1
|
Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
Collapse
Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| |
Collapse
|
2
|
Audett MR, Maresca TJ. The whole is greater than the sum of its parts: at the intersection of order, disorder, and kinetochore function. Essays Biochem 2020; 64:349-358. [PMID: 32756877 PMCID: PMC8011995 DOI: 10.1042/ebc20190069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022]
Abstract
The kinetochore (KT) field has matured tremendously since Earnshaw first identified CENP-A, CENP-B, and CENP-C [1,2]. In the past 35 years, the accumulation of knowledge has included: defining the parts list, identifying epistatic networks of interdependence within the parts list, understanding the spatial organization of subcomplexes into a massive structure - hundreds of megadaltons in size, and dissecting the functions of the KT in its entirety as well as of its individual parts. Like nearly all cell and molecular biology fields, the structure-function paradigm has been foundational to advances in the KT field. A point nicely highlighted by the fact that we are at the precipice of the in vitro reconstitution of a functional KT holo complex. Yet conventional notions of structure cannot provide a complete picture of the KT especially since it contains an abundance of unstructured or intrinsically disordered constituents. The combination of structured and disordered proteins within the KT results in an assembled system that is functionally greater than the sum of its parts.
Collapse
Affiliation(s)
- Margaux R Audett
- Biology Department, University of Massachusetts, Amherst, MA, U.S.A
| | - Thomas J Maresca
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, U.S.A
| |
Collapse
|
3
|
N2A Titin: Signaling Hub and Mechanical Switch in Skeletal Muscle. Int J Mol Sci 2020; 21:ijms21113974. [PMID: 32492876 PMCID: PMC7312179 DOI: 10.3390/ijms21113974] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Since its belated discovery, our understanding of the giant protein titin has grown exponentially from its humble beginning as a sarcomeric scaffold to recent recognition of its critical mechanical and signaling functions in active muscle. One uniquely useful model to unravel titin’s functions, muscular dystrophy with myositis (mdm), arose spontaneously in mice as a transposon-like LINE repeat insertion that results in a small deletion in the N2A region of titin. This small deletion profoundly affects hypertrophic signaling and muscle mechanics, thereby providing insights into the function of this specific region and the consequences of its dysfunction. The impact of this mutation is profound, affecting diverse aspects of the phenotype including muscle mechanics, developmental hypertrophy, and thermoregulation. In this review, we explore accumulating evidence that points to the N2A region of titin as a dynamic “switch” that is critical for both mechanical and signaling functions in skeletal muscle. Calcium-dependent binding of N2A titin to actin filaments triggers a cascade of changes in titin that affect mechanical properties such as elastic energy storage and return, as well as hypertrophic signaling. The mdm phenotype also points to the existence of as yet unidentified signaling pathways for muscle hypertrophy and thermoregulation, likely involving titin’s PEVK region as well as the N2A signalosome.
Collapse
|
4
|
Manfredini F, Romero AE, Pedroso I, Paccanaro A, Sumner S, Brown MJF. Neurogenomic Signatures of Successes and Failures in Life-History Transitions in a Key Insect Pollinator. Genome Biol Evol 2017; 9:3059-3072. [PMID: 29087523 PMCID: PMC5714134 DOI: 10.1093/gbe/evx220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 12/22/2022] Open
Abstract
Life-history transitions require major reprogramming at the behavioral and physiological level. Mating and reproductive maturation are known to trigger changes in gene transcription in reproductive tissues in a wide range of organisms, but we understand little about the molecular consequences of a failure to mate or become reproductively mature, and it is not clear to what extent these processes trigger neural as well as physiological changes. In this study, we examined the molecular processes underpinning the behavioral changes that accompany the major life-history transitions in a key pollinator, the bumblebee Bombus terrestris. We compared neuro-transcription in queens that succeeded or failed in switching from virgin and immature states, to mated and reproductively mature states. Both successes and failures were associated with distinct molecular profiles, illustrating how development during adulthood triggers distinct molecular profiles within a single caste of a eusocial insect. Failures in both mating and reproductive maturation were explained by a general up-regulation of brain gene transcription. We identified 21 genes that were highly connected in a gene coexpression network analysis: nine genes are involved in neural processes and four are regulators of gene expression. This suggests that negotiating life-history transitions involves significant neural processing and reprogramming, and not just changes in physiology. These findings provide novel insights into basic life-history transitions of an insect. Failure to mate or to become reproductively mature is an overlooked component of variation in natural systems, despite its prevalence in many sexually reproducing organisms, and deserves deeper investigation in the future.
