1
|
Yeganeh FA, Summerill C, Hu Z, Rahmani H, Taylor DW, Taylor KA. The cryo-EM 3D image reconstruction of isolated Lethocerus indicus Z-discs. J Muscle Res Cell Motil 2023; 44:271-286. [PMID: 37661214 PMCID: PMC10843718 DOI: 10.1007/s10974-023-09657-1] [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: 02/14/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023]
Abstract
The Z-disk of striated muscle defines the ends of the sarcomere, which repeats many times within the muscle fiber. Here we report application of cryoelectron tomography and subtomogram averaging to Z-disks isolated from the flight muscles of the large waterbug Lethocerus indicus. We use high salt solutions to remove the myosin containing filaments and use gelsolin to remove the actin filaments of the A- and I-bands leaving only the thin filaments within the Z-disk which were then frozen for cryoelectron microscopy. The Lethocerus Z-disk structure is similar in many ways to the previously studied Z-disk of the honeybee Apis mellifera. At the corners of the unit cell are positioned trimers of paired antiparallel F-actins defining a large solvent channel, whereas at the trigonal positions are positioned F-actin trimers converging slowly towards their (+) ends defining a small solvent channel through the Z-disk. These near parallel F-actins terminate at different Z-heights within the Z-disk. The two types of solvent channel in Lethocerus are similar in size compared to those of Apis which are very different in size. Two types of α-actinin crosslinks were observed between oppositely oriented actin filaments. In one of these, the α-actinin long axis is almost parallel to the F-actins it crosslinks. In the other, the α-actinins are at a small but distinctive angle with respect to the crosslinked actin filaments. The utility of isolated Z-disks for structure determination is discussed.
Collapse
Affiliation(s)
- Fatemeh Abbasi Yeganeh
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Corinne Summerill
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
- Department of Life and Earth Sciences, Perimeter College, Georgia State University, 33 Gilmer Street SE, Atlanta, GA, 30303, USA
| | - Zhongjun Hu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
- Facebook, Inc, 1 Hacker Way, Menlo Park, CA, 94025, USA
| | - Hamidreza Rahmani
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dianne W Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Kenneth A Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA.
| |
Collapse
|
2
|
Smith SM, Larocque G, Wood KM, Morris KL, Roseman AM, Sessions RB, Royle SJ, Smith CJ. Multi-modal adaptor-clathrin contacts drive coated vesicle assembly. EMBO J 2021; 40:e108795. [PMID: 34487371 PMCID: PMC8488560 DOI: 10.15252/embj.2021108795] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
Clathrin‐coated pits are formed by the recognition of membrane and cargo by the AP2 complex and the subsequent recruitment of clathrin triskelia. A role for AP2 in coated‐pit assembly beyond initial clathrin recruitment has not been explored. Clathrin binds the β2 subunit of AP2, and several binding sites have been identified, but our structural knowledge of these interactions is incomplete and their functional importance during endocytosis is unclear. Here, we analysed the cryo‐EM structure of clathrin cages assembled in the presence of β2 hinge‐appendage (β2HA). We find that the β2‐appendage binds in at least two positions in the cage, demonstrating that multi‐modal binding is a fundamental property of clathrin‐AP2 interactions. In one position, β2‐appendage cross‐links two adjacent terminal domains from different triskelia. Functional analysis of β2HA‐clathrin interactions reveals that endocytosis requires two clathrin interaction sites: a clathrin‐box motif on the hinge and the “sandwich site” on the appendage. We propose that β2‐appendage binding to more than one triskelion is a key feature of the system and likely explains why assembly is driven by AP2.
Collapse
Affiliation(s)
- Sarah M Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Gabrielle Larocque
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Kyle L Morris
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Alan M Roseman
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK
| | - Corinne J Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| |
Collapse
|
3
|
Abstract
After several decades studying different acto-myosin complexes at lower and intermediate resolution - limited by the electron microscope instrumentation available then - recent advances in imaging technology have been crucial for obtaining a number of excellent high-resolution 3D reconstructions from cryo electron microscopy. The resolution level reached now is about 3-4 Å, which allows unambiguous model building of filamentous actin on its own as well as that of actin filaments decorated with strongly bound myosin variants. The interface between actin and the myosin motor domain can now be described in detail, and the function of parts of the interface (such as, e.g., the cardiomyopathy loop) can be understood in a mechanistical way. Most recently, reconstructions of actin filaments decorated with different myosins, which show a strongly bound acto-myosin complex also in the presence of the nucleotide ADP, have become available. The comparison of these structures with the nucleotide-free Rigor state provide the first mechanistic description of force sensing. An open question is still the initial interaction of the motor domain of myosin with the actin filament. Such weakly interacting states have so far not been the subject of microscopical studies, even though high-resolution structures would be needed to shed light on the initial steps of phosphate release and power stroke initiation.
Collapse
|
4
|
Bradshaw M, Paul DM. After the revolution: how is Cryo-EM contributing to muscle research? J Muscle Res Cell Motil 2019; 40:93-98. [PMID: 31302812 PMCID: PMC6726666 DOI: 10.1007/s10974-019-09537-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022]
Abstract
The technique of electron microscopy (EM) has been fundamental to muscle research since the days of Huxley and Hanson. Direct observation of how proteins in the sarcomere are arranged and visualising the changes that occur upon activation have greatly increased our understanding of function. In the 1980s specimen preparation techniques for biological EM moved away from traditional fixing and staining. The technique known as cryo-electron microscopy (Cryo-EM) was developed, which involves rapidly freezing proteins in liquid ethane which maintains them in a near native state. Within the last 5 years there has been a step change in the achievable resolution using Cryo-EM. This ‘resolution revolution’ can be attributed to advances in detector technology, microscope automation and maximum likelihood image processing. In this article we look at how Cryo-EM has contributed to the field of muscle research in this post revolution era, focussing on recently published high resolution structures of sarcomeric proteins.
Collapse
Affiliation(s)
- Marston Bradshaw
- Department of Physiology & Pharmacology, University of Bristol, Bristol, BS8 1TD, UK
| | - Danielle M Paul
- Department of Physiology & Pharmacology, University of Bristol, Bristol, BS8 1TD, UK.
| |
Collapse
|
5
|
Marques MA, Parvatiyar MS, Yang W, de Oliveira GAP, Pinto JR. The missing links within troponin. Arch Biochem Biophys 2018; 663:95-100. [PMID: 30584890 DOI: 10.1016/j.abb.2018.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/18/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023]
Abstract
The cardiac contraction-relaxation cycle is controlled by a sophisticated set of machinery. Of particular interest, is the revelation that allosteric networks transmit effects of binding at one site to influence troponin complex dynamics and structural-mediated signaling in often distal, functional sites in the myofilament. Our recent observations provide compelling evidence that allostery can explain the function of large-scale macromolecular events. Here we elaborate on our recent findings of interdomain communication within troponin C, using cutting-edge structural biology approaches, and highlight the importance of unveiling the unknown, distant communication networks within this system to obtain more comprehensive knowledge of how allostery impacts cardiac physiology and disease.
Collapse
Affiliation(s)
- Mayra A Marques
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michelle S Parvatiyar
- Department of Nutrition, Food and Exercise Sciences, Florida State University, 107 Chieftan Way, Tallahassee, FL, 32306-1493, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, Kasha Laboratory Building, 91 Chieftan Way, Tallahassee, FL, 32306-4380, USA
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908-0733, USA.
| | - Jose R Pinto
- Department of Biomedical Sciences, Florida State University College of Medicine, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA.
| |
Collapse
|
6
|
Drulyte I, Johnson RM, Hesketh EL, Hurdiss DL, Scarff CA, Porav SA, Ranson NA, Muench SP, Thompson RF. Approaches to altering particle distributions in cryo-electron microscopy sample preparation. Acta Crystallogr D Struct Biol 2018; 74:560-571. [PMID: 29872006 PMCID: PMC6096488 DOI: 10.1107/s2059798318006496] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/26/2018] [Indexed: 11/23/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) can now be used to determine high-resolution structural information on a diverse range of biological specimens. Recent advances have been driven primarily by developments in microscopes and detectors, and through advances in image-processing software. However, for many single-particle cryo-EM projects, major bottlenecks currently remain at the sample-preparation stage; obtaining cryo-EM grids of sufficient quality for high-resolution single-particle analysis can require the careful optimization of many variables. Common hurdles to overcome include problems associated with the sample itself (buffer components, labile complexes), sample distribution (obtaining the correct concentration, affinity for the support film), preferred orientation, and poor reproducibility of the grid-making process within and between batches. This review outlines a number of methodologies used within the electron-microscopy community to address these challenges, providing a range of approaches which may aid in obtaining optimal grids for high-resolution data collection.
Collapse
Affiliation(s)
- Ieva Drulyte
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Rachel M. Johnson
- School of Biomedical Sciences, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry, Faculty of Mathematics and Physical Chemistry and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Emma L. Hesketh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Daniel L. Hurdiss
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Charlotte A. Scarff
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Sebastian A. Porav
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Neil A. Ranson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Rebecca F. Thompson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| |
Collapse
|
7
|
Actin genes and their expression in pacific white shrimp, Litopenaeus vannamei. Mol Genet Genomics 2017; 293:479-493. [PMID: 29189957 DOI: 10.1007/s00438-017-1397-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/18/2017] [Indexed: 10/18/2022]
Abstract
Actin is a multi-functional gene family that can be divided into muscle-type actins and non-muscle-type actins. In this study, 37 unigenes encoding actins were identified from RNA-Seq data of Pacific white shrimp, Litopenaeus vannamei. According to phylogenetic analysis, four and three cDNAs belong to cytoplasmic- and heart-type actins and were named LvActinCT and LvActinHT, respectively. 10 cDNAs belong to the slow-type skeletal muscle actins, and 18 belong to the fast-type skeletal muscle actins; they were designated LvActinSSK and LvActinFSK, respectively. Some muscle actin genes formed gene clusters in the genome. Multiple alternative transcription starts sites (ATSSs) were found for LvActinCT1. Based on the early developmental expression profile, almost all LvActins were highly expressed between the early limb bud and post-larval stages. Using LvActinSSK5 as probes, slow-type muscle was localized in pleopod muscle and superficial ventral muscle. We also found three actin genes that were down-regulated in the hemocytes of white spot syndrome virus (WSSV)- and Vibrio parahaemolyticus-infected L. vannamei. This study provides valuable information on the actin gene structure of shrimp, furthers our understanding of the shrimp muscle system and helps us develop strategies for disease control and sustainable shrimp farming.
