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106-489: SUMO proteins are similar to ubiquitin and are considered members of the ubiquitin-like protein family. SUMOylation is directed by an enzymatic cascade analogous to that involved in ubiquitination. In contrast to ubiquitin, SUMO is not used to tag proteins for degradation . Mature SUMO is produced when the last four amino acids of the C-terminus have been cleaved off to allow formation of an isopeptide bond between

212-483: A leucine zipper , which is a type of coiled-coil. These hydrophobic residues pack together in the interior of the helix bundle. In general, the fifth and seventh residues (the e and g positions) have opposing charges and form a salt bridge stabilized by electrostatic interactions. Fibrous proteins such as keratin or the "stalks" of myosin or kinesin often adopt coiled-coil structures, as do several dimerizing proteins. A pair of coiled-coils –

318-403: A substrate protein . This process most commonly binds the last amino acid of ubiquitin ( glycine 76) to a lysine residue on the substrate. An isopeptide bond is formed between the carboxyl group (COO ) of the ubiquitin's glycine and the epsilon- amino group (ε- NH 3 ) of the substrate's lysine. Trypsin cleavage of a ubiquitin-conjugated substrate leaves a di-glycine "remnant" that

424-476: A 3 10 helix is roughly −75°, whereas that for the π-helix is roughly −130°. The general formula for the rotation angle Ω per residue of any polypeptide helix with trans isomers is given by the equation The α-helix is tightly packed; there is almost no free space within the helix. The amino-acid side-chains are on the outside of the helix, and point roughly "downward" (i.e., toward the N-terminus), like

530-531: A C-terminal peptide is cleaved from the SUMO precursor by a protease (in human these are the SENP proteases or Ulp1 in yeast) to reveal a di-glycine motif. The obtained SUMO then becomes bound to an E1 enzyme (SUMO Activating Enzyme (SAE)) which is a heterodimer (subunits SAE1 and SAE2 ). It is then passed to an E2, which is a conjugating enzyme (Ubc9). Finally, one of a small number of E3 ligating proteins attaches it to

636-413: A UIM, and RAP80 then helps localize BRCA1 . This pathway will eventually recruit the necessary proteins for homologous recombination repair . Histones can be ubiquitinated, usually in the form of monoubiquitylation, although polyubiquitylated forms do occur. Histone ubiquitylation alters chromatin structure and allows the access of enzymes involved in transcription. Ubiquitin on histones also acts as

742-412: A binding site for proteins that either activate or inhibit transcription and also can induce further post-translational modifications of the protein. These effects can all modulate the transcription of genes. Deubiquitinating enzymes (deubiquitinases; DUBs) oppose the role of ubiquitylation by removing ubiquitin from substrate proteins. They are cysteine proteases that cleave the amide bond between

848-782: A chain (polyubiquitin) or attached to ribosomal subunits. DUBs cleave these proteins to produce active ubiquitin. They also recycle ubiquitin that has been bound to small nucleophilic molecules during the ubiquitylation process. Monoubiquitin is formed by DUBs that cleave ubiquitin from free polyubiquitin chains that have been previously removed from proteins. in proteome (amino acids) Affinity H. sapiens : 21 H. sapiens : 14 H. sapiens : ? H. sapiens : 25 H. sapiens : 16 H. sapiens : 98 H. sapiens : ? H. sapiens : 71 H. sapiens : 28 Ubiquitin-binding domains (UBDs) are modular protein domains that non-covalently bind to ubiquitin, these motifs control various cellular events. Detailed molecular structures are known for

954-437: A cold and went to bed. Being bored, he drew a polypeptide chain of roughly correct dimensions on a strip of paper and folded it into a helix, being careful to maintain the planar peptide bonds. After a few attempts, he produced a model with physically plausible hydrogen bonds. Pauling then worked with Corey and Branson to confirm his model before publication. In 1954, Pauling was awarded his first Nobel Prize "for his research into

1060-459: A component of an E3 ubiquitin ligase . VHL complex targets a member of the hypoxia-inducible transcription factor family (HIF) for degradation by interacting with the oxygen-dependent destruction domain under normoxic conditions. HIF activates downstream targets such as the vascular endothelial growth factor (VEGF), promoting angiogenesis . Mutations in VHL prevent degradation of HIF and thus lead to

1166-400: A four- helix bundle  – is a very common structural motif in proteins. For example, it occurs in human growth hormone and several varieties of cytochrome . The Rop protein , which promotes plasmid replication in bacteria, is an interesting case in which a single polypeptide forms a coiled-coil and two monomers assemble to form a four-helix bundle. The amino acids that make up

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1272-452: A helix and the propensity to extend a helix. At least five artists have made explicit reference to the α-helix in their work: Julie Newdoll in painting and Julian Voss-Andreae , Bathsheba Grossman , Byron Rubin, and Mike Tyka in sculpture. San Francisco area artist Julie Newdoll, who holds a degree in microbiology with a minor in art, has specialized in paintings inspired by microscopic images and molecules since 1990. Her painting "Rise of

1378-532: A helix, both because it cannot donate an amide hydrogen bond (having no amide hydrogen), and also because its sidechain interferes sterically with the backbone of the preceding turn – inside a helix, this forces a bend of about 30° in the helix's axis. However, proline is often seen as the first residue of a helix, it is presumed due to its structural rigidity. At the other extreme, glycine also tends to disrupt helices because its high conformational flexibility makes it entropically expensive to adopt

