Intermediate filament

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Intermediate filament tail domain
PDB 1ifr EBI.jpg
Structure of lamin a/c globular domain
Identifiers
SymbolIF_tail
Pfam PF00932
InterPro IPR001322
PROSITE PDOC00198
SCOP2 1ivt / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
Intermediate filament rod domain
PDB 1gk4 EBI.jpg
Human vimentin coil 2b fragment (cys2)
Identifiers
SymbolFilament
Pfam PF00038
InterPro IPR016044
PROSITE PDOC00198
SCOP2 1gk7 / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
Intermediate filament head (DNA binding) region
Identifiers
SymbolFilament_head
Pfam PF04732
InterPro IPR006821
SCOP2 1gk7 / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
Peripherin neuronal intermediate filament protein
Identifiers
SymbolPRPH
Alt. symbolsNEF4
NCBI gene 5630
HGNC 9461
OMIM 170710
RefSeq NM_006262.3
UniProt P41219
Other data
Locus Chr. 12 q13.12
Search for
Structures Swiss-model
Domains InterPro
Nestin neuronal stem cell intermediate filament protein
Identifiers
SymbolNES
NCBI gene 10763
HGNC 7756
OMIM 600915
RefSeq NP_006608
UniProt P48681
Other data
Locus Chr. 1 q23.1
Search for
Structures Swiss-model
Domains InterPro

Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. [1] [2] [3] Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma . [4]

Contents

Intermediate filaments are composed of a family of related proteins sharing common structural and sequence features. Initially designated 'intermediate' because their average diameter (10  nm) is between those of narrower microfilaments (actin) and wider myosin filaments found in muscle cells, the diameter of intermediate filaments is now commonly compared to actin microfilaments (7 nm) and microtubules (25 nm). [1] [5] Animal intermediate filaments are subcategorized into six types based on similarities in amino acid sequence and protein structure. [6] Most types are cytoplasmic, but one type, Type V is a nuclear lamin. Unlike microtubules, IF distribution in cells shows no good correlation with the distribution of either mitochondria or endoplasmic reticulum. [7]

Structure

Structure of intermediate filament Intermediate filament.svg
Structure of intermediate filament

The structure of proteins that form intermediate filaments (IF) was first predicted by computerized analysis of the amino acid sequence of a human epidermal keratin derived from cloned cDNAs. [8] Analysis of a second keratin sequence revealed that the two types of keratins share only about 30% amino acid sequence homology but share similar patterns of secondary structure domains. [9] As suggested by the first model, all IF proteins appear to have a central alpha-helical rod domain that is composed of four alpha-helical segments (named as 1A, 1B, 2A and 2B) separated by three linker regions. [9] [10]

The central building block of an intermediate filament is a pair of two intertwined proteins that is called a coiled-coil structure. This name reflects the fact that the structure of each protein is helical, and the intertwined pair is also a helical structure. Structural analysis of a pair of keratins shows that the two proteins that form the coiled-coil bind by hydrophobic interactions. [11] [12] The charged residues in the central domain do not have a major role in the binding of the pair in the central domain. [11]

Cytoplasmic IFs assemble into non-polar unit-length filaments (ULFs). Identical ULFs associate laterally into staggered, antiparallel, soluble tetramers, which associate head-to-tail into protofilaments that pair up laterally into protofibrils, four of which wind together into an intermediate filament. [13] Part of the assembly process includes a compaction step, in which ULF tighten and assume a smaller diameter. The reasons for this compaction are not well understood, and IF are routinely observed to have diameters ranging between 6 and 12 nm.

The N-terminus and the C-terminus of IF proteins are non-alpha-helical regions and show wide variation in their lengths and sequences across IF families. The N-terminal "head domain" binds DNA. [14] Vimentin heads are able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease may play an important role in HIV-1 associated cytopathogenesis and carcinogenesis. [15] Phosphorylation of the head region can affect filament stability. [16] The head has been shown to interact with the rod domain of the same protein. [17]

C-terminal "tail domain" shows extreme length variation between different IF proteins. [18]

The anti-parallel orientation of tetramers means that, unlike microtubules and microfilaments, which have a plus end and a minus end, IFs lack polarity and cannot serve as basis for cell motility and intracellular transport.