Collapse
|
8
|
Banerjee C, Hu Z, Huang Z, Warrington JA, Taylor DW, Trybus KM, Lowey S, Taylor KA. The structure of the actin-smooth muscle myosin motor domain complex in the rigor state. J Struct Biol 2017; 200:325-333. [PMID: 29038012 DOI: 10.1016/j.jsb.2017.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 01/08/2023]
Abstract
Myosin-based motility utilizes catalysis of ATP to drive the relative sliding of F-actin and myosin. The earliest detailed model based on cryo-electron microscopy (cryoEM) and X-ray crystallography postulated that higher actin affinity and lever arm movement were coupled to closure of a feature of the myosin head dubbed the actin-binding cleft. Several studies since then using crystallography of myosin-V and cryoEM structures of F-actin bound myosin-I, -II and -V have provided details of this model. The smooth muscle myosin II interaction with F-actin may differ from those for striated and non-muscle myosin II due in part to different lengths of important surface loops. Here we report a ∼6 Å resolution reconstruction of F-actin decorated with the nucleotide-free recombinant smooth muscle myosin-II motor domain (MD) from images recorded using a direct electron detector. Resolution is highest for F-actin and the actin-myosin interface (3.5-4 Å) and lowest (∼6-7 Å) for those parts of the MD at the highest radius. Atomic models built into the F-actin density are quite comparable to those previously reported for rabbit muscle actin and show density from the bound ADP. The atomic model of the MD, is quite similar to a recently published structure of vertebrate non-muscle myosin II bound to F-actin and a crystal structure of nucleotide free myosin-V. Larger differences are observed when compared to the cryoEM structure of F-actin decorated with rabbit skeletal muscle myosin subfragment 1. The differences suggest less closure of the 50 kDa domain in the actin bound skeletal muscle myosin structure.
Collapse
Affiliation(s)
- Chaity Banerjee
- Department of Computer Science, Florida State University, Tallahassee, FL 32306-4530, United States
| | - Zhongjun Hu
- Institute of Molecular Biophysics, Kasha Laboratory, Florida State University, Tallahassee, FL 32306-4380, United States
| | - Zhong Huang
- Institute of Molecular Biophysics, Kasha Laboratory, Florida State University, Tallahassee, FL 32306-4380, United States
| | - J Anthony Warrington
- Institute of Molecular Biophysics, Kasha Laboratory, Florida State University, Tallahassee, FL 32306-4380, United States
| | - Dianne W Taylor
- Institute of Molecular Biophysics, Kasha Laboratory, Florida State University, Tallahassee, FL 32306-4380, United States
| | - Kathleen M Trybus
- Health Science Research Facility 130, 149 Beaumont Avenue, Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT 05405, United States
| | - Susan Lowey
- Health Science Research Facility 130, 149 Beaumont Avenue, Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT 05405, United States
| | - Kenneth A Taylor
- Institute of Molecular Biophysics, Kasha Laboratory, Florida State University, Tallahassee, FL 32306-4380, United States.
| |
Collapse
|
9
|
Rangel-Zúñiga OA, Camargo A, Marin C, Peña-Orihuela P, Pérez-Martínez P, Delgado-Lista J, González-Guardia L, Yubero-Serrano EM, Tinahones FJ, Malagón MM, Pérez-Jiménez F, Roche HM, López-Miranda J. Proteome from patients with metabolic syndrome is regulated by quantity and quality of dietary lipids. BMC Genomics 2015; 16:509. [PMID: 26152126 PMCID: PMC4493955 DOI: 10.1186/s12864-015-1725-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/26/2015] [Indexed: 01/22/2023] Open
Abstract
Background Metabolic syndrome is a multi-component disorder associated to a high risk of cardiovascular disease. Its etiology is the result of a complex interaction between genetic and environmental factors, including dietary habits. We aimed to identify the target proteins modulated by the long-term consumption of four diets differing in the quality and quantity of lipids in the whole proteome of peripheral blood mononuclear cells (PBMC). Results A randomized, controlled trial conducted within the LIPGENE study assigned 24 MetS patients for 12 weeks each to 1 of 4 diets: a) high-saturated fatty acid (HSFA), b) high-monounsaturated fatty acid (HMUFA), c) low-fat, high-complex carbohydrate diets supplemented with placebo (LFHCC) and d) low-fat, high-complex carbohydrate diets supplemented with long chain (LC) n-3 polyunsaturated fatty acids (PUFA) (LFHCC n-3). We analyzed the changes induced in the proteome of both nuclear and cytoplasmic fractions of PBMC using 2-D proteomic analysis. Sixty-seven proteins were differentially expressed after the long-term consumption of the four diets. The HSFA diet induced the expression of proteins responding to oxidative stress, degradation of ubiquitinated proteins and DNA repair. However, HMUFA, LFHCC and LFHCC n-3 diets down-regulated pro-inflammatory and oxidative stress-related proteins and DNA repairing proteins. Conclusion The long-term consumption of HSFA, compared to HMUFA, LFHCC and LFHCC n-3, seems to increase the cardiovascular disease (CVD) risk factors associated with metabolic syndrome, such as inflammation and oxidative stress, and seem lead to DNA damage as a consequence of high oxidative stress. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1725-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Oriol Alberto Rangel-Zúñiga
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Antonio Camargo
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Carmen Marin
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Patricia Peña-Orihuela
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Pablo Pérez-Martínez
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Javier Delgado-Lista
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Lorena González-Guardia
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Elena M Yubero-Serrano
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Francisco J Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain. .,Endocrinology and Nutrition Service, Hospital Virgen de la Victoria, Málaga, Spain.
| | - María M Malagón
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain. .,Department of Cell Biology, Physiology, and Immunology, IMIBIC/Reina Sofia University Hospital/University of Córdoba, Cordoba, Spain.
| | - Francisco Pérez-Jiménez
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Helen M Roche
- UCD Institute of Food & Health/UCD Conway Institute, School of Public Health and Population Sciences, University College Dublin, Dublin, Ireland.
| | - José López-Miranda
- Lipids and Atherosclerosis Research Unit, IMIBIC/Reina Sofia University Hospital, University of Cordoba, Av. Menendez Pidal s/n. 14004, Córdoba, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
10
|
WAKABAYASHI T. Mechanism of the calcium-regulation of muscle contraction--in pursuit of its structural basis. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2015; 91:321-50. [PMID: 26194856 PMCID: PMC4631897 DOI: 10.2183/pjab.91.321] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/01/2015] [Indexed: 06/10/2023]
Abstract
The author reviewed the research that led to establish the structural basis for the mechanism of the calcium-regulation of the contraction of striated muscles. The target of calcium ions is troponin on the thin filaments, of which the main component is the double-stranded helix of actin. A model of thin filament was generated by adding tropomyosin and troponin. During the process to provide the structural evidence for the model, the troponin arm was found to protrude from the calcium-depleted troponin and binds to the carboxyl-terminal region of actin. As a result, the carboxyl-terminal region of tropomyosin shifts and covers the myosin-binding sites of actin to block the binding of myosin. At higher calcium concentrations, the troponin arm changes its partner from actin to the main body of calcium-loaded troponin. Then, tropomyosin shifts back to the position near the grooves of actin double helix, and the myosin-binding sites of actin becomes available to myosin resulting in force generation through actin-myosin interactions.
Collapse
Affiliation(s)
- Takeyuki WAKABAYASHI
- Department of Physics, Graduate School of Science, the University of Tokyo, Tokyo, Japan
- Department of Biosciences, Graduate School of Science and Engineering, Teikyo University, Tochigi, Japan
| |
Collapse
|
11
|
Lyumkis D, Julien JP, de Val N, Cupo A, Potter CS, Klasse PJ, Burton DR, Sanders RW, Moore JP, Carragher B, Wilson IA, Ward AB. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science 2013; 342:1484-90. [PMID: 24179160 PMCID: PMC3954647 DOI: 10.1126/science.1245627] [Citation(s) in RCA: 589] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1, and HR2 domains, as well as shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described.
Collapse
Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jean-Philippe Julien
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Albert Cupo
- Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Per Johan Klasse
- Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Dennis R. Burton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Rogier W. Sanders
- Weill Medical College of Cornell University, New York, New York 10021, USA
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, Netherlands
| | - John P. Moore
- Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA
| |
Collapse
|
12
|
Viswanathan MC, Kaushik G, Engler AJ, Lehman W, Cammarato A. A Drosophila melanogaster model of diastolic dysfunction and cardiomyopathy based on impaired troponin-T function. Circ Res 2013; 114:e6-17. [PMID: 24221941 DOI: 10.1161/circresaha.114.302028] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RATIONALE Regulation of striated muscle contraction is achieved by Ca2+ -dependent steric modulation of myosin cross-bridge cycling on actin by the thin filament troponin-tropomyosin complex. Alterations in the complex can induce contractile dysregulation and disease. For example, mutations between or near residues 112 to 136 of cardiac troponin-T, the crucial TnT1 (N-terminal domain of troponin-T)-tropomyosin-binding region, cause cardiomyopathy. The Drosophila upheld(101) Glu/Lys amino acid substitution lies C-terminally adjacent to this phylogenetically conserved sequence. OBJECTIVE Using a highly integrative approach, we sought to determine the molecular trigger of upheld(101) myofibrillar degeneration, to evaluate contractile performance in the mutant cardiomyocytes, and to examine the effects of the mutation on the entire Drosophila heart to elucidate regulatory roles for conserved TnT1 regions and provide possible mechanistic insight into cardiac dysfunction. METHODS AND RESULTS Live video imaging of Drosophila cardiac tubes revealed that the troponin-T mutation prolongs systole and restricts diastolic dimensions of the heart, because of increased numbers of actively cycling myosin cross-bridges. Elevated resting myocardial stiffness, consistent with upheld(101) diastolic dysfunction, was confirmed by an atomic force microscopy-based nanoindentation approach. Direct visualization of mutant thin filaments via electron microscopy and 3-dimensional reconstruction resolved destabilized tropomyosin positioning and aberrantly exposed myosin-binding sites under low Ca2+ conditions. CONCLUSIONS As a result of troponin-tropomyosin dysinhibition, upheld(101) hearts exhibited cardiac dysfunction and remodeling comparable to that observed during human restrictive cardiomyopathy. Thus, reversal of charged residues about the conserved tropomyosin-binding region of TnT1 may perturb critical intermolecular associations required for proper steric regulation, which likely elicits myopathy in our Drosophila model.
