Intermediate filaments: molecular architecture, assembly, dynamics and polymorphism

1999 ◽  
Vol 32 (2) ◽  
pp. 99-187 ◽  
Author(s):  
David A. D. Parry ◽  
Peter M. Steinert
Keyword(s):  
Intermediate Filaments ◽  
Intermediate Filament ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Lattice Structure ◽  
Coiled Coil ◽  
Salt Bridges ◽  
Molecular Architecture

1. Introduction 1002. Molecular architecture 1072.1 Primary structure 1082.1.1 Homologous regions 1092.1.2 Chain typing 1152.1.3 Post-translational modifications 1172.2 Secondary structure 1182.2.1 Central rod domain 1182.2.2 Head and tail domains 1192.3 Tertiary structure 1232.3.1 Coiled-coil rod domain 1232.3.1.1 Specificity through salt bridges 1242.3.1.2 Specificity through apolar interactions 1272.3.1.3 A consensus trigger sequence for two-stranded coiled-coils 1282.3.2 Discontinuities in the rod domain 1282.3.2.1 Links 1292.3.2.2 Stutter 1312.3.3 Head and tail domains 1312.4 Electron microscope observations 1333. Assembly 1363.1 Role of the coiled-coil rod domain 1373.2 Role of end domains 1413.3 Experimentally induced crosslinks and modes of assembly 1453.4 Naturally occurring crosslinks for tissue coordination 1543.5 STEM data 1544. Quaternary structure 1604.1 Protofilaments and protofibrils 1604.2 Head and tail domains 1634.3 Surface lattice structure 1644.4 Crystal studies on intermediate filament fragments 1685. Polymorphism 1695.1 Variations on a theme 1705.1.1 Axial structure 1705.1.2 Lateral structure 1716. Keratin intermediate filament chains in diseases 1727. Concluding remarks 1758. Acknowledgments 1769. References 176Three types of intracellular filament have been identified in eukaryotic cells, and together they constitute the key elements of the cytoskeleton. They are the microtubules, the actin-containing microfilaments and the intermediate filaments. The uniqueness of the former two types of filament in cells has been well known for a long time but, in contrast, the intermediate filaments have been a relative new-comer to the scene. The microtubules and the microfilaments have always been easy to distinguish from one another on the grounds of their respective sizes (microtubules are about 25 nm in diameter and microfilaments are about 7–10 nm in diameter). Additionally, microtubules were capable of being disaggregated by the action of colchicine, and microfilaments could be disassembled by other drugs or be decorated with heavy meromyosin to generate arrowhead-like structures. Importantly, in both microtubules and microfilaments the constituent protein subunits were arranged to give the filaments a directionality, and the ability of these filaments to function in vivo depended crucially on this feature of their structure. Microtubules, for example, are involved in mitosis, motility and transport within the cell: each of these functions is clearly a ‘directional’ one. With this background the discovery and characterization of the intermediate filaments can begin.

scholarly journals Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1

Open Biology ◽  
2014 ◽  
Vol 4 (3) ◽  
pp. 130172 ◽  
Author(s):  
Barbara Franke ◽  
Alexander Gasch ◽  
Dayté Rodriguez ◽  
Mohamed Chami ◽  
Muzamil M. Khan ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Quaternary Structure ◽  
E3 Ubiquitin Ligase ◽  
Coiled Coil ◽  
Trim Protein ◽  
Muscle Catabolism ◽  
And Function ◽  
Helical Region ◽  
Structural Significance

MuRF1 is an E3 ubiquitin ligase central to muscle catabolism. It belongs to the TRIM protein family characterized by a tripartite fold of RING, B-box and coiled-coil (CC) motifs, followed by variable C-terminal domains. The CC motif is hypothesized to be responsible for domain organization in the fold as well as for high-order assembly into functional entities. But data on CC from this family that can clarify the structural significance of this motif are scarce. We have characterized the helical region from MuRF1 and show that, contrary to expectations, its CC domain assembles unproductively, being the B2- and COS-boxes in the fold (respectively flanking the CC) that promote a native quaternary structure. In particular, the C-terminal COS-box seemingly forms an α-hairpin that packs against the CC, influencing its dimerization. This shows that a C-terminal variable domain can be tightly integrated within the conserved TRIM fold to modulate its structure and function. Furthermore, data from transfected muscle show that in MuRF1 the COS-box mediates the in vivo targeting of sarcoskeletal structures and points to the pharmacological relevance of the COS domain for treating MuRF1-mediated muscle atrophy.

scholarly journals Assembly of type IV neuronal intermediate filaments in nonneuronal cells in the absence of preexisting cytoplasmic intermediate filaments