Also, unlike actin or tubulin, intermediate filaments do not contain a binding site for a nucleoside triphosphate.

Cytoplasmic IFs do not undergo treadmilling like microtubules and actin fibers, but are dynamic. [19]

Biomechanical properties

IFs are rather deformable proteins that can be stretched several times their initial length. [20] The key to facilitate this large deformation is due to their hierarchical structure, which facilitates a cascaded activation of deformation mechanisms at different levels of strain. [12] Initially the coupled alpha-helices of unit-length filaments uncoil as they're strained, then as the strain increases they transition into beta-sheets, and finally at increased strain the hydrogen bonds between beta-sheets slip and the ULF monomers slide along each other. [12]

Types

There are about 70 different human genes coding for various intermediate filament proteins. However, different kinds of IFs share basic characteristics: In general, they are all polymers that measure between 9–11 nm in diameter when fully assembled.

Animal IFs are subcategorized into six types based on similarities in amino acid sequence and protein structure: [6]

Types I and II – acidic and basic keratins

Keratin intermediate filaments (stained red) around epithelial cells Epithelial-cells.jpg
Keratin intermediate filaments (stained red) around epithelial cells

These proteins are the most diverse among IFs and constitute type I (acidic) and type II (basic) IF proteins. The many isoforms are divided in two groups:

Regardless of the group, keratins are either acidic or basic. Acidic and basic keratins bind each other to form acidic-basic heterodimers and these heterodimers then associate to make a keratin filament. [6]

Cytokeratin filaments laterally associate with each other to create a thick bundle of ~50 nm radius. The optimal radius of such bundles is determined by the interplay between the long range electrostatic repulsion and short range hydrophobic attraction. [21] Subsequently, these bundles would intersect through junctions to form a dynamic network, spanning the cytoplasm of epithelial cells.

Type III

Vimentin fibers in fibroblasts Vimentin.jpg
Vimentin fibers in fibroblasts

There are four proteins classed as type III intermediate filament proteins, which may form homo- or heteropolymeric proteins.

Type IV

Type V – nuclear lamins

Lamins are fibrous proteins having structural function in the cell nucleus.

In metazoan cells, there are A and B type lamins, which differ in their length and pI. Human cells have three differentially regulated genes. B-type lamins are present in every cell. B type lamins, lamin B1 and B2, are expressed from the LMNB1 and LMNB2 genes on 5q23 and 19q13, respectively. A-type lamins are only expressed following gastrulation. Lamin A and C are the most common A-type lamins and are splice variants of the LMNA gene found at 1q21.

These proteins localize to two regions of the nuclear compartment, the nuclear lamina—a proteinaceous structure layer subjacent to the inner surface of the nuclear envelope and throughout the nucleoplasm in the nucleoplasmic veil.

Comparison of the lamins to vertebrate cytoskeletal IFs shows that lamins have an extra 42 residues (six heptads) within coil 1b. The c-terminal tail domain contains a nuclear localization signal (NLS), an Ig-fold-like domain, and in most cases a carboxy-terminal CaaX box that is isoprenylated and carboxymethylated (lamin C does not have a CAAX box). Lamin A is further processed to remove the last 15 amino acids and its farnesylated cysteine.

During mitosis, lamins are phosphorylated by MPF, which drives the disassembly of the lamina and the nuclear envelope. [6]

Type VI

Vertebrate-only. Related to type I-IV. Used to contain other newly discovered IF proteins not yet assigned to a type. [25]

Function

Cell adhesion

At the plasma membrane, some keratins or desmin interact with desmosomes (cell-cell adhesion) and hemidesmosomes (cell-matrix adhesion) via adapter proteins.

Associated proteins

Filaggrin binds to keratin fibers in epidermal cells. Plectin links vimentin to other vimentin fibers, as well as to microfilaments, microtubules, and myosin II. Kinesin is being researched and is suggested to connect vimentin to tubulin via motor proteins.