Collapse
Affiliation(s)
- Meera Cozhimuttam Viswanathan
- From the Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (M.C.V., A.C.); Department of Bioengineering, University of California, San Diego, La Jolla, CA (G.K., A.J.E.); and Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA (W.L.)
| | | | | | | | | |
Collapse
|
13
|
Gomibuchi Y, Uyeda TQP, Wakabayashi T. Bulkiness or aromatic nature of tyrosine-143 of actin is important for the weak binding between F-actin and myosin-ADP-phosphate. Biochem Biophys Res Commun 2013; 441:844-8. [PMID: 24211213 DOI: 10.1016/j.bbrc.2013.10.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 10/28/2013] [Indexed: 11/24/2022]
Abstract
Actin filaments (F-actin) interact with myosin and activate its ATPase to support force generation. By comparing crystal structures of G-actin and the quasi-atomic model of F-actin based on high-resolution cryo-electron microscopy, the tyrosine-143 was found to be exposed more than 60Å(2) to the solvent in F-actin. Because tyrosine-143 flanks the hydrophobic cleft near the hydrophobic helix that binds to myosin, the mutant actins, of which the tyrosine-143 was replaced with tryptophan, phenylalanine, or isoleucine, were generated using the Dictyostelium expression system. It polymerized significantly poorly when induced by NaCl, but almost normally by KCl. In the presence of phalloidin and KCl, the extents of the polymerization of all the mutant actins were comparable to that of the wild-type actin so that the actin-activated myosin ATPase activity could be reliably compared. The affinity of skeletal heavy meromyosin to F-actin and the maximum ATPase activity (Vmax) were estimated by a double reciprocal plot. The Tyr143Trp-actin showed the higher affinity (smaller Kapp) than that of the wild-type actin, with the Vmax being almost unchanged. The Kapp and Vmax of the Tyr143Phe-actin were similar to those of the wild-type actin. However, the activation by Tyr143Ile-actin was much smaller than the wild-type actin and the accurate determination of Kapp was difficult. Comparison of the myosin ATPase activated by the various mutant actins at the same concentration of F-actin showed that the extent of activation correlates well with the solvent-accessible surface areas (ASA) of the replaced amino acid molecule. Because 1/Kapp reflects the affinity of F-actin for the myosin-ADP-phosphate intermediate (M.ADP.Pi) through the weak binding, these data suggest that the bulkiness or the aromatic nature of the tyrosin-143 is important for the initial binding of the M.ADP.Pi intermediate with F-actin but not for later processes such as the phosphate release.
Collapse
Affiliation(s)
- Yuki Gomibuchi
- Graduate School of Science and Engineering, Teikyo University, Toyosatodai 1-1, Utsunomiya 320-8551, Japan
| | | | | |
Collapse
|
14
|
Gonzalez MA, Cope J, Rank KC, Chen CJ, Tittmann P, Rayment I, Gilbert SP, Hoenger A. Common mechanistic themes for the powerstroke of kinesin-14 motors. J Struct Biol 2013; 184:335-44. [PMID: 24099757 PMCID: PMC3851574 DOI: 10.1016/j.jsb.2013.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 09/19/2013] [Accepted: 09/25/2013] [Indexed: 01/06/2023]
Abstract
Kar3Cik1 is a heterodimeric kinesin-14 from Saccharomyces cerevisiae involved in spindle formation during mitosis and karyogamy in mating cells. Kar3 represents a canonical kinesin motor domain that interacts with microtubules under the control of ATP-hydrolysis. In vivo, the localization and function of Kar3 is differentially regulated by its interacting stoichiometrically with either Cik1 or Vik1, two closely related motor homology domains that lack the nucleotide-binding site. Indeed, Vik1 structurally resembles the core of a kinesin head. Despite being closely related, Kar3Cik1 and Kar3Vik1 are each responsible for a distinct set of functions in vivo and also display different biochemical behavior in vitro. To determine a structural basis for their distinct functional abilities, we used cryo-electron microscopy and helical reconstruction to investigate the 3-D structure of Kar3Cik1 complexed to microtubules in various nucleotide states and compared our 3-D data of Kar3Cik1 with that of Kar3Vik1 and the homodimeric kinesin-14 Ncd from Drosophila melanogaster. Due to the lack of an X-ray crystal structure of the Cik1 motor homology domain, we predicted the structure of this Cik1 domain based on sequence similarity to its relatives Vik1, Kar3 and Ncd. By molecular docking into our 3-D maps, we produced a detailed near-atomic model of Kar3Cik1 complexed to microtubules in two distinct nucleotide states, a nucleotide-free state and an ATP-bound state. Our data show that despite their functional differences, heterodimeric Kar3Cik1 and Kar3Vik1 and homodimeric Ncd, all share striking structural similarities at distinct nucleotide states indicating a common mechanistic theme within the kinesin-14 family.
Collapse
Affiliation(s)
- Miguel A. Gonzalez
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | - Julia Cope
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | - Katherine C. Rank
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Chun Ju Chen
- Department of Biology and the Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter Tittmann
- EMEZ, Swiss Federal Institute of Technology, Hoenggerberg, 8093 Zuerich, Switzerland
| | - Ivan Rayment
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Susan P. Gilbert
- Department of Biology and the Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Andreas Hoenger
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| |
Collapse
|
15
|
Young A, Stoilova-McPhie S, Rothnie A, Vallis Y, Harvey-Smith P, Ranson N, Kent H, Brodsky FM, Pearse BMF, Roseman A, Smith CJ. Hsc70-induced changes in clathrin-auxilin cage structure suggest a role for clathrin light chains in cage disassembly. Traffic 2013; 14:987-96. [PMID: 23710728 PMCID: PMC3776051 DOI: 10.1111/tra.12085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/21/2013] [Accepted: 05/25/2013] [Indexed: 01/28/2023]
Abstract
The molecular chaperone, Hsc70, together with its co-factor, auxilin, facilitates the ATP-dependent removal of clathrin during clathrin-mediated endocytosis in cells. We have used cryo-electron microscopy to determine the 3D structure of a complex of clathrin, auxilin401-910 and Hsc70 at pH 6 in the presence of ATP, frozen within 20 seconds of adding Hsc70 in order to visualize events that follow the binding of Hsc70 to clathrin and auxilin before clathrin disassembly. In this map, we observe density beneath the vertex of the cage that we attribute to bound Hsc70. This density emerges asymmetrically from the clathrin vertex, suggesting preferential binding by Hsc70 for one of the three possible sites at the vertex. Statistical comparison with a map of whole auxilin and clathrin previously published by us reveals the location of statistically significant differences which implicate involvement of clathrin light chains in structural rearrangements which occur after Hsc70 is recruited. Clathrin disassembly assays using light scattering suggest that loss of clathrin light chains reduces the efficiency with which auxilin facilitates this reaction. These data support a regulatory role for clathrin light chains in clathrin disassembly in addition to their established role in regulating clathrin assembly.
Collapse
Affiliation(s)
- Anna Young
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Uddowla MH, Salma U, Kim HW. Molecular characterization of four actin cDNAs and effects of 20-hydroxyecdysone on their expression in swimming crab,Portunus trituberculatus(Miers, 1876). Anim Cells Syst (Seoul) 2013. [DOI: 10.1080/19768354.2013.799100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
17
|
Regulation of actin-myosin interaction by conserved periodic sites of tropomyosin. Proc Natl Acad Sci U S A 2012; 109:18425-30. [PMID: 23091026 DOI: 10.1073/pnas.1212754109] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cooperative activation of actin-myosin interaction by tropomyosin (Tm) is central to regulation of contraction in muscle cells and cellular and intracellular movements in nonmuscle cells. The steric blocking model of muscle regulation proposed 40 y ago has been substantiated at both the kinetic and structural levels. Even with atomic resolution structures of the major players, how Tm binds and is designed for regulatory function has remained a mystery. Here we show that a set of periodically distributed evolutionarily conserved surface residues of Tm is required for cooperative regulation of actomyosin. Based on our results, we propose a model of Tm on a structure of actin-Tm-myosin in the "open" (on) state showing potential electrostatic interactions of the residues with both actin and myosin. The sites alternate with a second set of conserved surface residues that are important for actin binding in the inhibitory state in the absence of myosin. The transition from the closed to open states requires the sites identified here, even when troponin + Ca(2+) is present. The evolutionarily conserved residues are important for actomyosin regulation, a universal function of Tm that has a common structural basis and mechanism.
Collapse
|
18
|
Suphamungmee W, Nakamura F, Hartwig JH, Lehman W. Electron microscopy and 3D reconstruction reveals filamin Ig domain binding to F-actin. J Mol Biol 2012; 424:248-56. [PMID: 23041423 DOI: 10.1016/j.jmb.2012.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/24/2012] [Accepted: 09/28/2012] [Indexed: 11/24/2022]
Abstract
Filamin A (FLNa) is an actin-binding protein that cross-links F-actin into networks of orthogonally branched filaments. FLNa also directs the networks to integrins while responding to mechanochemical signaling pathways. Flexible, 160-nm-long FLNa molecules are tail-to-tail dimers, each subunit of which contains an N-terminal calponin homology (CH)/actin-binding domain connected by a series of 24 immunoglobulin (Ig) repeats to a dimerization site at their C-terminal end. Whereas the contribution of the CH domains to F-actin affinity is weak (apparent K(a)~10(5)), the binding of the intact protein to F-actin is strong (apparent K(a)~10(8)), suggesting involvement of additional parts of the molecule in this association. Indeed, previous results indicate that Ig repeats along FLNa contribute significantly to the strength of the actin filament interaction. In the current study, we used electron microscopy and three-dimensional reconstruction to elucidate the structural basis of the Ig repeat-F-actin binding. We find that FLNa density is clearly delineated in reconstructions of F-actin complexed either with a four-Ig-repeat segment of FLNa containing Ig repeat 10 or with immunoglobulin-like filamin A repeat (IgFLNa)10 alone. The mass attributable to IgFLNa10 lies peripherally along the actin helix over the N-terminus of actin subdomain 1. The IgFLNa10 interaction appears to be specific, since no other individual Ig repeat or fragment of the FLNa molecule examined, besides ones with IgFLNa10 or CH domains, decorated F-actin filaments or were detected in reconstructions. We conclude that the combined interactions of CH domains and the IgFLNa10 repeat provide the binding strength of the whole FLNa molecule and propose a model for the association of IgFLNa10 on actin filaments.