1993 ◽  
Vol 122 (6) ◽  
pp. 1323-1335 ◽  
Author(s):  
GY Ching ◽  
RK Liem
Keyword(s):  
Intermediate Filaments ◽  
Intermediate Filament ◽  
Cultured Cells ◽  
Neuronal Cell ◽  
Intermediate Filament Protein ◽  
Amino Acid Residues ◽  
Intermediate Filament Proteins ◽  
Transfected Cells ◽  
Type Iv

We report here on the in vivo assembly of alpha-internexin, a type IV neuronal intermediate filament protein, in transfected cultured cells, comparing its assembly properties with those of the neurofilament triplet proteins (NF-L, NF-M, and NF-H). Like the neurofilament triplet proteins, alpha-internexin coassembles with vimentin into filaments. To study the assembly characteristics of these proteins in the absence of a preexisting filament network, transient transfection experiments were performed with a non-neuronal cell line lacking cytoplasmic intermediate filaments. The results showed that only alpha-internexin was able to self-assemble into extensive filamentous networks. In contrast, the neurofilament triplet proteins were incapable of homopolymeric assembly into filamentous arrays in vivo. NF-L coassembled with either NF-M or NF-H into filamentous structures in the transfected cells, but NF-M could not form filaments with NF-H. alpha-internexin could coassemble with each of the neurofilament triplet proteins in the transfected cells to form filaments. When all but 2 and 10 amino acid residues were removed from the tail domains of NF-L and NF-M, respectively, the resulting NF-L and NF-M deletion mutants retained the ability to coassemble with alpha-internexin into filamentous networks. These mutants were also capable of forming filaments with other wild-type neurofilament triplet protein subunits. These results suggest that the tail domains of NF-L and NF-M are dispensable for normal coassembly of each of these proteins with other type IV intermediate filament proteins to form filaments.

scholarly journals The Centrosomal, Putative Tumor Suppressor Protein TACC2 Is Dispensable for Normal Development, and Deficiency Does Not Lead to Cancer

2004 ◽  
Vol 24 (14) ◽  
pp. 6403-6409 ◽  
Author(s):  
Michael M. Schuendeln ◽  
Roland P. Piekorz ◽  
Christian Wichmann ◽  
Youngsoo Lee ◽  
Peter J. McKinnon ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Cell Cycle Progression ◽  
Tumor Development ◽  
Coiled Coil ◽  
Physiological Role ◽  
Tumor Suppressor Protein ◽  
Wild Type ◽  
Mouse Development

ABSTRACT TACC2 is a member of the transforming acidic coiled-coil-containing protein family and is associated with the centrosome-spindle apparatus during cell cycling. In vivo, the TACC2 gene is expressed in various splice forms predominantly in postmitotic tissues, including heart, muscle, kidney, and brain. Studies of human breast cancer samples and cell lines suggest a putative role of TACC2 as a tumor suppressor protein. To analyze the physiological role of TACC2, we generated mice lacking TACC2. TACC2-deficient mice are viable, develop normally, are fertile, and lack phenotypic changes compared to wild-type mice. Furthermore, TACC2 deficiency does not lead to an increased incidence of tumor development. Finally, in TACC2-deficient embryonic fibroblasts, proliferation and cell cycle progression as well as centrosome numbers are comparable to those in wild-type cells. Therefore, TACC2 is not required, nonredundantly, for mouse development and normal cell proliferation and is not a tumor suppressor protein.

scholarly journals alpha-Internexin, a 66-kD intermediate filament-binding protein from mammalian central nervous tissues.

1985 ◽  
Vol 101 (4) ◽  
pp. 1316-1322 ◽  
Author(s):  
J S Pachter ◽  
R K Liem
Keyword(s):  
Optic Nerve ◽  
Intermediate Filaments ◽  
Intermediate Filament ◽  
Peptide Mapping ◽  
Exchange Chromatography ◽  
Filament Assembly ◽  
Antigen Antibody

In this paper we describe a 66-kD protein that co-purifies with intermediate filaments from rat optic nerve and spinal cord but can be separated further by ion-exchange chromatography. This protein is distinct from the 68-kD neurofilament subunit protein as judged by isoelectric focusing, immunoblotting, peptide mapping, and tests of polymerization competence. This protein is avidly recognized by the monoclonal anti-intermediate filament antigen antibody, previously demonstrated to recognize a common antigenic determinant in all five known classes of intermediate filaments. Also, when isolated this protein binds to various intermediate filament subunit proteins, which suggests an in vivo interaction with the intermediate filament cytoskeleton, and it appears to be axonally transported in the rat optic nerve. Because of this ability to bind to intermediate filaments in situ and in vitro we have named this protein alpha-internexin. A possible functional role for the protein in organizing filament assembly and distribution is discussed.

scholarly journals Expression of plectin mutant cDNA in cultured cells indicates a role of COOH-terminal domain in intermediate filament association.