Keratin filaments in epithelial cells link to desmosomes (desmosomes connect the cytoskeleton together) through plakoglobin, desmoplakin, desmogleins, and desmocollins; desmin filaments are connected in a similar way in heart muscle cells.

Diseases arising from mutations in IF genes

In other organisms

IF proteins are universal among animals in the form of a nuclear lamin. The Hydra has an additional "nematocilin" derived from the lamin. Cytoplasmic IFs (type I-IV) are only found in Bilateria; they also arose from a gene duplication event involving "type V" nuclear lamin. In addition, a few other diverse types of eukaryotes have lamins, suggesting an early origin of the protein. [25]

There was not really a concrete definition of an "intermediate filament protein", in the sense that the size or shape-based definition does not cover a monophyletic group. With the inclusion of unusual proteins like the network-forming beaded lamins (type VI), the current classification is moving to a clade containing nuclear lamin and its many descendants, characterized by sequence similarity as well as the exon structure. Functionally-similar proteins out of this clade, like crescentins, alveolins, tetrins, and epiplasmins, are therefore only "IF-like". They likely arose through convergent evolution. [25]

Related Research Articles

<span class="mw-page-title-main">Keratin</span> Structural fibrous protein

Keratin is one of a family of structural fibrous proteins also known as scleroproteins. Alpha-keratin (α-keratin) is a type of keratin found in vertebrates. It is the key structural material making up scales, hair, nails, feathers, horns, claws, hooves, and the outer layer of skin among vertebrates. Keratin also protects epithelial cells from damage or stress. Keratin is extremely insoluble in water and organic solvents. Keratin monomers assemble into bundles to form intermediate filaments, which are tough and form strong unmineralized epidermal appendages found in reptiles, birds, amphibians, and mammals. Excessive keratinization participate in fortification of certain tissues such as in horns of cattle and rhinos, and armadillos' osteoderm. The only other biological matter known to approximate the toughness of keratinized tissue is chitin. Keratin comes in two types, the primitive, softer forms found in all vertebrates and harder, derived forms found only among sauropsids.

<span class="mw-page-title-main">Cytoskeleton</span> Network of filamentous proteins that forms the internal framework of cells

The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is composed of similar proteins in the various organisms. It is composed of three main components: microfilaments, intermediate filaments, and microtubules, and these are all capable of rapid growth or disassembly depending on the cell's requirements.

<span class="mw-page-title-main">Lamin</span>

Lamins, also known as nuclear lamins are fibrous proteins in type V intermediate filaments, providing structural function and transcriptional regulation in the cell nucleus. Nuclear lamins interact with inner nuclear membrane proteins to form the nuclear lamina on the interior of the nuclear envelope. Lamins have elastic and mechanosensitive properties, and can alter gene regulation in a feedback response to mechanical cues. Lamins are present in all animals but are not found in microorganisms, plants or fungi. Lamin proteins are involved in the disassembling and reforming of the nuclear envelope during mitosis, the positioning of nuclear pores, and programmed cell death. Mutations in lamin genes can result in several genetic laminopathies, which may be life-threatening.

<span class="mw-page-title-main">Keratin 6A</span>

Keratin 6A is one of the 27 different type II keratins expressed in humans. Keratin 6A was the first type II keratin sequence determined. Analysis of the sequence of this keratin together with that of the first type I keratin led to the discovery of the four helical domains in the central rod of keratins. In humans Keratin 6A is encoded by the KRT6A gene.

Type II keratins constitutes the Type II intermediate filaments (IFs) of the intracytoplasmatic cytoskeleton, which is present in all mammalian epithelial cells. The type 2 cytokeratins consist of basic or neutral, high molecular weight proteins which in vivo are arranged in pairs of heterotypic Type I and Type II keratin chains, coexpressed during differentiation of simple and stratified epithelial tissues. It has been seen that Type II Keratins are developed before Type 1 keratins during human embryonic development.

<span class="mw-page-title-main">Keratin 10</span> Protein-coding gene in the species Homo sapiens

Keratin, type I cytoskeletal 10 also known as cytokeratin-10 (CK-10) or keratin-10 (K10) is a protein that in humans is encoded by the KRT10 gene. Keratin 10 is a type I keratin.