Collapse
Affiliation(s)
- Worawit Suphamungmee
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | | |
Collapse
|
19
|
Behrmann E, Müller M, Penczek PA, Mannherz HG, Manstein DJ, Raunser S. Structure of the rigor actin-tropomyosin-myosin complex. Cell 2012; 150:327-38. [PMID: 22817895 DOI: 10.1016/j.cell.2012.05.037] [Citation(s) in RCA: 267] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/13/2012] [Accepted: 05/20/2012] [Indexed: 01/13/2023]
Abstract
Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions within the complex and the trajectory of tropomyosin movement between its "open" and "closed" positions on the actin filament. Here, we report the 8 Å resolution structure of the rigor (nucleotide-free) actin-tropomyosin-myosin complex determined by cryo-electron microscopy. The pseudoatomic model of the complex, obtained from fitting crystal structures into the map, defines the large interface involving two adjacent actin monomers and one tropomyosin pseudorepeat per myosin contact. Severe forms of hereditary myopathies are linked to mutations that critically perturb this interface. Myosin binding results in a 23 Å shift of tropomyosin along actin. Complex domain motions occur in myosin, but not in actin. Based on our results, we propose a structural model for the tropomyosin-dependent modulation of myosin binding to actin.
Collapse
Affiliation(s)
- Elmar Behrmann
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | | | | | | | | | | |
Collapse
|
20
|
Unwin N, Fujiyoshi Y. Gating movement of acetylcholine receptor caught by plunge-freezing. J Mol Biol 2012; 422:617-634. [PMID: 22841691 PMCID: PMC3443390 DOI: 10.1016/j.jmb.2012.07.010] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/06/2012] [Accepted: 07/10/2012] [Indexed: 11/19/2022]
Abstract
The nicotinic acetylcholine (ACh) receptor converts transiently to an open-channel form when activated by ACh released into the synaptic cleft. We describe here the conformational change underlying this event, determined by electron microscopy of ACh-sprayed and freeze-trapped postsynaptic membranes. ACh binding to the α subunits triggers a concerted rearrangement in the ligand-binding domain, involving an ~1-Å outward displacement of the extracellular portion of the β subunit where it interacts with the juxtaposed ends of α-helices shaping the narrow membrane-spanning pore. The β-subunit helices tilt outward to accommodate this displacement, destabilising the arrangement of pore-lining helices, which in the closed channel bend inward symmetrically to form a central hydrophobic gate. Straightening and tangential motion of the pore-lining helices effect channel opening by widening the pore asymmetrically and increasing its polarity in the region of the gate. The pore-lining helices of the α(γ) and δ subunits, by flexing between alternative bent and straight conformations, undergo the greatest movements. This coupled allosteric transition shifts the structure from a tense (closed) state toward a more relaxed (open) state.
Collapse
Affiliation(s)
- Nigel Unwin
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
| | - Yoshinori Fujiyoshi
- Department of Biophysics, Faculty of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|
21
|
Behrmann E, Tao G, Stokes DL, Egelman EH, Raunser S, Penczek PA. Real-space processing of helical filaments in SPARX. J Struct Biol 2012; 177:302-13. [PMID: 22248449 DOI: 10.1016/j.jsb.2011.12.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 11/18/2022]
Abstract
We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional features include a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy.
Collapse
Affiliation(s)
- Elmar Behrmann
- Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | | | | | | | | | | |
Collapse
|
22
|
Jensen MH, Watt J, Hodgkinson J, Gallant C, Appel S, El-Mezgueldi M, Angelini TE, Morgan KG, Lehman W, Moore JR. Effects of basic calponin on the flexural mechanics and stability of F-actin. Cytoskeleton (Hoboken) 2012; 69:49-58. [PMID: 22135101 PMCID: PMC3355516 DOI: 10.1002/cm.20548] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Revised: 10/28/2011] [Accepted: 11/14/2011] [Indexed: 01/12/2023]
Abstract
The cellular actin cytoskeleton plays a central role in the ability of cells to properly sense, propagate, and respond to external stresses and other mechanical stimuli. Calponin, an actin-binding protein found both in muscle and non-muscle cells, has been implicated in actin cytoskeletal organization and regulation. In this work, we studied the mechanical and structural interaction of actin with basic calponin, a differentiation marker in smooth muscle cells, on a single filament level. We imaged fluorescently labeled thermally fluctuating actin filaments and found that at moderate calponin binding densities, actin filaments were more flexible, evident as a reduction in persistence length from 8.0 to 5.8 μm. When calponin-decorated actin filaments were subjected to shear, we observed a marked reduction of filament lengths after decoration with calponin, which we argue was due to shear-induced filament rupture rather than depolymerization. This increased shear susceptibility was exacerbated with calponin concentration. Cryo-electron microscopy results confirmed previously published negative stain electron microscopy results and suggested alterations in actin involving actin subdomain 2. A weakening of F-actin intermolecular association is discussed as the underlying cause of the observed mechanical perturbations.
Collapse
Affiliation(s)
- Mikkel Herholdt Jensen
- Boston University, School of Medicine, Boston, MA
- Boston University, Department of Physics, Boston, MA
| | - James Watt
- Boston University, School of Medicine, Boston, MA
| | - Julie Hodgkinson
- Medical School Hannover, Department of Molecular and Cell Physiology, Hannover, Germany
| | - Cynthia Gallant
- Boston University, Department of Health Sciences, Boston, MA
| | - Sarah Appel
- Boston University, Department of Health Sciences, Boston, MA
| | | | - Thomas E. Angelini
- University of Florida, Department of Mechanical and Aerospace Engineering, Gainesville, FL
| | | | | | | |
Collapse
|
23
|
Bouchet-Marquis C, Pagratis M, Kirmse R, Hoenger A. Metallothionein as a clonable high-density marker for cryo-electron microscopy. J Struct Biol 2012; 177:119-27. [PMID: 22068155 PMCID: PMC3261350 DOI: 10.1016/j.jsb.2011.10.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 11/24/2022]
Abstract
Cryo-electron microscopy is expanding its scope from macromolecules towards much larger and more complex cellular specimens such as organelles, cells and entire tissues. While isolated macromolecular specimens are typically composed of only very few different components that may be recognized by their shape, size or state of polymerization, cellular specimens combine large numbers of proteinaceous structures as well as nucleic acids and lipid arrays. Consequently, an unambiguous identification of these structures within the context of a whole cell may create a very difficult challenge. On plastic-embedded specimens, or Tokuyasu sections (Tokuyasu, 1980), epitopes that are exposed at the surface can be tagged by antibodies. However, vitrified sections have to be kept at strict cryo-conditions (below -140 °C) and therefore do not allow any post-sectioning treatment of the specimens other than data acquisition in the microscope. Hence, the labels have to be placed into the specimen before freezing. Here we report on the application of a small metal-clustering protein, metallothionein (MTH), as a clonable label capable of clustering metal atoms into a high-density particle with high spatial resolution. We tested MTH as a label for kinesin-decorated microtubules (MTs) as well as the building blocks of desmin intermediate filaments (IFs).
Collapse
Affiliation(s)
| | | | | | - Andreas Hoenger
- Dept. of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder CO, 80309-0347, USA
| |
Collapse
|
24
|
Fisher LS, Ward A, Milligan RA, Unwin N, Potter CS, Carragher B. A helical processing pipeline for EM structure determination of membrane proteins. Methods 2011; 55:350-62. [PMID: 21964395 PMCID: PMC3262078 DOI: 10.1016/j.ymeth.2011.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/07/2011] [Accepted: 09/13/2011] [Indexed: 01/27/2023] Open
Abstract
Electron crystallography plays a key role in the structural biology of integral membrane proteins (IMPs) by offering one of the most direct means of providing insight into the functional state of these molecular machines in their lipid-associated forms, and also has the potential to facilitate examination of physiologically relevant transitional states and complexes. Helical or tubular crystals, which are the natural product of proteins crystallizing on the surface of a cylindrical vesicle, offer some unique advantages, such as three-dimensional (3D) information from a single view, compared to other crystalline forms. While a number of software packages are available for processing images of helical crystals to produce 3D electron density maps, widespread exploitation of helical image reconstruction is limited by a lack of standardized approaches and the initial effort and specialized expertise required. Our goal is to develop an integrated pipeline to enable structure determination by transmission electron microscopy (TEM) of IMPs in the form of tubular crystals. We describe here the integration of standard Fourier-Bessel helical analysis techniques into Appion, an integrated, database-driven pipeline.
Collapse
Affiliation(s)
- Lauren S. Fisher
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Andrew Ward
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Ronald A. Milligan
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Nigel Unwin
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| |
Collapse
|
25
|
Miki M, Makimura S, Saitoh T, Bunya M, Sugahara Y, Ueno Y, Kimura-Sakiyama C, Tobita H. A three-dimensional FRET analysis to construct an atomic model of the actin-tropomyosin complex on a reconstituted thin filament. J Mol Biol 2011; 414:765-82. [PMID: 22051514 DOI: 10.1016/j.jmb.2011.10.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 11/29/2022]
Abstract
Fluorescence resonance energy transfer (FRET) was used to construct an atomic model of the actin-tropomyosin (Tm) complex on a reconstituted thin filament. We generated five single-cysteine mutants in the 146-174 region of rabbit skeletal muscle α-Tm. An energy donor probe was attached to a single-cysteine Tm residue, while an energy acceptor probe was located in actin Gln41, actin Cys374, or the actin nucleotide binding site. From these donor-acceptor pairs, FRET efficiencies were determined with and without Ca(2+). Using the atomic coordinates for F-actin and Tm, we searched all possible arrangements for Tm segment 146-174 on F-actin to calculate the FRET efficiency for each donor-acceptor pair in each arrangement. By minimizing the squared sum of deviations for the calculated FRET efficiencies from the observed FRET efficiencies, we determined the location of the Tm segment on the F-actin filament. Furthermore, we generated a set of five single-cysteine mutants in each of the four Tm regions 41-69, 83-111, 216-244, and 252-279. Using the same procedures, we determined each segment's location on the F-actin filament. In the best-fit model, Tm runs along actin residues 217-236, which were reported to compose the Tm binding site. Electrostatic, hydrogen-bonding, and hydrophobic interactions are involved in actin and Tm binding. The C-terminal region of Tm was observed to contact actin more closely than did the N-terminal region. Tm contacts more residues on actin without Ca(2+) than with it. Ca(2+)-induced changes on the actin-Tm contact surface strongly affect the F-actin structure, which is important for muscle regulation.