Collapse
Affiliation(s)
- Fabio Manfredini
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Alfonso E Romero
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Inti Pedroso
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alberto Paccanaro
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, United Kingdom
- Present address: Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| |
Collapse
|
5
|
Bang ML. Animal Models of Congenital Cardiomyopathies Associated With Mutations in Z-Line Proteins. J Cell Physiol 2016; 232:38-52. [PMID: 27171814 DOI: 10.1002/jcp.25424] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/10/2016] [Indexed: 01/15/2023]
Abstract
The cardiac Z-line at the boundary between sarcomeres is a multiprotein complex connecting the contractile apparatus with the cytoskeleton and the extracellular matrix. The Z-line is important for efficient force generation and transmission as well as the maintenance of structural stability and integrity. Furthermore, it is a nodal point for intracellular signaling, in particular mechanosensing and mechanotransduction. Mutations in various genes encoding Z-line proteins have been associated with different cardiomyopathies, including dilated cardiomyopathy, hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy, restrictive cardiomyopathy, and left ventricular noncompaction, and mutations even within the same gene can cause widely different pathologies. Animal models have contributed to a great advancement in the understanding of the physiological function of Z-line proteins and the pathways leading from mutations in Z-line proteins to cardiomyopathy, although genotype-phenotype prediction remains a great challenge. This review presents an overview of the currently available animal models for Z-line and Z-line associated proteins involved in human cardiomyopathies with special emphasis on knock-in and transgenic mouse models recapitulating the clinical phenotypes of human cardiomyopathy patients carrying mutations in Z-line proteins. Pros and cons of mouse models will be discussed and a future outlook will be given. J. Cell. Physiol. 232: 38-52, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research, UOS Milan, National Research Council and Humanitas Clinical and Research Center, Rozzano, Milan, Italy.
| |
Collapse
|
6
|
(Intrinsically disordered) splice variants in the proteome: implications for novel drug discovery. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0384-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
7
|
Abstract
Efficient muscle contraction in skeletal muscle is predicated on the regulation of actin filament lengths. In one long-standing model that was prominent for decades, the giant protein nebulin was proposed to function as a 'molecular ruler' to specify the lengths of the thin filaments. This theory was questioned by many observations, including experiments in which the length of nebulin was manipulated in skeletal myocytes; this approach revealed that nebulin functions to stabilize filamentous actin, allowing thin filaments to reach mature lengths. In addition, more recent data, mostly from in vivo models and identification of new interacting partners, have provided evidence that nebulin is not merely a structural protein. Nebulin plays a role in numerous cellular processes including regulation of muscle contraction, Z-disc formation, and myofibril organization and assembly.
Collapse
Affiliation(s)
- Miensheng Chu
- Department of Cellular and Molecular Medicine and the Sarver Molecular Cardiovascular Research Program, The University of Arizona, 1656 East Mabel, MRB315, Tucson, AZ 85724, USA
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine and the Sarver Molecular Cardiovascular Research Program, The University of Arizona, 1656 East Mabel, MRB315, Tucson, AZ 85724, USA
| | - Christopher T Pappas
- Department of Cellular and Molecular Medicine and the Sarver Molecular Cardiovascular Research Program, The University of Arizona, 1656 East Mabel, MRB315, Tucson, AZ 85724, USA
| |
Collapse
|
8
|
Abstract
The members of the nebulin protein family, including nebulin, nebulette, LASP-1, LASP-2, and N-RAP, contain various numbers of nebulin repeats and bind to actin, but are otherwise heterogeneous with regard to size, expression pattern, and function. This review focuses on the roles of nebulin family members in the heart. Nebulin is the largest member predominantly expressed in skeletal muscle, where it stretches along the thin filament. In heart, nebulin is detectable only at low levels and its absence has no apparent effects. Nebulette is similar in structure to the nebulin C-terminal Z-line region and specifically expressed in heart. Nebulette gene mutations have been identified in dilated cardiomyopathy patients and transgenic mice overexpressing nebulette mutants partially recapitulate the human pathology. In contrast, nebulette knockout mice show no functional phenotype, but exhibit Z-line widening. LASP-2 is an isoform of nebulette expressed in multiple tissues, including the heart. It is present in the Z-line and intercalated disc and able to bind and cross-link filamentous actin. LASP-1 is similar in structure to LASP-2, but expressed only in non-muscle tissue. N-RAP is present in myofibril precursors during myofibrillogenesis and thought to be involved in myofibril assembly, while it is localized at the intercalated disc in adult heart. Additional in vivo models are required to provide further insights into the functions of nebulin family members in the heart.
Collapse
Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research, UOS Milan, National Research Council
| | | |
Collapse
|
9
|
Fang Q, Indzhykulian AA, Mustapha M, Riordan GP, Dolan DF, Friedman TB, Belyantseva IA, Frolenkov GI, Camper SA, Bird JE. The 133-kDa N-terminal domain enables myosin 15 to maintain mechanotransducing stereocilia and is essential for hearing. eLife 2015; 4. [PMID: 26302205 PMCID: PMC4592939 DOI: 10.7554/elife.08627] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/22/2015] [Indexed: 11/13/2022] Open
Abstract
The precise assembly of inner ear hair cell stereocilia into rows of increasing height is critical for mechanotransduction and the sense of hearing. Yet, how the lengths of actin-based stereocilia are regulated remains poorly understood. Mutations of the molecular motor myosin 15 stunt stereocilia growth and cause deafness. We found that hair cells express two isoforms of myosin 15 that differ by inclusion of an 133-kDa N-terminal domain, and that these isoforms can selectively traffic to different stereocilia rows. Using an isoform-specific knockout mouse, we show that hair cells expressing only the small isoform remarkably develop normal stereocilia bundles. However, a critical subset of stereocilia with active mechanotransducer channels subsequently retracts. The larger isoform with the 133-kDa N-terminal domain traffics to these specialized stereocilia and prevents disassembly of their actin core. Our results show that myosin 15 isoforms can navigate between functionally distinct classes of stereocilia, and are independently required to assemble and then maintain the intricate hair bundle architecture.