<span class="mw-page-title-main">Cytokeratin</span> Keratin protein

Cytokeratins are keratin proteins found in the intracytoplasmic cytoskeleton of epithelial tissue. They are an important component of intermediate filaments, which help cells resist mechanical stress. Expression of these cytokeratins within epithelial cells is largely specific to particular organs or tissues. Thus they are used clinically to identify the cell of origin of various human tumors.

<span class="mw-page-title-main">Desmin</span> Mammalian protein found in humans

Desmin is a protein that in humans is encoded by the DES gene. Desmin is a muscle-specific, type III intermediate filament that integrates the sarcolemma, Z disk, and nuclear membrane in sarcomeres and regulates sarcomere architecture.

<span class="mw-page-title-main">Vimentin</span> Type III intermediate filament protein

Vimentin is a structural protein that in humans is encoded by the VIM gene. Its name comes from the Latin vimentum which refers to an array of flexible rods.

<span class="mw-page-title-main">Peripherin</span> Protein-coding gene in the species Homo sapiens

Peripherin is a type III intermediate filament protein expressed mainly in neurons of the peripheral nervous system. It is also found in neurons of the central nervous system that have projections toward peripheral structures, such as spinal motor neurons. Its size, structure, and sequence/location of protein motifs is similar to other type III intermediate filament proteins such as desmin, vimentin and glial fibrillary acidic protein. Like these proteins, peripherin can self-assemble to form homopolymeric filamentous networks, but it can also heteropolymerize with neurofilaments in several neuronal types. This protein in humans is encoded by the PRPH gene. Peripherin is thought to play a role in neurite elongation during development and axonal regeneration after injury, but its exact function is unknown. It is also associated with some of the major neuropathologies that characterize amyotropic lateral sclerosis (ALS), but despite extensive research into how neurofilaments and peripherin contribute to ALS, their role in this disease is still unidentified.

<span class="mw-page-title-main">Glial fibrillary acidic protein</span> Type III intermediate filament protein

Glial fibrillary acidic protein (GFAP) is a protein that is encoded by the GFAP gene in humans. It is a type III intermediate filament (IF) protein that is expressed by numerous cell types of the central nervous system (CNS), including astrocytes and ependymal cells during development. GFAP has also been found to be expressed in glomeruli and peritubular fibroblasts taken from rat kidneys, Leydig cells of the testis in both hamsters and humans, human keratinocytes, human osteocytes and chondrocytes and stellate cells of the pancreas and liver in rats.

Neurofilaments (NF) are classed as type IV intermediate filaments found in the cytoplasm of neurons. They are protein polymers measuring 10 nm in diameter and many micrometers in length. Together with microtubules (~25 nm) and microfilaments (7 nm), they form the neuronal cytoskeleton. They are believed to function primarily to provide structural support for axons and to regulate axon diameter, which influences nerve conduction velocity. The proteins that form neurofilaments are members of the intermediate filament protein family, which is divided into six types based on their gene organization and protein structure. Types I and II are the keratins which are expressed in epithelia. Type III contains the proteins vimentin, desmin, peripherin and glial fibrillary acidic protein (GFAP). Type IV consists of the neurofilament proteins NF-L, NF-M, NF-H and α-internexin. Type V consists of the nuclear lamins, and type VI consists of the protein nestin. The type IV intermediate filament genes all share two unique introns not found in other intermediate filament gene sequences, suggesting a common evolutionary origin from one primitive type IV gene.

<span class="mw-page-title-main">Plectin</span> Mammalian protein found in Homo sapiens

Plectin is a giant protein found in nearly all mammalian cells which acts as a link between the three main components of the cytoskeleton: actin microfilaments, microtubules and intermediate filaments. In addition, plectin links the cytoskeleton to junctions found in the plasma membrane that structurally connect different cells. By holding these different networks together, plectin plays an important role in maintaining the mechanical integrity and viscoelastic properties of tissues.