Collapse
Affiliation(s)
- Masao Miki
- Division of Applied Chemistry and Biotechnology, Graduate School of Engineering Science, University of Fukui, Fukui 910-8507, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
26
|
CYRKLAFF M, ROOS N, GROSS H, DUBOCHET J. Particle-surface interaction in thin vitrified films for cryo-electron microscopy. J Microsc 2011. [DOI: 10.1111/j.1365-2818.1994.tb03476.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Li XE, Tobacman LS, Mun JY, Craig R, Fischer S, Lehman W. Tropomyosin position on F-actin revealed by EM reconstruction and computational chemistry. Biophys J 2011; 100:1005-13. [PMID: 21320445 DOI: 10.1016/j.bpj.2010.12.3697] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 12/03/2010] [Accepted: 12/09/2010] [Indexed: 12/18/2022] Open
Abstract
Electron microscopy and fiber diffraction studies of reconstituted F-actin-tropomyosin filaments reveal the azimuthal position of end-to-end linked tropomyosin molecules on the surface of actin. However, the longitudinal z-position of tropomyosin along F-actin is still uncertain. Without this information, atomic models of F-actin-tropomyosin filaments, free of constraints imposed by troponin or other actin-binding proteins, cannot be formulated, and thus optimal interfacial contacts between actin and tropomyosin remain unknown. Here, a computational search assessing electrostatic interactions for multiple azimuthal locations, z-positions, and pseudo-rotations of tropomyosin on F-actin was performed. The information gleaned was used to localize tropomyosin on F-actin, yielding an atomic model characterized by protein-protein contacts that primarily involve clusters of basic amino acids on actin subdomains 1 and 3 juxtaposed against acidic residues on the successive quasi-repeating units of tropomyosin. A virtually identical model generated by docking F-actin and tropomyosin atomic structures into electron microscopy reconstructions of F-actin-tropomyosin validated the above solution. Here, the z-position of tropomyosin alongside F-actin was defined by matching the seven broad and narrow motifs that typify tropomyosin's twisting superhelical coiled-coil to the wide and tapering tropomyosin densities seen in surface views of F-actin-tropomyosin reconstructions. The functional implications of the F-actin-tropomyosin models determined in this work are discussed.
Collapse
Affiliation(s)
- Xiaochuan Edward Li
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, USA
| | | | | | | | | | | |
Collapse
|
28
|
Abstract
Helical symmetry is commonly used for building macromolecular assemblies. Helical symmetry is naturally present in viruses and cytoskeletal filaments and also occurs during crystallization of isolated proteins, such as Ca-ATPase and the nicotinic acetyl choline receptor. Structure determination of helical assemblies by electron microscopy has a long history dating back to the original work on three-dimensional (3D) reconstruction. A helix offers distinct advantages for structure determination. Not only can one improve resolution by averaging across the constituent subunits, but each helical assembly provides multiple views of these subunits and thus provides a complete 3D data set. This review focuses on Fourier methods of helical reconstruction, covering the theoretical background, a step-by-step guide to the process, and a practical example based on previous work with Ca-ATPase. Given recent results from helical reconstructions at atomic resolution and the development of graphical user interfaces to aid in the process, these methods are likely to continue to make an important contribution to the field of structural biology.
Collapse
Affiliation(s)
- Ruben Diaz
- Cryo-electron Microscopy Facility, New York Structural Biology Center, New York, USA
| | | | | |
Collapse
|
29
|
Galińska A, Hatch V, Craig R, Murphy AM, Van Eyk JE, Wang CLA, Lehman W, Foster DB. The C terminus of cardiac troponin I stabilizes the Ca2+-activated state of tropomyosin on actin filaments. Circ Res 2009; 106:705-11. [PMID: 20035081 DOI: 10.1161/circresaha.109.210047] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RATIONALE Ca(2+) control of troponin-tropomyosin position on actin regulates cardiac muscle contraction. The inhibitory subunit of troponin, cardiac troponin (cTn)I is primarily responsible for maintaining a tropomyosin conformation that prevents crossbridge cycling. Despite extensive characterization of cTnI, the precise role of its C-terminal domain (residues 193 to 210) is unclear. Mutations within this region are associated with restrictive cardiomyopathy, and C-terminal deletion of cTnI, in some species, has been associated with myocardial stunning. OBJECTIVE We sought to investigate the effect of a cTnI deletion-removal of 17 amino acids from the C terminus- on the structure of troponin-regulated tropomyosin bound to actin. METHODS AND RESULTS A truncated form of human cTnI (cTnI(1-192)) was expressed and reconstituted with troponin C and troponin T to form a mutant troponin. Using electron microscopy and 3D image reconstruction, we show that the mutant troponin perturbs the positional equilibrium dynamics of tropomyosin in the presence of Ca(2+). Specifically, it biases tropomyosin position toward an "enhanced C-state" that exposes more of the myosin-binding site on actin than found with wild-type troponin. CONCLUSIONS In addition to its well-established role of promoting the so-called "blocked-state" or "B-state," cTnI participates in proper stabilization of tropomyosin in the "Ca(2+)-activated state" or "C-state." The last 17 amino acids perform this stabilizing role. The data are consistent with a "fly-casting" model in which the mobile C terminus of cTnI ensures proper conformational switching of troponin-tropomyosin. Loss of actin-sensing function within this domain, by pathological proteolysis or cardiomyopathic mutation, may be sufficient to perturb tropomyosin conformation.
Collapse
Affiliation(s)
- Agnieszka Galińska
- Department of Physiology & Biophysics, Boston University School of Medicine, 72 E Concord St., Boston, MA 02118, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Electron microscopy and three-dimensional reconstruction of native thin filaments reveal species-specific differences in regulatory strand densities. Biochem Biophys Res Commun 2009; 391:193-7. [PMID: 19900412 DOI: 10.1016/j.bbrc.2009.11.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 11/05/2009] [Indexed: 11/24/2022]
Abstract
Throughout the animal kingdom striated muscle contraction is regulated by the thin filament troponin-tropomyosin complex. Homologous regulatory components are shared among vertebrate and arthropod muscles; however, unique protein extensions and/or components characterize the latter. The Troponin T (TnT) isoforms of Drosophila indirect flight and tarantula femur muscle for example contain distinct C-terminal extensions and are approximately 20% larger overall than their vertebrate counterpart. Using electron microscopy and three-dimensional helical reconstruction of native Drosophila, tarantula and frog muscle thin filaments we have identified species-specific differences in tropomyosin regulatory strand densities. The strands on the arthropod thin filaments were significantly larger in diameter than those from vertebrates, although not significantly different from each other. These findings reflect differences in the regulatory troponin-tropomyosin complex, which are likely due to the larger TnT molecules aligning and extending along much of the tropomyosin strands' length. Such an arrangement potentially alters the physical properties of the regulatory strands and may help establish contractile characteristics unique to certain arthropod muscles.
Collapse
|
31
|
Lehman W, Galińska-Rakoczy A, Hatch V, Tobacman LS, Craig R. Structural basis for the activation of muscle contraction by troponin and tropomyosin. J Mol Biol 2009; 388:673-81. [PMID: 19341744 DOI: 10.1016/j.jmb.2009.03.060] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 03/23/2009] [Accepted: 03/25/2009] [Indexed: 11/19/2022]
Abstract
The molecular regulation of striated muscle contraction couples the binding and dissociation of Ca(2+) on troponin (Tn) to the movement of tropomyosin on actin filaments. In turn, this process exposes or blocks myosin binding sites on actin, thereby controlling myosin crossbridge dynamics and consequently muscle contraction. Using 3D electron microscopy, we recently provided structural evidence that a C-terminal extension of TnI is anchored on actin at low Ca(2+) and competes with tropomyosin for a common site to drive tropomyosin to the B-state location, a constrained, relaxing position on actin that inhibits myosin-crossbridge association. Here, we show that release of this constraint at high Ca(2+) allows a second segment of troponin, probably representing parts of TnT or the troponin core domain, to promote tropomyosin movement on actin to the Ca(2+)-induced C-state location. With tropomyosin stabilized in this position, myosin binding interactions can begin. Tropomyosin appears to oscillate to a higher degree between respective B- and C-state positions on troponin-free filaments than on fully regulated filaments, suggesting that tropomyosin positioning in both states is troponin-dependent. By biasing tropomyosin to either of these two positions, troponin appears to have two distinct structural functions; in relaxed muscles at low Ca(2+), troponin operates as an inhibitor, while in activated muscles at high Ca(2+), it acts as a promoter to initiate contraction.
Collapse
Affiliation(s)
- William Lehman
- Department of Physiology and Biophysics, Boston University, School of Medicine, Boston, MA 02118, USA.
| | | | | | | | | |
Collapse
|
32
|
Kim BK, Kim KS, Oh CW, Mykles DL, Lee SG, Kim HJ, Kim HW. Twelve actin-encoding cDNAs from the American lobster, Homarus americanus: cloning and tissue expression of eight skeletal muscle, one heart, and three cytoplasmic isoforms. Comp Biochem Physiol B Biochem Mol Biol 2009; 153:178-84. [PMID: 19258044 DOI: 10.1016/j.cbpb.2009.02.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 02/23/2009] [Accepted: 02/24/2009] [Indexed: 11/26/2022]
Abstract
Lobster muscles express a diverse array of myofibrillar protein isoforms. Three fiber types (fast, slow-twitch or S1, and slow-tonic or S2) differ qualitatively and quantitatively in myosin heavy and light chains, troponin-T, -I, and -C, paramyosin, and tropomyosin variants. However, little is known about the diversity of actin isoforms present in crustacean tissues. In this report we characterized cDNAs that encode twelve actin isoforms in the American lobster, Homarus americanus: eight from skeletal muscle (Ha-ActinSK1-8), one from heart (Ha-ActinHT1), and three cytoplasmic type actins from hepatopancreas (Ha-ActinCT1-3). All twelve cDNAs were products of distinct genes, as indicated by differences in the 3'-untranslated regions (UTRs). The open reading frames specified polypeptides 376 or 377 amino acids in length. Although key amino residues are conserved in the lobster actins, variations in nearby sequences may affect actin polymerization and/or interactions with other myofibrillar proteins. Quantitative reverse transcription-polymerase chain reaction showed muscle fiber type- and tissue-specific expression patterns. Ha-Actin-HT1 was expressed exclusively in heart (87% of the total; 12% of the total was Ha-ActinCT1). Ha-ActinCT1 was expressed in all tissues, while CT2 and CT3 were expressed only in hepatopancreas, with Ha-ActinCT2 as the major isoform (93% of the total). Ha-ActinSK1 and SK2 were the major isoforms (88% and 12% of the total, respectively) in the S1 fibers of crusher claw closer muscle. Fast fibers in the cutter claw closer and deep abdominal muscles differed in SK isoforms. Ha-ActinSK3, SK4, and SK5 were the major isoforms in cutter claw closer muscle (12%, 48%, and 37% of the total, respectively). Ha-ActinSK5 and SK8 were the major isoforms in deep abdominal flexor (31% and 65% of the total, respectively) and extensor (46% and 53% of the total, respectively) muscles, with SK6 and SK7 expressed at low levels. These data indicate that fast fibers in cutter claw and abdominal muscles show a phenotypic plasticity with respect to the expression of actin isoforms and may constitute discrete subtypes that differ in contractile properties.