Collapse
Affiliation(s)
- Qing Fang
- Department of Human Genetics, University of Michigan, Ann Arbor, United States
| | | | - Mirna Mustapha
- Department of Human Genetics, University of Michigan, Ann Arbor, United States
| | - Gavin P Riordan
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, United States
| | - David F Dolan
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, United States
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, United States
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, United States
| | | | - Sally A Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, United States
| | - Jonathan E Bird
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, United States
| |
Collapse
|
10
|
Mastrototaro G, Liang X, Li X, Carullo P, Piroddi N, Tesi C, Gu Y, Dalton ND, Peterson KL, Poggesi C, Sheikh F, Chen J, Bang ML. Nebulette knockout mice have normal cardiac function, but show Z-line widening and up-regulation of cardiac stress markers. Cardiovasc Res 2015; 107:216-25. [PMID: 25987543 DOI: 10.1093/cvr/cvv156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 04/26/2015] [Indexed: 02/06/2023] Open
Abstract
AIMS Nebulette is a 109 kDa modular protein localized in the sarcomeric Z-line of the heart. In vitro studies have suggested a role of nebulette in stabilizing the thin filament, and missense mutations in the nebulette gene were recently shown to be causative for dilated cardiomyopathy and endocardial fibroelastosis in human and mice. However, the role of nebulette in vivo has remained elusive. To provide insights into the function of nebulette in vivo, we generated and studied nebulette-deficient (nebl(-) (/-)) mice. METHODS AND RESULTS Nebl(-) (/-) mice were generated by replacement of exon 1 by Cre under the control of the endogenous nebulette promoter, allowing for lineage analysis using the ROSA26 Cre reporter strain. This revealed specific expression of nebulette in the heart, consistent with in situ hybridization results. Nebl(-) (/-) mice exhibited normal cardiac function both under basal conditions and in response to transaortic constriction as assessed by echocardiography and haemodynamic analyses. Furthermore, histological, IF, and western blot analysis showed no cardiac abnormalities in nebl(-) (/-) mice up to 8 months of age. In contrast, transmission electron microscopy showed Z-line widening starting from 5 months of age, suggesting that nebulette is important for the integrity of the Z-line. Furthermore, up-regulation of cardiac stress responsive genes suggests the presence of chronic cardiac stress in nebl(-) (/-) mice. CONCLUSION Nebulette is dispensable for normal cardiac function, although Z-line widening and up-regulation of cardiac stress markers were found in nebl(-) (/-) heart. These results suggest that the nebulette disease causing mutations have dominant gain-of-function effects.
Collapse
Affiliation(s)
- Giuseppina Mastrototaro
- Humanitas Clinical and Research Center, Via Manzoni 113, 20089 Rozzano, Milan, Italy University of Milano-Bicocca, Milan, Italy
| | - Xingqun Liang
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613C, USA
| | - Xiaodong Li
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613C, USA
| | - Pierluigi Carullo
- Humanitas Clinical and Research Center, Via Manzoni 113, 20089 Rozzano, Milan, Italy Institute of Genetic and Biomedical Research, UOS Milan, National Research Council, Milan, Italy
| | - Nicoletta Piroddi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Chiara Tesi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Yusu Gu
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613C, USA
| | - Nancy D Dalton
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613C, USA
| | - Kirk L Peterson
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613C, USA
| | - Corrado Poggesi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Farah Sheikh
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613C, USA
| | - Ju Chen
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0613C, USA
| | - Marie-Louise Bang
- Humanitas Clinical and Research Center, Via Manzoni 113, 20089 Rozzano, Milan, Italy Institute of Genetic and Biomedical Research, UOS Milan, National Research Council, Milan, Italy
| |
Collapse
|
11
|
Uversky VN. Wrecked regulation of intrinsically disordered proteins in diseases: pathogenicity of deregulated regulators. Front Mol Biosci 2014; 1:6. [PMID: 25988147 PMCID: PMC4428494 DOI: 10.3389/fmolb.2014.00006] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/06/2014] [Indexed: 12/14/2022] Open
Abstract
Biologically active proteins without stable tertiary structure are common in all known proteomes. Functions of these intrinsically disordered proteins (IDPs) are typically related to regulation, signaling, and control. Cellular levels of these important regulators are tightly regulated by a variety mechanisms ranging from firmly controlled expression to precisely targeted degradation. Functions of IDPs are controlled by binding to specific partners, alternative splicing, and posttranslational modifications among other means. In the norm, right amounts of precisely activated IDPs have to be present in right time at right places. Wrecked regulation brings havoc to the ordered world of disordered proteins, leading to protein misfolding, misidentification, and missignaling that give rise to numerous human diseases, such as cancer, cardiovascular disease, neurodegenerative diseases, and diabetes. Among factors inducing pathogenic transformations of IDPs are various cellular mechanisms, such as chromosomal translocations, damaged splicing, altered expression, frustrated posttranslational modifications, aberrant proteolytic degradation, and defective trafficking. This review presents some of the aspects of deregulated regulation of IDPs leading to human diseases.