Crescentin is a protein which is a bacterial relative of the intermediate filaments found in eukaryotic cells. Just as tubulins and actins, the other major cytoskeletal proteins, have prokaryotic homologs in, respectively, the FtsZ and MreB proteins, intermediate filaments are linked to the crescentin protein. Some of its homologs are erroneously labelled Chromosome segregation protein ParA. This protein family is found in Caulobacter and Methylobacterium.

<span class="mw-page-title-main">Desmoplakin</span> Protein found in humans

Desmoplakin is a protein in humans that is encoded by the DSP gene. Desmoplakin is a critical component of desmosome structures in cardiac muscle and epidermal cells, which function to maintain the structural integrity at adjacent cell contacts. In cardiac muscle, desmoplakin is localized to intercalated discs which mechanically couple cardiac cells to function in a coordinated syncytial structure. Mutations in desmoplakin have been shown to play a role in dilated cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy, where it may present with acute myocardial injury; striate palmoplantar keratoderma, Carvajal syndrome and paraneoplastic pemphigus.

<span class="mw-page-title-main">Keratin 5</span>

Keratin 5, also known as KRT5, K5, or CK5, is a protein that is encoded in humans by the KRT5 gene. It dimerizes with keratin 14 and forms the intermediate filaments (IF) that make up the cytoskeleton of basal epithelial cells. This protein is involved in several diseases including epidermolysis bullosa simplex and breast and lung cancers.

<span class="mw-page-title-main">Synemin</span> Protein found in humans

Synemin, also known as desmuslin, is a protein that in humans is encoded by the SYNM gene. Synemin is an intermediate filament (IF) family member. IF proteins are cytoskeletal proteins that confer resistance to mechanical stress and are encoded by a dispersed multigene family. This protein has been found to form a linkage between desmin, which is a subunit of the IF network, and the extracellular matrix, and provides an important structural support in muscle.

<span class="mw-page-title-main">IFFO1</span> Protein-coding gene in the species Homo sapiens

Intermediate filament family orphan 1 is a protein that in humans is encoded by the IFFO1 gene. IFFO1 has uncharacterized function and a weight of 61.98 kDa. IFFO1 proteins play an important role in the cytoskeleton and the nuclear envelope of most eukaryotic cell types.

Alpha-keratin, or α-keratin, is a type of keratin found in mammalian vertebrates. This protein is the primary component in hairs, horns, claws, nails and the epidermis layer of the skin. α-keratin is a fibrous structural protein, meaning it is made up of amino acids that form a repeating secondary structure. The secondary structure of α-keratin is very similar to that of a traditional protein α-helix and forms a coiled coil. Due to its tightly wound structure, it can function as one of the strongest biological materials and has various functions in mammals, from predatory claws to hair for warmth. α-keratin is synthesized through protein biosynthesis, utilizing transcription and translation, but as the cell matures and is full of α-keratin, it dies, creating a strong non-vascular unit of keratinized tissue.