Collapse
Affiliation(s)
- Bo Kwang Kim
- Department of Marine Biology, Pukyong National University, Busan, 608-737 South Korea
| | | | | | | | | | | | | |
Collapse
|
33
|
Aulisa L, Forraz N, McGuckin C, Hartgerink JD. Inhibition of cancer cell proliferation by designed peptide amphiphiles. Acta Biomater 2009; 5:842-53. [PMID: 19249722 DOI: 10.1016/j.actbio.2008.11.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 11/05/2008] [Accepted: 11/06/2008] [Indexed: 12/27/2022]
Abstract
HOX genes encode conserved transcription factors that control the morphological diversification along the anteroposterior body axis. HOX proteins bind to DNA through a highly conserved 60 amino acid sequence called the homeodomain, and greater DNA binding specificity and stability are achieved when it forms complexes with cofactors such as PBX and MEIS in humans. In particular, HOX proteins from paralog groups 1-8, interact with PBX proteins via a specific and highly conserved hydrophobic six amino acid sequence localized in the N-terminal region of HOX. In several oncogenic transformations, deregulated HOX gene expression has been observed, indicating an involvement of these transcriptional regulators in carcinogenesis and metastasis. Inhibition of the HOX-PBX interaction could be a strategy to control the abnormal proliferation of these cancer cells. In this study we describe a small designed peptide amphiphile (PA) which self-assembles into micelles and shows inhibition of T3M4 pancreatic cancer cells, K562 leukemia cells and MJT1 melanoma cells while non-cancerous fibroblast NIH 3T3 cells are less affected. This molecule contains three critical regions: a 9-amino-acid sequence designed to disrupt HOX/PBX/DNA complex formation, a 16-amino-acid sequence to deliver the peptide into the cell and a 16-carbon-acyl chain which we show leads to the molecule's self-assembly and significantly enhances the effectiveness of the molecule to slow cell proliferation.
Collapse
Affiliation(s)
- Lorenzo Aulisa
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | | | | | | |
Collapse
|
34
|
Patel DA, Root DD. Close proximity of myosin loop 3 to troponin determined by triangulation of resonance energy transfer distance measurements. Biochemistry 2009; 48:357-69. [PMID: 19108638 DOI: 10.1021/bi801554m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cooperative activation of the thin filament is known to be influenced by the tight binding of myosin to actin, but the molecular mechanism underlying this contribution of myosin is not well understood. To better understand the structural relationship of myosin with the regulatory troponin complex, resonance energy transfer measurements were used to map the location of troponin relative to a neighboring myosin bound to actin using atomic models. Using a chicken troponin T isoform that contains a single cysteine near the binding interface between troponins T, I, and C, this uniquely labeled cysteine on troponin was found to be remarkably near loop 3 of myosin. This loop has previously been localized near the actin and myosin interface by chemical cross-linking methods, but its functional contributions have not been established. The implications of this close proximity are examined by molecular modeling, which suggests that only restricted conformations of actomyosin can accommodate the presence of troponin at this location near the cross-bridge. This potential for interaction between troponin and myosin heads that bind near it along the thin filament raises the possibility of models in which direct myosin and troponin interactions may play a role in the regulatory mechanism.
Collapse
Affiliation(s)
- Dipesh A Patel
- University of North Texas, P.O. Box 305220, Denton, Texas 76203-5220, USA
| | | |
Collapse
|
35
|
Davis J, Westfall MV, Townsend D, Blankinship M, Herron TJ, Guerrero-Serna G, Wang W, Devaney E, Metzger JM. Designing heart performance by gene transfer. Physiol Rev 2008; 88:1567-651. [PMID: 18923190 DOI: 10.1152/physrev.00039.2007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The birth of molecular cardiology can be traced to the development and implementation of high-fidelity genetic approaches for manipulating the heart. Recombinant viral vector-based technology offers a highly effective approach to genetically engineer cardiac muscle in vitro and in vivo. This review highlights discoveries made in cardiac muscle physiology through the use of targeted viral-mediated genetic modification. Here the history of cardiac gene transfer technology and the strengths and limitations of viral and nonviral vectors for gene delivery are reviewed. A comprehensive account is given of the application of gene transfer technology for studying key cardiac muscle targets including Ca(2+) handling, the sarcomere, the cytoskeleton, and signaling molecules and their posttranslational modifications. The primary objective of this review is to provide a thorough analysis of gene transfer studies for understanding cardiac physiology in health and disease. By comparing results obtained from gene transfer with those obtained from transgenesis and biophysical and biochemical methodologies, this review provides a global view of cardiac structure-function with an eye towards future areas of research. The data presented here serve as a basis for discovery of new therapeutic targets for remediation of acquired and inherited cardiac diseases.
Collapse
Affiliation(s)
- Jennifer Davis
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Littlefield KP, Ward AB, Chappie JS, Reedy MK, Bernstein SI, Milligan RA, Reedy MC. Similarities and differences between frozen-hydrated, rigor acto-S1 complexes of insect flight and chicken skeletal muscles. J Mol Biol 2008; 381:519-28. [PMID: 18588896 DOI: 10.1016/j.jmb.2008.06.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 06/06/2008] [Accepted: 06/11/2008] [Indexed: 11/25/2022]
Abstract
The structure and function of myosin crossbridges in asynchronous insect flight muscle (IFM) have been elucidated in situ using multiple approaches. These include generating "atomic" models of myosin in multiple contractile states by rebuilding the crystal structure of chicken subfragment 1 (S1) to fit IFM crossbridges in lower-resolution electron microscopy tomograms and by "mapping" the functional effects of genetically substituted, isoform-specific domains, including the converter domain, in chimeric IFM myosin to sequences in the crystal structure of chicken S1. We prepared helical reconstructions (approximately 25 A resolution) to compare the structural characteristics of nucleotide-free myosin0 S1 bound to actin (acto-S1) isolated from chicken skeletal muscle (CSk) and the flight muscles of Lethocerus (Leth) wild-type Drosophila (wt Dros) and a Drosophila chimera (IFI-EC) wherein the converter domain of the indirect flight muscle myosin isoform has been replaced by the embryonic skeletal myosin converter domain. Superimposition of the maps of the frozen-hydrated acto-S1 complexes shows that differences between CSk and IFM S1 are limited to the azimuthal curvature of the lever arm: the regulatory light-chain (RLC) region of chicken skeletal S1 bends clockwise (as seen from the pointed end of actin) while those of IFM S1 project in a straight radial direction. All the IFM S1s are essentially identical other than some variation in the azimuthal spread of density in the RLC region. This spread is most pronounced in the IFI-EC S1, consistent with proposals that the embryonic converter domain increases the compliance of the IFM lever arm affecting the function of the myosin motor. These are the first unconstrained models of IFM S1 bound to actin and the first direct comparison of the vertebrate and invertebrate skeletal myosin II classes, the latter for which, data on the structure of discrete acto-S1 complexes, are not readily available.
Collapse
|
37
|
Galińska-Rakoczy A, Engel P, Xu C, Jung H, Craig R, Tobacman LS, Lehman W. Structural basis for the regulation of muscle contraction by troponin and tropomyosin. J Mol Biol 2008; 379:929-35. [PMID: 18514658 DOI: 10.1016/j.jmb.2008.04.062] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 04/24/2008] [Accepted: 04/28/2008] [Indexed: 01/13/2023]
Abstract
The molecular switching mechanism governing skeletal and cardiac muscle contraction couples the binding of Ca2+ on troponin to the movement of tropomyosin on actin filaments. Despite years of investigation, this mechanism remains unclear because it has not yet been possible to directly assess the structural influence of troponin on tropomyosin that causes actin filaments, and hence myosin-crossbridge cycling and contraction, to switch on and off. A C-terminal domain of troponin I is thought to be intimately involved in inducing tropomyosin movement to an inhibitory position that blocks myosin-crossbridge interaction. Release of this regulatory, latching domain from actin after Ca2+ binding to TnC (the Ca2+ sensor of troponin that relieves inhibition) presumably allows tropomyosin movement away from the inhibitory position on actin, thus initiating contraction. However, the structural interactions of the regulatory domain of TnI (the "inhibitory" subunit of troponin) with tropomyosin and actin that cause tropomyosin movement are unknown, and thus, the regulatory process is not well defined. Here, thin filaments were labeled with an engineered construct representing C-terminal TnI, and then, 3D electron microscopy was used to resolve where troponin is anchored on actin-tropomyosin. Electron microscopy reconstruction showed how TnI binding to both actin and tropomyosin at low Ca2+ competes with tropomyosin for a common site on actin and drives tropomyosin movement to a constrained, relaxing position to inhibit myosin-crossbridge association. Thus, the observations reported reveal the structural mechanism responsible for troponin-tropomyosin-mediated steric interference of actin-myosin interaction that regulates muscle contraction.
Collapse
Affiliation(s)
- Agnieszka Galińska-Rakoczy
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Moores CA, Milligan RA. Visualisation of a kinesin-13 motor on microtubule end mimics. J Mol Biol 2008; 377:647-54. [PMID: 18294653 DOI: 10.1016/j.jmb.2008.01.079] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 01/17/2008] [Accepted: 01/23/2008] [Indexed: 11/25/2022]
Abstract
An expanding collection of proteins localises to microtubule ends to regulate cytoskeletal dynamics and architecture by unknown molecular mechanisms. Electron microscopy is invaluable for studying microtubule structure, but because microtubule ends are heterogeneous, their structures are difficult to determine. We therefore investigated whether tubulin oligomers induced by the drug dolastatin could mimic microtubule ends. The microtubule end-dependent ATPase of kinesin-13 motors is coupled to microtubule depolymerisation. Significantly, kinesin-13 motor ATPase activity is stimulated by dolastatin-tubulin oligomers, suggesting, first, that these oligomers share properties with microtubule ends and, second, that the physical presence of an end is less important than terminal tubulin flexibility for microtubule end recognition by the kinesin-13 motor. Using electron microscopy, we visualised the kinesin-13 motor-dolastatin-tubulin oligomer interaction in nucleotide states mimicking steps in the ATPase cycle. This enabled us to detect conformational changes that the motor undergoes during depolymerisation. Our data suggest that such tubulin oligomers can be used to examine other microtubule end-binding proteins.