Collapse
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida Tampa, FL, USA ; Biology Department, Faculty of Science, King Abdulaziz University Jeddah, Saudi Arabia ; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences Moscow, Russia
| |
Collapse
|
12
|
Macaluso F, Isaacs AW, Di Felice V, Myburgh KH. Acute change of titin at mid-sarcomere remains despite 8 wk of plyometric training. J Appl Physiol (1985) 2014; 116:1512-9. [DOI: 10.1152/japplphysiol.00420.2013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The purpose of this study was to investigate skeletal muscle changes induced by an acute bout of plyometric exercise (PlyEx) both before and after PlyEx training, to understand if titin is affected differently after PlyEx training. Healthy untrained individuals ( N = 11) completed the 1stPlyEx (10 × 10 squat-jumps, 1-min rest). Thereafter, six subjects completed 8 wk of PlyEx, while five controls abstained from any jumping activity. Seven days after the last training session, all subjects completed the 2ndPlyEx. Blood samples were collected before and 6 h and 1, 2, 3, and 4 days after each acute bout of PlyEx, and muscle biopsies 4 days before and 3 days after each acute bout of PlyEx. The 1stPlyEx induced an increase in circulating myoglobin concentration. Muscle sample analysis revealed Z-disk streaming, a stretch or a fragmentation of titin (immunogold), and increased calpain-3 autolysis. After training, 2ndPlyEx did not induce Z-disk streaming or calpain-3 activation. The previously observed post-1stPlyEx positional change of the titin COOH terminus was still present pre-2ndPlyEx, in all trained and all control subjects. Only two controls presented with Z-disk streaming after 2ndPlyEx, while calpain-3 activation was absent in all controls. Eccentric explosive exercise induced a stretch or fragmentation of titin, which presented as a positional change of the COOH terminus. Calpain-3 activation does not occur when titin is already stretched before explosive jumping. Enzymatic digestion results in titin fragmentation, but since an increase in calpain-3 autolysis was visible only after the 1stPlyEx acute bout, fragmentation cannot explain the prolonged positional change.
Collapse
Affiliation(s)
- F. Macaluso
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa; and
- Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche, Università di Palermo, Palermo, Italy
| | - A. W. Isaacs
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa; and
| | - V. Di Felice
- Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche, Università di Palermo, Palermo, Italy
| | - K. H. Myburgh
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa; and
| |
Collapse
|
13
|
Abstract
The giant protein titin forms a unique filament network in cardiomyocytes, which engages in both mechanical and signaling functions of the heart. TTN, which encodes titin, is also a major human disease gene. In this review, we cover the roles of cardiac titin in normal and failing hearts, with a special emphasis on the contribution of titin to diastolic stiffness. We provide an update on disease-associated titin mutations in cardiac and skeletal muscles and summarize what is known about the impact of protein-protein interactions on titin properties and functions. We discuss the importance of titin-isoform shifts and titin phosphorylation, as well as titin modifications related to oxidative stress, in adjusting the diastolic stiffness of the healthy and the failing heart. Along the way we distinguish among titin alterations in systolic and in diastolic heart failure and ponder the evidence for titin stiffness as a potential target for pharmacological intervention in heart disease.
Collapse
Affiliation(s)
- Wolfgang A Linke
- From the Department of Cardiovascular Physiology, Ruhr University Bochum, Bochum, Germany
| | | |
Collapse
|
14
|
Ball KA, Wemmer DE, Head-Gordon T. Comparison of structure determination methods for intrinsically disordered amyloid-β peptides. J Phys Chem B 2014; 118:6405-16. [PMID: 24410358 PMCID: PMC4066902 DOI: 10.1021/jp410275y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intrinsically disordered proteins (IDPs) represent a new frontier in structural biology since the primary characteristic of IDPs is that structures need to be characterized as diverse ensembles of conformational substates. We compare two general but very different ways of combining NMR spectroscopy with theoretical methods to derive structural ensembles for the disease IDPs amyloid-β 1-40 and amyloid-β 1-42, which are associated with Alzheimer's Disease. We analyze the performance of de novo molecular dynamics and knowledge-based approaches for generating structural ensembles by assessing their ability to reproduce a range of NMR experimental observables. In addition to the comparison of computational methods, we also evaluate the relative value of different types of NMR data for refining or validating the IDP structural ensembles for these important disease peptides.
Collapse
Affiliation(s)
- K Aurelia Ball
- Graduate Group in Biophysics , Berkeley, California 94720, United States
| | | | | |
Collapse
|
15
|
Abstract
Giant muscle proteins (e.g., titin, nebulin, and obscurin) play a seminal role in muscle elasticity, stretch response, and sarcomeric organization. Each giant protein consists of multiple tandem structural domains, usually arranged in a modular fashion spanning 500 kDa to 4 MDa. Although many of the domains are similar in structure, subtle differences create a unique function of each domain. Recent high and low resolution structural and dynamic studies now suggest more nuanced overall protein structures than previously realized. These findings show that atomic structure, interactions between tandem domains, and intrasarcomeric environment all influence the shape, motion, and therefore function of giant proteins. In this article we will review the current understanding of titin, obscurin, and nebulin structure, from the atomic level through the molecular level.