1993 ◽  
Vol 121 (3) ◽  
pp. 607-619 ◽  
Author(s):  
G Wiche ◽  
D Gromov ◽  
A Donovan ◽  
M J Castañón ◽  
E Fuchs
Keyword(s):  
Intermediate Filaments ◽  
Intermediate Filament ◽  
Cultured Cells ◽  
Globular Domain ◽  
Mutant Proteins ◽  
Terminal Domain ◽  
Confocal Immunofluorescence Microscopy ◽  
Terminal Repeats ◽  
Carboxy Terminal

Plectin is an intermediate filament (IF) binding protein of exceptionally large size. Its molecular structure, revealed by EM and predicted by its sequence, indicates an NH2-terminal globular domain, a long rodlike central domain, and a globular COOH-terminal domain containing six highly homologous repeat regions. To examine the role of the various domains in mediating plectin's interaction with IFs, we have constructed rat cDNAs encoding truncated plectin mutants under the control of the SV-40 promoter. Mutant proteins expressed in mammalian COS and PtK2 cells could be distinguished from endogenous wild type plectin by virtue of a short carboxy-terminal antigenic peptide (P tag). As shown by conventional and confocal immunofluorescence microscopy, the transient expression of plectin mutants containing all six or the last four of the repeat regions of the COOH-terminus, or the COOH-terminus and the rod, associated with IF networks of both the vimentin and the cytokeratin type and eventually caused their collapse into perinuclear aggregates. Similar effects were observed upon expression of a protein encoded by a full length cDNA construct. Microtubules and microfilaments were unaffected. Unexpectedly, mutants containing the rod without any of the COOH-terminal repeats, accumulated almost exclusively within the nuclei of cells. When the rod was extended by the first one and a half of the COOH-terminal repeats, mutant proteins showed a partial cytoplasmic distribution, although association with intermediate filaments was not observed. Nuclear and diffuse cytoplasmic distribution was also observed upon expression of the NH2-terminal domain without rod. These results indicate that sequences located roughly within the last two thirds of the globular COOH-terminus are indispensable for association of plectin with intermediate filaments in living cells.

scholarly journals The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

2017 ◽  
Vol 28 (23) ◽  
pp. 3298-3314 ◽  
Author(s):  
Shruthi Viswanath ◽  
Massimiliano Bonomi ◽  
Seung Joong Kim ◽  
Vadim A. Klenchin ◽  
Keenan C. Taylor ◽  
...  
Keyword(s):  
Cell Biology ◽  
Spindle Pole Body ◽  
Coiled Coil ◽  
Resonance Energy ◽  
Spindle Pole ◽  
Physical Structure ◽  
Molecular Architecture ◽  
X Ray ◽  
Pole Body

Microtubule-organizing centers (MTOCs) form, anchor, and stabilize the polarized network of microtubules in a cell. The central MTOC is the centrosome that duplicates during the cell cycle and assembles a bipolar spindle during mitosis to capture and segregate sister chromatids. Yet, despite their importance in cell biology, the physical structure of MTOCs is poorly understood. Here we determine the molecular architecture of the core of the yeast spindle pole body (SPB) by Bayesian integrative structure modeling based on in vivo fluorescence resonance energy transfer (FRET), small-angle x-ray scattering (SAXS), x-ray crystallography, electron microscopy, and two-hybrid analysis. The model is validated by several methods that include a genetic analysis of the conserved PACT domain that recruits Spc110, a protein related to pericentrin, to the SPB. The model suggests that calmodulin can act as a protein cross-linker and Spc29 is an extended, flexible protein. The model led to the identification of a single, essential heptad in the coiled-coil of Spc110 and a minimal PACT domain. It also led to a proposed pathway for the integration of Spc110 into the SPB.

Plectin: A Cytolinker by Design

1999 ◽  
Vol 380 (2) ◽  
pp. 151-158 ◽  
Author(s):  
F.A. Steinböck ◽  
G. Wiche
Keyword(s):  
Intermediate Filaments ◽  
Intermediate Filament ◽  
Transmembrane Protein ◽  
Coiled Coil ◽  
Cytoskeletal Protein ◽  
Terminal Domain ◽  
Junctional Proteins ◽  
Molecular Backbone ◽  
Cytoskeletal Elements

Abstract Plectin is a cytoskeletal protein of > 500 kDa that forms dumbbell-shaped homodimers comprising a central parallel α-helical coiled coil rod domain flanked by globular domains, thus providing a molecular backbone ideally suited to mediate the protein's interactions with an array of other cytoskeletal elements. Plectin self-associates and interacts with actin and intermediate filament cytoskeleton networks at opposite ends, and it binds at both ends to the hemidesmosomal transmembrane protein integrin beta-4, and likely to other junctional proteins. The central coiled coil rod domain can form bridges over long stretches and serves as a flexible linker between the structurally diverse N-terminal domain and the highly conserved C-terminal domain. Plectin is also a target of p34cdc2 kinase that regulates its dissociation from intermediate filaments during mitosis.