Collapse
Affiliation(s)
- Carolyn A Moores
- School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.
| | | |
Collapse
|
39
|
Affiliation(s)
- Kenneth A Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | | | | | | |
Collapse
|
40
|
Murakami K, Yumoto F, Ohki SY, Yasunaga T, Tanokura M, Wakabayashi T. Structural basis for calcium-regulated relaxation of striated muscles at interaction sites of troponin with actin and tropomyosin. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 592:71-86. [PMID: 17278357 DOI: 10.1007/978-4-431-38453-3_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In summary, we have shown that the TnI-TnC-TnT2 ternary complex (-52 kDa) has a mobile actin-binding domain (-6.1 kDa) that tumbles independently of the core domain. By docking the mobile domain and the core domain into the cryo-EM map obtained for thin filaments at low Ca2+, a model for actin-troponin interaction has been obtained. This model shows the atomic details of interactions of actin with the mobile domain and suggests the mechanism by which troponin generates a shift in the azimuthal position of tropomyosin in response to changes in Ca2+ levels. In this model the mobile domain of troponin interacts with three actins and one troponin interacts with four actin molecules. The relationship between myosin and the mobile domain suggests that the latter may work as a fail-safe latch to secure a relaxed state. The model also provides insights into many mutations associated with human cardiomyopathy and has implications for the function of other actin-binding proteins. Coordinates of the mobile domain have been deposited in the Protein Data Bank under accession codes 1VDI (low Ca2+) and 1VDJ (high Ca2+). Chemical shifts of the mobile domain have been deposited in the BMRB under accession ID 18140.
Collapse
Affiliation(s)
- Kenji Murakami
- Department of Biosciences, School of Science and Engineering, Teikyo University, Toyosatodai 1-1, Utsunomiya 320-8551, Japan
| | | | | | | | | | | |
Collapse
|
41
|
Cheng A, Yeager M. Bootstrap resampling for voxel-wise variance analysis of three-dimensional density maps derived by image analysis of two-dimensional crystals. J Struct Biol 2006; 158:19-32. [PMID: 17187989 PMCID: PMC2840724 DOI: 10.1016/j.jsb.2006.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2005] [Revised: 08/18/2006] [Accepted: 10/05/2006] [Indexed: 10/24/2022]
Abstract
Difference density maps are commonly used in structural biology for identifying conformational changes in macromolecular complexes. For interpretation of the results, it is essential to estimate the variance or standard deviation of the difference density and the distribution of errors in space. In order to compare three-dimensional density maps of gap junction channels with and without the C-terminal regulatory domain, we developed a bootstrap resampling method for estimation of the voxel-wise standard deviation. The bootstrap approach has been successfully used for estimating the sampling distribution from a limited data set and for estimating the statistical properties of the derived quantities [Efron, B., 1979. Bootstrap methods: another look at the jackknife. Ann. Stat. 7, 1-26]. In our application, the standard deviation map can be estimated by bootstrapping the images. Our results show that, apart from the symmetry axes and small regions bordering the lumen of the extracellular vestibule, difference maps normalized by the mean of the standard deviation map can be used as a good approximation of the t-test map of the gap junction crystals.
Collapse
Affiliation(s)
- Anchi Cheng
- The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | | |
Collapse
|
42
|
Poole KJV, Lorenz M, Evans G, Rosenbaum G, Pirani A, Craig R, Tobacman LS, Lehman W, Holmes KC. A comparison of muscle thin filament models obtained from electron microscopy reconstructions and low-angle X-ray fibre diagrams from non-overlap muscle. J Struct Biol 2006; 155:273-84. [PMID: 16793285 DOI: 10.1016/j.jsb.2006.02.020] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Accepted: 02/14/2006] [Indexed: 10/24/2022]
Abstract
The regulation of striated muscle contraction involves changes in the interactions of troponin and tropomyosin with actin thin filaments. In resting muscle, myosin-binding sites on actin are thought to be blocked by the coiled-coil protein tropomyosin. During muscle activation, Ca2+ binding to troponin alters the tropomyosin position on actin, resulting in cyclic actin-myosin interactions that accompany muscle contraction. Evidence for this steric regulation by troponin-tropomyosin comes from X-ray data [Haselgrove, J.C., 1972. X-ray evidence for a conformational change in the actin-containing filaments of verterbrate striated muscle. Cold Spring Habor Symp. Quant. Biol. 37, 341-352; Huxley, H.E., 1972. Structural changes in actin and myosin-containing filaments during contraction. Cold Spring Habor Symp. Quant. Biol. 37, 361-376; Parry, D.A., Squire, J.M., 1973. Structural role of tropomyosin in muscle regulation: analysis of the X-ray diffraction patterns from relaxed and contracting muscles. J. Mol. Biol. 75, 33-55] and electron microscope (EM) data [Spudich, J.A., Huxley, H.E., Finch, J., 1972. Regulation of skeletal muscle contraction. II. Structural studies of the interaction of the tropomyosin-troponin complex with actin. J. Mol. Biol. 72, 619-632; O'Brien, E.J., Gillis, J.M., Couch, J., 1975. Symmetry and molecular arrangement in paracrystals of reconstituted muscle thin filaments. J. Mol. Biol. 99, 461-475; Lehman, W., Craig, R., Vibert, P., 1994. Ca2+-induced tropomyosin movement in Limulus thin filaments revealed by three-dimensional reconstruction. Nature 368, 65-67] each with its own particular strengths and limitations. Here we bring together some of the latest information from EM analysis of single thin filaments from Pirani et al. [Pirani, A., Xu, C., Hatch, V., Craig, R., Tobacman, L.S., Lehman, W. (2005). Single particle analysis of relaxed and activated muscle thin filaments. J. Mol. Biol. 346, 761-772], with synchrotron X-ray data from non-overlapped muscle fibres to refine the models of the striated muscle thin filament. This was done by incorporating current atomic-resolution structures of actin, tropomyosin, troponin and myosin subfragment-1. Fitting these atomic coordinates to EM reconstructions, we present atomic models of the thin filament that are entirely consistent with a steric regulatory mechanism. Furthermore, fitting the atomic models against diffraction data from skinned muscle fibres, stretched to non-overlap to preclude crossbridge binding, produced very similar results, including a large Ca2+-induced shift in tropomyosin azimuthal location but little change in the actin structure or apparent alteration in troponin position.
Collapse
Affiliation(s)
- Katrina J V Poole
- Arbeitsgruppe Biophysik, Max Planck Institut für medizinische Forschung, 69120 Heidelberg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Pant K, Chereau D, Hatch V, Dominguez R, Lehman W. Cortactin binding to F-actin revealed by electron microscopy and 3D reconstruction. J Mol Biol 2006; 359:840-7. [PMID: 16697006 DOI: 10.1016/j.jmb.2006.03.065] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 03/17/2006] [Accepted: 03/31/2006] [Indexed: 01/01/2023]
Abstract
Cortactin and WASP activate Arp2/3-mediated actin filament nucleation and branching. However, different mechanisms underlie activation by the two proteins, which rely on distinct actin-binding modules and modes of binding to actin filaments. It is generally thought that cortactin binds to "mother" actin filaments, while WASP donates actin monomers to Arp2/3-generated "daughter" filament branches. Interestingly, cortactin also binds WASP in addition to F-actin and the Arp2/3 complex. However, the structural basis for the role of cortactin in filament branching remains unknown, making interpretation difficult. Here, electron microscopy and 3D reconstruction were carried out on F-actin decorated with the actin-binding repeating domain of cortactin, revealing conspicuous density on F-actin attributable to cortactin that is located on a consensus-binding site on subdomain-1 of actin subunits. Strikingly, the binding of cortactin widens the gap between the two long-pitch filament strands. Although other proteins have been found to alter the structure of the filament, the cortactin-induced conformational change appears unique. The results are consistent with a mechanism whereby alterations of the F-actin structure may facilitate recruitment of the Arp2/3 complex to the "mother" filament in the cortex of cells. In addition, cortactin may act as a structural adapter protein, stabilizing nascent filament branches while mediating the simultaneous recruitment of Arp2/3 and WASP.
Collapse
Affiliation(s)
- Kiran Pant
- Department of Physiology & Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
| | | | | | | | | |
Collapse
|
44
|
Hizlan D, Mishima M, Tittmann P, Gross H, Glotzer M, Hoenger A. Structural analysis of the ZEN-4/CeMKLP1 motor domain and its interaction with microtubules. J Struct Biol 2006; 153:73-84. [PMID: 16361109 DOI: 10.1016/j.jsb.2005.10.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 10/17/2005] [Accepted: 10/27/2005] [Indexed: 11/25/2022]
Abstract
The centralspindlin complex is required for the assembly and maintenance of the central spindle during late anaphase and the completion of cytokinesis. It is composed of two copies each of the kinesin-like protein ZEN-4, a Caenorhabditis elegans MKLP-1 (Kinesin-6 family), and the RhoGAP CYK-4. By using cryo-electron microscopy and helical 3D reconstruction, we are investigating the structural features of the interactions between monomeric and dimeric motor domain constructs of ZEN-4 and microtubules. We have calculated helically averaged 3D maps of microtubules decorated with ZEN-4 motor domain in the presence of AMP-PNP, ADP, ADP-AlF(4)(-), and nucleotide-free conditions. We used statistical difference mapping to compare these maps among each other and to related maps obtained from microtubules decorated with a well-characterized Kinesin-1 motor domain from Neurospora crassa. Thereby, we found distinct structural features in microtubule-ZEN-4 complexes that may directly relate to the functional properties of ZEN-4 and centralspindlin. Furthermore, we investigated the location, structure, and function of a highly conserved extension of approximately 50 residues unique to the Kinesin-6 subfamily, located in the motor core loop6/beta4 region.