Collapse
Affiliation(s)
- Logan C Meyer
- Department of Chemistry and Biochemistry, James Madison University Harrisonburg, VA, USA
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University Harrisonburg, VA, USA
| |
Collapse
|
16
|
Yamamoto DL, Vitiello C, Zhang J, Gokhin DS, Castaldi A, Coulis G, Piaser F, Filomena MC, Eggenhuizen PJ, Kunderfranco P, Camerini S, Takano K, Endo T, Crescenzi M, Luther PKL, Lieber RL, Chen J, Bang ML. The nebulin SH3 domain is dispensable for normal skeletal muscle structure but is required for effective active load bearing in mouse. J Cell Sci 2013; 126:5477-89. [PMID: 24046450 DOI: 10.1242/jcs.137026] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nemaline myopathy (NM) is a congenital myopathy with an estimated incidence of 150,000 live births. It is caused by mutations in thin filament components, including nebulin, which accounts for about 50% of the cases. The identification of NM cases with nonsense mutations resulting in loss of the extreme C-terminal SH3 domain of nebulin suggests an important role of the nebulin SH3 domain, which is further supported by the recent demonstration of its role in IGF-1-induced sarcomeric actin filament formation through targeting of N-WASP to the Z-line. To provide further insights into the functional significance of the nebulin SH3 domain in the Z-disk and to understand the mechanisms by which truncations of nebulin lead to NM, we took two approaches: (1) an affinity-based proteomic screening to identify novel interaction partners of the nebulin SH3 domain; and (2) generation and characterization of a novel knockin mouse model with a premature stop codon in the nebulin gene, eliminating its C-terminal SH3 domain (NebΔSH3 mouse). Surprisingly, detailed analyses of NebΔSH3 mice revealed no structural or histological skeletal muscle abnormalities and no changes in gene expression or localization of interaction partners of the nebulin SH3 domain, including myopalladin, palladin, zyxin and N-WASP. Also, no significant effect on peak isometric stress production, passive tensile stress or Young's modulus was found. However, NebΔSH3 muscle displayed a slightly altered force-frequency relationship and was significantly more susceptible to eccentric contraction-induced injury, suggesting that the nebulin SH3 domain protects against eccentric contraction-induced injury and possibly plays a role in fine-tuning the excitation-contraction coupling mechanism.
Collapse
Affiliation(s)
- Daniel L Yamamoto
- Institute of Biomedical Technologies, National Research Council, 20090 Milan, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Eulitz S, Sauer F, Pelissier MC, Boisguerin P, Molt S, Schuld J, Orfanos Z, Kley RA, Volkmer R, Wilmanns M, Kirfel G, van der Ven PFM, Fürst DO. Identification of Xin-repeat proteins as novel ligands of the SH3 domains of nebulin and nebulette and analysis of their interaction during myofibril formation and remodeling. Mol Biol Cell 2013; 24:3215-26. [PMID: 23985323 PMCID: PMC3810769 DOI: 10.1091/mbc.e13-04-0202] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The striated muscle–specific actin-binding proteins Xin and Xirp2 are identified as novel ligands of the SH3 domains of the thin filament ruler nebulin and nebulette. The interaction is spatially restricted to structures associated with myofibril development or remodeling, indicating a role for these proteins in myofibril assembly and repair. The Xin actin-binding repeat–containing proteins Xin and XIRP2 are exclusively expressed in striated muscle cells, where they are believed to play an important role in development. In adult muscle, both proteins are concentrated at attachment sites of myofibrils to the membrane. In contrast, during development they are localized to immature myofibrils together with their binding partner, filamin C, indicating an involvement of both proteins in myofibril assembly. We identify the SH3 domains of nebulin and nebulette as novel ligands of proline-rich regions of Xin and XIRP2. Precise binding motifs are mapped and shown to bind both SH3 domains with micromolar affinity. Cocrystallization of the nebulette SH3 domain with the interacting XIRP2 peptide PPPTLPKPKLPKH reveals selective interactions that conform to class II SH3 domain–binding peptides. Bimolecular fluorescence complementation experiments in cultured muscle cells indicate a temporally restricted interaction of Xin-repeat proteins with nebulin/nebulette during early stages of myofibril development that is lost upon further maturation. In mature myofibrils, this interaction is limited to longitudinally oriented structures associated with myofibril development and remodeling. These data provide new insights into the role of Xin actin-binding repeat–containing proteins (together with their interaction partners) in myofibril assembly and after muscle damage.
Collapse
Affiliation(s)
- Stefan Eulitz
- Institute for Cell Biology, University of Bonn, D-53121 Bonn, Germany European Molecular Biology Laboratory-Hamburg/Deutsches Elektronen-Synchrotron, D-22603 Hamburg, Germany Department of Medicinal Immunology, Charité-University Medicine Berlin, D-13353 Berlin, Germany Department of Neurology, Neuromuscular Center Ruhrgebiet, University Hospital Bergmannsheil, Ruhr-University Bochum, D-44789 Bochum, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Theillet FX, Kalmar L, Tompa P, Han KH, Selenko P, Dunker AK, Daughdrill GW, Uversky VN. The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24360. [PMID: 28516008 PMCID: PMC5424786 DOI: 10.4161/idp.24360] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 03/17/2013] [Indexed: 11/19/2022]
Abstract
A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.
