5 (87.7%). CONCLUSION AND CLINICAL RELEVANCE TMs are the major allergens in allergy to crustaceans. Auto-antibodies against human TM isoform 5 have been implicated as a causative agent in inflammatory bowel disease (IBD). Intriguingly, six of the 10 tilapia allergic patients had also been diagnosed with IBD, corroborating a connection between allergy and IBD. To our knowledge, this is the first report of tropomyosin from vertebrates as an allergen.
Collapse
Affiliation(s)
- R Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Haidian, Beijing, 100083, PR China
| | | | | | | | | |
Collapse
|
49
|
Barua B. Periodicities designed in the tropomyosin sequence and structure define its functions. BIOARCHITECTURE 2013; 3:51-6. [PMID: 23887197 DOI: 10.4161/bioa.25616] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Tropomyosin is an actin binding protein that regulates actin filament dynamics and its interactions with actin binding proteins such as myosin, tropomodulin, formin, Arp2/3 and ADF-cofilin in most eukaryotic cells. Tropomyosin is the prototypical two-chained, α-helical coiled coil protein that associates end-to-end and binds to both sides of the actin filament. Each tropomyosin molecule spans four to seven actin monomers in the filament, depending on the size of the tropomyosin. Tropomyosins have a periodic heptad repeat sequence that is characteristic of coiled coil proteins as well as additional periodicities required for its interaction with the actin filament, where each periodic repeat interacts with one actin molecule. This review addresses the role of periodic features of the Tm molecule in carrying out its universal functions of binding to the actin filament and its regulation and the specific features that may determine the isoform specificity of tropomyosins.
Collapse
Affiliation(s)
- Bipasha Barua
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Piscataway, NJ, USA.
| |
Collapse
|
50
|
Coffee Castro-Zena PG, Root DD. Asymmetric myosin binding to the thin filament as revealed by a fluorescent nanocircuit. Arch Biochem Biophys 2013; 535:14-21. [PMID: 23274408 PMCID: PMC3627744 DOI: 10.1016/j.abb.2012.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 12/07/2012] [Accepted: 12/11/2012] [Indexed: 11/15/2022]
Abstract
The interplay between myosin, actin, and striated muscle regulatory proteins involves complex cooperative interactions that propagate along the thin filament. A repeating unit of the tropomyosin dimer, troponin heterotrimer, and the actin protofilament heptamer is sometimes assumed to be able to bind myosin at any of its seven actins when activated even though the regulatory proteins are asymmetrically positioned along this repeating unit. Analysis of the impact of this asymmetry on actin and myosin interactions by sensitized emission luminescence resonance energy transfer spectroscopy and a unique fluorescent nanocircuit design reveals that the troponin affects the structure and function of myosin heads bound nearby in a different manner than myosin heads bound further away from the troponin. To test this hypothesis, a fluorescent nanocircuit reported the position of the myosin lever arm only when the myosin was bound adjacent to the troponin, or in controls, only when the myosin was bound distant from the troponin. Confirming the hypothesis, the myosin lever arm is predominantly in the pre powerstroke orientation when bound near troponin, but is predominantly in the post powerstroke orientation when bound distant from troponin. These data are consistent with the hypothesis that troponin is responsible for the formation of myosin binding target zones along the thin filament.
Collapse
|