Collapse
Affiliation(s)
- Dilem Hizlan
- European Molecular Biology Laboratory, Structural Biology and Biocomputing Programme, Heidelberg, Germany
| | | | | | | | | | | |
Collapse
|
45
|
Roseman AM, Berriman JA, Wynne SA, Butler PJG, Crowther RA. A structural model for maturation of the hepatitis B virus core. Proc Natl Acad Sci U S A 2005; 102:15821-6. [PMID: 16247012 PMCID: PMC1276056 DOI: 10.1073/pnas.0504874102] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus, a widespread and serious human pathogen, replicates by reverse transcription of an RNA intermediate. The virus consists of an inner nucleocapsid or core, surrounded by a lipid envelope containing virally encoded surface proteins. Using electron cryomicroscopy, we compare the structures of the bacterially expressed RNA-containing core particle and the mature DNA-containing core particle extracted from virions. We show that the mature core contains 240 subunits in a T = 4 arrangement similar to that in expressed core (T is the triangulation number and the icosahedral shell contains 60 T subunits). During the infective cycle, the core assembles in an immature state around a complex of viral pregenomic RNA and polymerase. After reverse transcription with concomitant degradation of the RNA, the now mature core buds through a cellular membrane containing the surface proteins to become enveloped. Envelopment must not happen before reverse transcription is completed, so it has been hypothesized that a change in capsid structure may signal maturation. Our results show significant differences in structure between the RNA- and DNA-containing cores. One such difference is in a hydrophobic pocket, formed largely from residues that, on mutation, lead to abnormal secretion. We suggest that the changes we see are related to maturation and control of envelopment, and we propose a mechanism based on DNA synthesis for their triggering.
Collapse
Affiliation(s)
- Alan M Roseman
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
| | | | | | | | | |
Collapse
|
46
|
Murakami K, Yumoto F, Ohki SY, Yasunaga T, Tanokura M, Wakabayashi T. Structural basis for Ca2+-regulated muscle relaxation at interaction sites of troponin with actin and tropomyosin. J Mol Biol 2005; 352:178-201. [PMID: 16061251 DOI: 10.1016/j.jmb.2005.06.067] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 06/17/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
Troponin and tropomyosin on actin filaments constitute a Ca2+-sensitive switch that regulates the contraction of vertebrate striated muscle through a series of conformational changes within the actin-based thin filament. Troponin consists of three subunits: an inhibitory subunit (TnI), a Ca2+-binding subunit (TnC), and a tropomyosin-binding subunit (TnT). Ca2+-binding to TnC is believed to weaken interactions between troponin and actin, and triggers a large conformational change of the troponin complex. However, the atomic details of the actin-binding sites of troponin have not been determined. Ternary troponin complexes have been reconstituted from recombinant chicken skeletal TnI, TnC, and TnT2 (the C-terminal region of TnT), among which only TnI was uniformly labelled with 15N and/or 13C. By applying NMR spectroscopy, the solution structures of a "mobile" actin-binding domain (approximately 6.1 kDa) in the troponin ternary complex (approximately 52 kDa) were determined. The mobile domain appears to tumble independently of the core domain of troponin. Ca2+-induced changes in the chemical shift and line shape suggested that its tumbling was more restricted at high Ca2+ concentrations. The atomic details of interactions between actin and the mobile domain of troponin were defined by docking the mobile domain into the cryo-electron microscopy (cryo-EM) density map of thin filament at low [Ca2+]. This allowed the determination of the 3D position of residue 133 of TnI, which has been an important landmark to incorporate the available information. This enabled unique docking of the entire globular head region of troponin into the thin filament cryo-EM map at a low Ca2+ concentration. The resultant atomic model suggests that troponin interacted electrostatically with actin and caused the shift of tropomyosin to achieve muscle relaxation. An important feature is that the coiled-coil region of troponin pushed tropomyosin at a low Ca2+ concentration. Moreover, the relationship between myosin and the mobile domain on actin filaments suggests that the latter works as a fail-safe latch.
Collapse
Affiliation(s)
- Kenji Murakami
- Department of Biosciences, School of Science and Engineering, Teikyo University, Toyosatodai 1-1, Utsunomiya 320-8551, Japan
| | | | | | | | | | | |
Collapse
|
47
|
Cammarato A, Craig R, Sparrow JC, Lehman W. E93K charge reversal on actin perturbs steric regulation of thin filaments. J Mol Biol 2005; 347:889-94. [PMID: 15784249 DOI: 10.1016/j.jmb.2005.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Revised: 02/08/2005] [Accepted: 02/09/2005] [Indexed: 11/27/2022]
Abstract
Contraction in striated muscles is regulated by Ca2+-dependent movement of tropomyosin-troponin on thin filaments. Interactions of charged amino acid residues between the surfaces of tropomyosin and actin are believed to play an integral role in this steric mechanism by influencing the position of tropomyosin on the filaments. To investigate this possibility further, thin filaments were isolated from troponin-regulated, indirect flight muscles of Drosophila mutants that express actin with an amino acid charge reversal at residue 93 located at the interface between actin subdomains 1 and 2, in which a lysine residue is substituted for a glutamic acid. Electron microscopy and 3D helical reconstruction were employed to evaluate the structural effects of the mutation. In the absence of Ca2+, tropomyosin was in a position that blocked the myosin-binding sites on actin, as previously found with wild-type filaments. However, in the presence of Ca2+, tropomyosin position in the mutant filaments was much more variable than in the wild-type ones. In most cases (approximately 60%), tropomyosin remained in the blocking position despite the presence of Ca2+, failing to undergo a normal Ca2+-induced change in position. Thus, switching of a negative to a positive charge at position 93 on actin may stabilize negatively charged tropomyosin in the Ca2+-free state regardless of Ca2+ levels, an alteration that, in turn, is likely to interfere with steric regulation and consequently muscle activation. These results highlight the importance of actin's surface charges in determining the distribution of tropomyosin positions on thin filaments derived from troponin-regulated striated muscles.
Collapse
Affiliation(s)
- Anthony Cammarato
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
| | | | | | | |
Collapse
|
48
|
Abstract
Troponin is the regulatory complex of the myofibrillar thin filament that plays a critical role in regulating excitation-contraction coupling in the heart. Troponin is composed of three distinct gene products: troponin C (cTnC), the 18-kD Ca(2+)-binding subunit; troponin I (cTnI), the approximately 23-kD inhibitory subunit that prevents contraction in the absence of Ca2+ binding to cTnC; and troponin T (cTnT), the approximately 35-kD subunit that attaches troponin to tropomyosin (Tm) and to the myofibrillar thin filament. Over the past 45 years, extensive biochemical, biophysical, and structural studies have helped to elucidate the molecular basis of troponin function and thin filament activation in the heart. At the onset of systole, Ca2+ binds to the N-terminal Ca2+ binding site of cTnC initiating a conformational change in cTnC, which catalyzes protein-protein associations activating the myofibrillar thin filament. Thin filament activation in turn facilitates crossbridge cycling, myofibrillar activation, and contraction of the heart. The intrinsic length-tension properties of cardiac myocytes as well as the Frank-Starling properties of the intact heart are mediated primarily through Ca(2+)-responsive thin filament activation. cTnC, cTnI, and cTnT are encoded by distinct single-copy genes in the human genome, each of which is expressed in a unique cardiac-restricted developmentally regulated fashion. Elucidation of the transcriptional programs that regulate troponin transcription and gene expression has provided insights into the molecular mechanisms that regulate and coordinate cardiac myocyte differentiation and provided unanticipated insights into the pathogenesis of cardiac hypertrophy. Autosomal dominant mutations in cTnI and cTnT have been identified and are associated with familial hypertrophic and restrictive cardiomyopathies.
Collapse
Affiliation(s)
- Michael S Parmacek
- Department of Medicine, University of Pennsylvania School of Medicine, 3400 Spruce St., 9123 Founders Pavilion, Philadelphia, PA 19104, USA.
| | | |
Collapse
|
49
|
Chen Y, Lehrer SS. Distances between Tropomyosin Sites Across the Muscle Thin Filament Using Luminescence Resonance Energy Transfer: Evidence for Tropomyosin Flexibility. Biochemistry 2004; 43:11491-9. [PMID: 15350135 DOI: 10.1021/bi049186v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To obtain information about the interaction of tropomyosin (Tm) with actin associated with the regulatory states of the muscle thin filament, we used luminescence resonance energy transfer (LRET) between Tb(3+) as a donor and rhodamine as an acceptor. A novel Tb(3+) chelator, S-(2-nitro-5-thiobenzoate)cysteaminyl-DTPA-Cs124, was synthesized, which specifically labels Cys groups in proteins. With the Tb chelate as the donor and tetramethylrhodamine-5-maleimide as the acceptor, both bound to specific Cys groups of Tm, we obtained 67 A as the distance between Tm's across the actin filament, a much shorter value than that obtained from structural studies (72-86 A). The difference appears to be due to submillisecond motion associated with Tm flexibility, which brings the probes closer during the millisecond lifetime of the donor. Ca(2+) did not change the energy transfer with the reconstituted thin filament, but myosin subfragment 1 decreased the transfer, consistent with either a 5-6 A increase in distance or, more likely, a decrease in flexibility.
Collapse
Affiliation(s)
- Yaodong Chen
- Muscle and Motility Group, 64 Grove Street, Boston Biomedical Research Institute, Watertown, Massachusetts 02472, USA.
| | | |
Collapse
|
50
|
Santarella RA, Skiniotis G, Goldie KN, Tittmann P, Gross H, Mandelkow EM, Mandelkow E, Hoenger A. Surface-decoration of microtubules by human tau. J Mol Biol 2004; 339:539-53. [PMID: 15147841 DOI: 10.1016/j.jmb.2004.04.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2004] [Revised: 03/31/2004] [Accepted: 04/05/2004] [Indexed: 11/23/2022]
Abstract
Tau is a neuronal, microtubule-associated protein that stabilizes microtubules and promotes neurite outgrowth. Tau is largely unfolded in solution and presumably forms mostly random coil. Because of its hydrophilic nature and flexible structure, tau complexed to microtubules is largely invisible by standard electron microscopy methods. We applied a combination of high-resolution metal-shadowing and cryo-electron microscopy to study the interactions between tau and microtubules. We used recombinant tau variants with different domain compositions, (1) full length tau, (2) the repeat domain that mediates microtubule binding (K19), and (3) two GFP-tau fusion proteins that contain a globular marker (GFP) attached to full-length tau at either end. All of these constructs bind exclusively to the outside of microtubules. Most of the tau-related mass appears randomly distributed, creating a "halo" of low-density mass spread across the microtubule surface. Only a small fraction of tau creates a periodic signal at an 8 nm interval, centered on alpha-tubulin subunits. Our data suggest that tau retains most of its disordered structure even when bound to the microtubule surface. Hence, it binds along, as well as across protofilaments. Nevertheless, even minute concentrations of tau have a strong stabilizing effect and effectively scavenge unpolymerized tubulin.
Collapse
Affiliation(s)
- Rachel A Santarella
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117, Heidelberg, Germany
| | | | | | | | | | | | | | | |
Collapse
|