Collapse
Affiliation(s)
- Francois-Xavier Theillet
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - Lajos Kalmar
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium.,Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics; University of Science and Technology; Daejeon, Yuseong-gu, Korea.,Biomedical Translational Research Center; Division of Convergent Biomedical Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Yuseong-gu, Korea
| | - Philipp Selenko
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Department of Biochemistry and Molecular Biology; Indiana University School of Medicine; Indianapolis, IN USA
| | - Gary W Daughdrill
- Center for Drug Discovery and Innovation; Department of Cell Biology, Microbiology and Molecular Biology; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
| |
Collapse
|
19
|
Tsai WL, Forbes JG, Wang K. Engineering of an elastic scaffolding polyprotein based on an SH3-binding intrinsically disordered titin PEVK module. Protein Expr Purif 2012; 85:187-99. [PMID: 22910563 PMCID: PMC3463739 DOI: 10.1016/j.pep.2012.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/24/2012] [Accepted: 08/03/2012] [Indexed: 01/21/2023]
Abstract
Titin is a large elastic protein found in muscle that maintains the elasticity and structural integrity of the sarcomere. The PEVK region of titin is intrinsically disordered, highly elastic and serves as a hub to bind signaling proteins. Systematic investigation of the structure and affinity profile of the PEVK region will provide important information about the functions of titin. Since PEVK is highly heterogeneous due to extensive differential splicing from more than one hundred exons, we engineered and expressed polyproteins that consist of a defined number of identical single exon modules. These customized polyproteins reduce heterogeneity, amplify interactions of less dominant modules, and most importantly, provide tags for atomic force microscopy and allow more readily interpretable data from single-molecule techniques. Expression and purification of recombinant polyprotein with repeat regions presented many technical challenges: recombination events in tandem repeats of identical DNA sequences exacerbated by high GC content, toxicity of polymer plasmid and expressed protein to the bacteria; early truncation of proteins expressed with different numbers of modules; and extreme sensitivity to proteolysis. We have investigated a number of in vitro and in vivo bacterial and yeast expression systems, as well as baculoviral systems as potential solutions to these problems. We successfully expressed and purified in gram quantities a polyprotein derived from human titin exon 172 using Pichia pastoris yeast. This study provides valuable insights into the technical challenges regarding the engineering and purification of a tandem repeat sequence of an intrinsically disordered biopolymer.
Collapse
Affiliation(s)
- Wanxia Li Tsai
- Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH/DHHS, Bethesda, MD 20892-8024, USA.
| | | | | |
Collapse
|
20
|
Abstract
Protein-protein interactions (PPIs) govern all aspects of cell function and, as such, are a major target for research and therapeutic intervention. A major rate-limiting step in PPI research is the expression and purification of full-length proteins. The use of peptides to study PPIs significantly facilitates the structural and biophysical characterization of PPIs as well as the effort to develop drugs to control PPIs. Here we describe examples for the use of peptides to study PPI and some of the important experimental methods that are used in the field. Peptides have proved to be excellent tools to study PPIs and have been contributing both for understanding mechanisms of PPIs as well as for drug design for PPI modulation.
Collapse
|
21
|
Voelkel T, Linke WA. Conformation-regulated mechanosensory control via titin domains in cardiac muscle. Pflugers Arch 2011; 462:143-54. [PMID: 21347754 PMCID: PMC3114084 DOI: 10.1007/s00424-011-0938-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 12/19/2022]
Abstract
The giant filamentous protein titin is ideally positioned in the muscle sarcomere to sense mechanical stimuli and transform them into biochemical signals, such as those triggering cardiac hypertrophy. In this review, we ponder the evidence for signaling hotspots along the titin filament involved in mechanosensory control mechanisms. On the way, we distinguish between stress and strain as triggers of mechanical signaling events at the cardiac sarcomere. Whereas the Z-disk and M-band regions of titin may be prominently involved in sensing mechanical stress, signaling hotspots within the elastic I-band titin segment may respond primarily to mechanical strain. Common to both stress and strain sensor elements is their regulation by conformational changes in protein domains.