scholarly journals Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal Its Essential Role in Replication

2006 ◽  
Vol 80 (17) ◽  
pp. 8566-8581 ◽  
Author(s):  
Xuehua Zhong ◽  
Neocles Leontis ◽  
Shuiming Qian ◽  
Asuka Itaya ◽  
Yijun Qi ◽  
...  
Keyword(s):  
Essential Role ◽  
Tertiary Structure ◽  
Matrix Analysis ◽  
Base Pairs ◽  
Rna Motifs ◽  
Viroid Infection ◽  
Functional Analyses

ABSTRACT RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented in which core non-Watson-Crick base pairs are precisely specified. Isostericity matrix analysis of these base pairs showed that the model accounts for the reported natural sequence variations and viable experimental mutations in loop E motifs of PSTVd and other viroids. Furthermore, isostericity matrix analysis allowed us to design disruptive, as well as compensatory, mutations of PSTVd loop E. Functional analyses of such mutants by in vitro and in vivo experiments demonstrated that loop E structural integrity is crucial for replication, specifically during transcription. Our results suggest that the PSTVd loop E motif exists and functions in vivo and provide loss-of-function genetic evidence for the essential role of a viroid RNA three-dimensional motif in rolling-circle replication. The use of isostericity matrix analysis of non-Watson-Crick base pairing to rationalize mutagenesis of tertiary motifs and systematic in vitro and in vivo functional assays of mutants offers a novel, comprehensive approach to elucidate the tertiary-structure-function relationships for RNA motifs of general biological significance.

scholarly journals Structural and Functional Analysis of Essential pre-mRNA Splicing Factor Prp19p

2005 ◽  
Vol 25 (1) ◽  
pp. 451-460 ◽  
Author(s):  
Melanie D. Ohi ◽  
Craig W. Vander Kooi ◽  
Joshua A. Rosenberg ◽  
Liping Ren ◽  
Justin P. Hirsch ◽  
...  
Keyword(s):  
Functional Data ◽  
Coiled Coil ◽  
Single Copy ◽  
Coiled Coils ◽  
Binding Partner ◽  
Central Stalk ◽  
Interaction Surface

ABSTRACT U-box-containing Prp19p is an integral component of the Prp19p-associated complex (the nineteen complex, or NTC) that is essential for activation of the spliceosome. Prp19p makes numerous protein-protein contacts with other NTC components and is required for NTC stability. Here we show that Prp19p forms a tetramer in vitro and in vivo and we map the domain required for its oligomerization to a central tetrameric coiled-coil. Biochemical and in vivo analyses are consistent with Prp19p tetramerization providing an interaction surface for a single copy of its binding partner, Cef1p. Electron microscopy showed that the isolated Prp19p tetramer is an elongated particle consisting of four globular WD40 domains held together by a central stalk consisting of four N-terminal U-boxes and four coiled-coils. These structural and functional data provide a basis for understanding the role of Prp19p as a key architectural component of the NTC.

scholarly journals Dimerization of the ATRIP Protein through the Coiled-Coil Motif and Its Implication to the Maintenance of Stalled Replication Forks

2005 ◽  
Vol 16 (12) ◽  
pp. 5551-5562 ◽  
Author(s):  
Eisuke Itakura ◽  
Isao Sawada ◽  
Akira Matsuura
Keyword(s):  
Mammalian Cells ◽  
Coiled Coil ◽  
Genotoxic Stress ◽  
Replication Forks ◽  
Cycle Arrest ◽  
Coiled Coil Domain ◽  
Functional Complex ◽  
Stalled Replication Forks

ATR (ATM and Rad3-related), a PI kinase-related kinase (PIKK), has been implicated in the DNA structure checkpoint in mammalian cells. ATR associates with its partner protein ATRIP to form a functional complex in the nucleus. In this study, we investigated the role of the ATRIP coiled-coil domain in ATR-mediated processes. The coiled-coil domain of human ATRIP contributes to self-dimerization in vivo, which is important for the stable translocation of the ATR-ATRIP complex to nuclear foci that are formed after exposure to genotoxic stress. The expression of dimerization-defective ATRIP diminishes the maintenance of replication forks during treatment with replication inhibitors. By contrast, it does not compromise the G2/M checkpoint after IR-induced DNA damage. These results show that there are two critical functions of ATR-ATRIP after the exposure to genotoxic stress: maintenance of the integrity of replication machinery and execution of cell cycle arrest, which are separable and are achieved via distinct mechanisms. The former function may involve the concentrated localization of ATR to damaged sites for which the ATRIP coiled-coil motif is critical.

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