References

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  2. ↑ Chang L, Goldman RD (August 2004). "Intermediate filaments mediate cytoskeletal crosstalk". Nature Reviews. Molecular Cell Biology. 5 (8): 601–13. doi:10.1038/nrm1438. PMID   15366704. S2CID   31835055.
  3. ↑ Traub, P. (2012), Intermediate Filaments: A Review, Springer Berlin Heidelberg, p. 33, ISBN   978-3-642-70230-3
  4. ↑ Karabinos A, Riemer D, Erber A, Weber K (October 1998). "Homologues of vertebrate type I, II and III intermediate filament (IF) proteins in an invertebrate: the IF multigene family of the cephalochordate Branchiostoma". FEBS Letters. 437 (1–2): 15–8. doi: 10.1016/S0014-5793(98)01190-9 . PMID   9804163. S2CID   7886395.
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  15. ↑ Shoeman RL, Hüttermann C, Hartig R, Traub P (January 2001). "Amino-terminal polypeptides of vimentin are responsible for the changes in nuclear architecture associated with human immunodeficiency virus type 1 protease activity in tissue culture cells". Molecular Biology of the Cell. 12 (1): 143–54. doi:10.1091/mbc.12.1.143. PMC   30574 . PMID   11160829.
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  18. ↑ Quinlan R, Hutchison C, Lane B (1995). "Intermediate filament proteins". Protein Profile. 2 (8): 795–952. PMID   8771189.
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  20. ↑ Herrmann H, Bär H, Kreplak L, Strelkov SV, Aebi U (July 2007). "Intermediate filaments: from cell architecture to nanomechanics". Nature Reviews. Molecular Cell Biology. 8 (7): 562–73. doi:10.1038/nrm2197. PMID   17551517. S2CID   27115011.Qin Z, Kreplak L, Buehler MJ (October 2009). "Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments". PLOS ONE. 4 (10): e7294. Bibcode:2009PLoSO...4.7294Q. doi: 10.1371/journal.pone.0007294 . PMC   2752800 . PMID   19806221.Kreplak L, Fudge D (January 2007). "Biomechanical properties of intermediate filaments: from tissues to single filaments and back". BioEssays. 29 (1): 26–35. doi:10.1002/bies.20514. PMID   17187357. S2CID   6560740.Qin Z, Buehler MJ, Kreplak L (January 2010). "A multi-scale approach to understand the mechanobiology of intermediate filaments". Journal of Biomechanics. 43 (1): 15–22. doi:10.1016/j.jbiomech.2009.09.004. PMID   19811783.Qin Z, Kreplak L, Buehler MJ (October 2009). "Nanomechanical properties of vimentin intermediate filament dimers". Nanotechnology. 20 (42): 425101. Bibcode:2009Nanot..20P5101Q. doi:10.1088/0957-4484/20/42/425101. PMID   19779230. S2CID   6870454.
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  22. ↑ Brodehl A, Gaertner-Rommel A, Milting H (August 2018). "Molecular insights into cardiomyopathies associated with desmin (DES) mutations". Biophysical Reviews. 10 (4): 983–1006. doi:10.1007/s12551-018-0429-0. PMC   6082305 . PMID   29926427.
  23. ↑ "SYNC – Syncoilin – Homo sapiens (Human) – SYNC gene & protein". www.uniprot.org. Retrieved 20 December 2021.
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  27. ↑ Bermúdez-Jiménez FJ, Carriel V, Brodehl A, Alaminos M, Campos A, Schirmer I, et al. (April 2018). "Novel Desmin Mutation p.Glu401Asp Impairs Filament Formation, Disrupts Cell Membrane Integrity, and Causes Severe Arrhythmogenic Left Ventricular Cardiomyopathy/Dysplasia". Circulation. 137 (15): 1595–1610. doi: 10.1161/CIRCULATIONAHA.117.028719 . hdl: 10481/89514 . PMID   29212896. S2CID   4715358.
  28. ↑ Protonotarios A, Brodehl A, Asimaki A, Jager J, Quinn E, Stanasiuk C, et al. (December 2020). "The novel desmin variant p.Leu115Ile is associated with a unique form of biventricular Arrhythmogenic Cardiomyopathy". The Canadian Journal of Cardiology. 37 (6): 857–866. doi:10.1016/j.cjca.2020.11.017. PMID   33290826. S2CID   228078648.
  29. ↑ Klauke B, Kossmann S, Gaertner A, Brand K, Stork I, Brodehl A, et al. (December 2010). "De novo desmin-mutation N116S is associated with arrhythmogenic right ventricular cardiomyopathy". Human Molecular Genetics. 19 (23): 4595–607. doi: 10.1093/hmg/ddq387 . PMID   20829228.
  30. ↑ Brodehl A, Hedde PN, Dieding M, Fatima A, Walhorn V, Gayda S, et al. (May 2012). "Dual color photoactivation localization microscopy of cardiomyopathy-associated desmin mutants". The Journal of Biological Chemistry. 287 (19): 16047–57. doi: 10.1074/jbc.M111.313841 . PMC   3346104 . PMID   22403400.
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Further reading

This article incorporates text from the public domain Pfam and InterPro: IPR001322
This article incorporates text from the public domain Pfam and InterPro: IPR006821
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