Collapse
Affiliation(s)
- Tobias Voelkel
- Department of Cardiovascular Physiology, Institute of Physiology, Ruhr University Bochum, MA 3/56, 44780 Bochum, Germany
| | - Wolfgang A. Linke
- Department of Cardiovascular Physiology, Institute of Physiology, Ruhr University Bochum, MA 3/56, 44780 Bochum, Germany
| |
Collapse
|
22
|
Forbes JG, Flaherty DB, Ma K, Qadota H, Benian GM, Wang K. Extensive and modular intrinsically disordered segments in C. elegans TTN-1 and implications in filament binding, elasticity and oblique striation. J Mol Biol 2010; 398:672-89. [PMID: 20346955 PMCID: PMC2908218 DOI: 10.1016/j.jmb.2010.03.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/17/2010] [Accepted: 03/17/2010] [Indexed: 11/26/2022]
Abstract
TTN-1, a titin like protein in Caenorhabditis elegans, is encoded by a single gene and consists of multiple Ig and fibronectin 3 domains, a protein kinase domain and several regions containing tandem short repeat sequences. We have characterized TTN-1's sarcomere distribution, protein interaction with key myofibrillar proteins as well as the conformation malleability of representative motifs of five classes of short repeats. We report that two antibodies developed to portions of TTN-1 detect an approximately 2-MDa polypeptide on Western blots. In addition, by immunofluorescence staining, both of these antibodies localize to the I-band and may extend into the outer edge of the A-band in the obliquely striated muscle of the nematode. Six different 300-residue segments of TTN-1 were shown to variously interact with actin and/or myosin in vitro. Conformations of synthetic peptides of representative copies of each of the five classes of repeats--39-mer PEVT, 51-mer CEEEI, 42-mer AAPLE, 32-mer BLUE and 30-mer DispRep--were investigated by circular dichroism at different temperatures, ionic strengths and solvent polarities. The PEVT, CEEEI, DispRep and AAPLE peptides display a combination of a polyproline II helix and an unordered structure in aqueous solution and convert in trifluoroethanol to alpha-helix (PEVT, CEEEI, DispRep) and beta-turn (AAPLE) structures, respectively. The octads in BLUE motifs form unstable alpha-helix-like structures coils in aqueous solution and negligible heptad-based, alpha-helical coiled-coils. The alpha-helical structure, as modeled by threading and molecular dynamics simulations, tends to form helical bundles and crosses based on its 8-4-2-2 hydrophobic helical patterns and charge arrays on its surface. Our finding indicates that APPLE, PEVT, CEEEI and DispRep regions are all intrinsically disordered and highly reminiscent of the conformational malleability and elasticity of vertebrate titin PEVK segments. The proposed presence of long, modular and unstable alpha-helical oligomerization domains in the BLUE region of TTN-1 could bundle TTN-1 and stabilize oblique striation of the sarcomere.
Collapse
Affiliation(s)
- Jeffrey G. Forbes
- Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Denise B. Flaherty
- Department of Pathology, Emory University, Whitehead Biomedical Research Building, Atlanta, GA 30332, USA
- Collegium of the Natural Sciences, Eckerd College, St. Petersburg, FL 33711
| | - Kan Ma
- Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hiroshi Qadota
- Department of Pathology, Emory University, Whitehead Biomedical Research Building, Atlanta, GA 30332, USA
| | - Guy M. Benian
- Department of Pathology, Emory University, Whitehead Biomedical Research Building, Atlanta, GA 30332, USA
| | - Kuan Wang
- Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
23
|
Kontrogianni-Konstantopoulos A, Ackermann MA, Bowman AL, Yap SV, Bloch RJ. Muscle giants: molecular scaffolds in sarcomerogenesis. Physiol Rev 2009; 89:1217-67. [PMID: 19789381 PMCID: PMC3076733 DOI: 10.1152/physrev.00017.2009] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Myofibrillogenesis in striated muscles is a highly complex process that depends on the coordinated assembly and integration of a large number of contractile, cytoskeletal, and signaling proteins into regular arrays, the sarcomeres. It is also associated with the stereotypical assembly of the sarcoplasmic reticulum and the transverse tubules around each sarcomere. Three giant, muscle-specific proteins, titin (3-4 MDa), nebulin (600-800 kDa), and obscurin (approximately 720-900 kDa), have been proposed to play important roles in the assembly and stabilization of sarcomeres. There is a large amount of data showing that each of these molecules interacts with several to many different protein ligands, regulating their activity and localizing them to particular sites within or surrounding sarcomeres. Consistent with this, mutations in each of these proteins have been linked to skeletal and cardiac myopathies or to muscular dystrophies. The evidence that any of them plays a role as a "molecular template," "molecular blueprint," or "molecular ruler" is less definitive, however. Here we review the structure and function of titin, nebulin, and obscurin, with the literature supporting a role for them as scaffolding molecules and the contradictory evidence regarding their roles as molecular guides in sarcomerogenesis.
Collapse
|
24
|
Fernando P, Sandoz JS, Ding W, de Repentigny Y, Brunette S, Kelly JF, Kothary R, Megeney LA. Bin1 SRC homology 3 domain acts as a scaffold for myofiber sarcomere assembly. J Biol Chem 2009; 284:27674-86. [PMID: 19633357 DOI: 10.1074/jbc.m109.029538] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In skeletal muscle development, the genes and regulatory factors that govern the specification of myocytes are well described. Despite this knowledge, the mechanisms that regulate the coordinated assembly of myofiber proteins into the functional contractile unit or sarcomere remain undefined. Here we explored the hypothesis that modular domain proteins such as Bin1 coordinate protein interactions to promote sarcomere formation. We demonstrate that Bin1 facilitates sarcomere organization through protein-protein interactions as mediated by the Src homology 3 (SH3) domain. We observed a profound disorder in myofiber size and structural organization in a murine model expressing the Bin1 SH3 region. In addition, satellite cell-derived myogenesis was limited despite the accumulation of skeletal muscle-specific proteins. Our experiments revealed that the Bin1 SH3 domain formed transient protein complexes with both actin and myosin filaments and the pro-myogenic kinase Cdk5. Bin1 also associated with a Cdk5 phosphorylation domain of titin. Collectively, these observations suggest that Bin1 displays protein scaffold-like properties and binds with sarcomeric factors important in directing sarcomere protein assembly and myofiber maturation.
Collapse
Affiliation(s)
- Pasan Fernando
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa, Ontario K1H 8L6, Canada.
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Cortese MS, Uversky VN, Dunker AK. Intrinsic disorder in scaffold proteins: getting more from less. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2008; 98:85-106. [PMID: 18619997 DOI: 10.1016/j.pbiomolbio.2008.05.007] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Regulation, recognition and cell signaling involve the coordinated actions of many players. Signaling scaffolds, with their ability to bring together proteins belonging to common and/or interlinked pathways, play crucial roles in orchestrating numerous events by coordinating specific interactions among signaling proteins. This review examines the roles of intrinsic disorder (ID) in signaling scaffold protein function. Several well-characterized scaffold proteins with structurally and functionally characterized ID regions are used here to illustrate the importance of ID for scaffolding function. These examples include scaffolds that are mostly disordered, only partially disordered or those in which the ID resides in a scaffold partner. Specific scaffolds discussed include RNase, voltage-activated potassium channels, axin, BRCA1, GSK-3beta, p53, Ste5, titin, Fus3, BRCA1, MAP2, D-AKAP2 and AKAP250. Among the mechanisms discussed are: molecular recognition features, fly-casting, ease of encounter complex formation, structural isolation of partners, modulation of interactions between bound partners, masking of intramolecular interaction sites, maximized interaction surface per residue, toleration of high evolutionary rates, binding site overlap, allosteric modification, palindromic binding, reduced constraints for alternative splicing, efficient regulation via posttranslational modification, efficient regulation via rapid degradation, protection of normally solvent-exposed sites, enhancing the plasticity of interaction and molecular crowding. We conclude that ID can enhance scaffold function by a diverse array of mechanisms. In other words, scaffold proteins utilize several ID-facilitated mechanisms to enhance function, and by doing so, get more functionality from less structure.
Collapse
Affiliation(s)
- Marc S Cortese
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | | |
Collapse
|
26
|
Hegedus T, Serohijos AWR, Dokholyan NV, He L, Riordan JR. Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. J Mol Biol 2008; 378:1052-63. [PMID: 18423665 DOI: 10.1016/j.jmb.2008.03.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 03/11/2008] [Accepted: 03/15/2008] [Indexed: 01/09/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-dependent chloride channel that is mutated in cystic fibrosis, an inherited disease of high morbidity and mortality. The phosphorylation of its approximately 200 amino acid R domain by protein kinase A is obligatory for channel gating under normal conditions. The R domain contains more than ten PKA phosphorylation sites. No individual site is essential but phosphorylation of increasing numbers of sites enables progressively greater channel activity. In spite of numerous studies of the role of the R domain in CFTR regulation, its mechanism of action remains largely unknown. This is because neither its structure nor its interactions with other parts of CFTR have been completely elucidated. Studies have shown that the R domain lacks well-defined secondary structural elements and is an intrinsically disordered region of the channel protein. Here, we have analyzed the disorder pattern and employed computational methods to explore low-energy conformations of the R domain. The specific disorder and secondary structure patterns detected suggest the presence of molecular recognition elements (MoREs) that may mediate phosphorylation-regulated intra- and inter-domain interactions. Simulations were performed to generate an ensemble of accessible R domain conformations. Although the calculated structures may represent more compact conformers than occur in vivo, their secondary structure propensities are consistent with predictions and published experimental data. Equilibrium simulations of a mimic of a phosphorylated R domain showed that it exhibited an increased radius of gyration. In one possible interpretation of these findings, by changing its size, the globally unstructured R domain may act as an entropic spring to perturb the packing of membrane-spanning sequences that constitute the ion permeability pathway and thereby activate channel gating.
Collapse
Affiliation(s)
- Tamás Hegedus
- Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA.
| | | | | | | | | |
Collapse
|
27
|
Cavnar PJ, Olenych SG, Keller TCS. Molecular identification and localization of cellular titin, a novel titin isoform in the fibroblast stress fiber. ACTA ACUST UNITED AC 2007; 64:418-33. [PMID: 17366640 DOI: 10.1002/cm.20193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We previously discovered a large titin-like protein-c-titin-in chicken epithelial brush border and human blood platelet extracts that binds alpha-actinin and organizes arrays of myosin II bipolar filaments in vitro. RT-PCR analysis of total RNA from human megakaryoblastic (CHRF-288-11) and mouse fibroblast (3T3) nonmuscle cells reveal sequences identical to known titin gene exon sequences that encode parts of the Z-line, I-band, PEVK domain, A-band, and M-line regions of striated muscle titins. In the nonmuscle cells, these sequences are differentially spliced in patterns not reported for any striated muscle titin isoform. Rabbit polyclonal antibodies raised against expressed protein fragments encoded by the Z-repeat and kinase domain regions react with the c-titin band in Western blot analysis of platelet extracts and immunoprecipitate c-titin in whole platelet extracts. Immunofluorescent localization demonstrates that the majority of the c-titin colocalizes with alpha-actinin and actin in 3T3 and Indian Muntjac deer skin fibroblast stress fibers. Our results suggest that differential expression of titin gene exons in nonmuscle cells yields multiple novel isoforms of the protein c-titin that are associated with the actin stress fiber structures.
Collapse
Affiliation(s)
- Peter J Cavnar
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370, USA
| | | | | |
Collapse
|