1484-438: A high degree of similarity to each other and are distinct from SUMO-1. SUMO-4 shows similarity to SUMO-2/3 but differs in having a Proline instead of Glutamine at position 90. As a result, SUMO-4 isn't processed and conjugated under normal conditions, but is used for modification of proteins under stress-conditions like starvation. During mitosis, SUMO-2/3 localize to centromeres and condensed chromosomes, whereas SUMO-1 localizes to

1590-425: A highly characteristic sequence motif known as a heptad repeat , in which the motif repeats itself every seven residues along the sequence ( amino acid residues, not DNA base-pairs). The first and especially the fourth residues (known as the a and d positions) are almost always hydrophobic ; the fourth residue is typically leucine  – this gives rise to the name of the structural motif called

1696-608: A molecular glue to facilitate the assembly of large protein complexes in repair foci. Also, SUMOylation can alter a protein's biochemical activities and interactions. SUMOylation plays a role in the major DNA repair pathways of base excision repair , nucleotide excision repair , non-homologous end joining and homologous recombinational repair. SUMOylation also facilitates error prone translation synthesis. SUMO proteins are small; most are around 100 amino acids in length and 12 kDa in mass . The exact length and mass varies between SUMO family members and depends on which organism

1802-642: A number of UBDs, binding specificity determines their mechanism of action and regulation, and how it regulates cellular proteins and processes. The ubiquitin pathway has been implicated in the pathogenesis of a wide range of diseases and disorders, including: Ubiquitin is implicated in neurodegenerative diseases associated with proteostasis dysfunction, including Alzheimer's disease , motor neuron disease , Huntington's disease and Parkinson's disease . Transcript variants encoding different isoforms of ubiquilin-1 are found in lesions associated with Alzheimer's and Parkinson's disease. Higher levels of ubiquilin in

1908-432: A particular helix can be plotted on a helical wheel , a representation that illustrates the orientations of the constituent amino acids (see the article for leucine zipper for such a diagram). Often in globular proteins , as well as in specialized structures such as coiled-coils and leucine zippers , an α-helix will exhibit two "faces" – one containing predominantly hydrophobic amino acids oriented toward

2014-493: A particular lysine, cysteine, serine, threonine or N-terminus of the target protein. Polyubiquitylation occurs when the C-terminus of another ubiquitin is linked to one of the seven lysine residues or the first methionine on the previously added ubiquitin molecule, creating a chain. This process repeats several times, leading to the addition of several ubiquitins. Only polyubiquitylation on defined lysines, mostly on K48 and K29,

2120-411: A process known as proteolysis . Multi-ubiquitin chains at least four ubiquitin molecules long must be attached to a lysine residue on the condemned protein in order for it to be recognised by the 26S proteasome . This is a barrel-shape structure comprising a central proteolytic core made of four ring structures, flanked by two cylinders that selectively allow entry of ubiquitylated proteins. Once inside,

2226-625: A pronounced double minimum at around 208 and 222 nm. Infrared spectroscopy is rarely used, since the α-helical spectrum resembles that of a random coil (although these might be discerned by, e.g., hydrogen-deuterium exchange ). Finally, cryo electron microscopy is now capable of discerning individual α-helices within a protein, although their assignment to residues is still an active area of research. Long homopolymers of amino acids often form helices if soluble. Such long, isolated helices can also be detected by other methods, such as dielectric relaxation , flow birefringence , and measurements of

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2332-425: A protein substrate, further ubiquitin molecules can be added to the first, yielding a polyubiquitin chain. These chains are made by linking the glycine residue of a ubiquitin molecule to a lysine of ubiquitin bound to a substrate. Ubiquitin has seven lysine residues and an N-terminus that serves as points of ubiquitination; they are K6, K11, K27, K29, K33, K48, K63 and M1, respectively. Lysine 48-linked chains were

2438-425: A signal for protein degradation through the 26S proteasome , it could also serve for other fundamental cellular processes, in endocytosis , enzymatic activation and DNA repair. Moreover, since ubiquitylation functions to tightly regulate the cellular level of cyclins , its misregulation is expected to have severe impacts. First evidence of the importance of the ubiquitin/proteasome pathway in oncogenic processes

2544-498: A single substrate molecule by an isopeptide linkage, and conjugates were found to be rapidly degraded with the release of free APF-1. Soon after APF-1-protein conjugation was characterised, APF-1 was identified as ubiquitin. The carboxyl group of the C-terminal glycine residue of ubiquitin (Gly76) was identified as the moiety conjugated to substrate lysine residues. MQIFV K TLTG K TITLEVEPSDTIENV K A K IQD K EGIPPD Ubiquitin

2650-469: A small fraction of a given protein is SUMOylated and this modification is rapidly reversed by the action of deSUMOylating enzymes. SUMOylation of target proteins has been shown to cause a number of different outcomes including altered localization and binding partners. The SUMO-1 modification of RanGAP1 (the first identified SUMO substrate) leads to its trafficking from cytosol to nuclear pore complex. The SUMO modification of ninein leads to its movement from

2756-508: A small number of diagrams, Heliquest can be used for helical wheels, and NetWheels can be used for helical wheels and helical nets. To programmatically generate a large number of diagrams, helixvis can be used to draw helical wheels and wenxiang diagrams in the R and Python programming languages. Since the α-helix is defined by its hydrogen bonds and backbone conformation, the most detailed experimental evidence for α-helical structure comes from atomic-resolution X-ray crystallography such as

2862-578: A subunit of the proteasome: S5a/Rpn10. This is achieved by a ubiquitin-interacting motif (UIM) found in a hydrophobic patch in the C-terminal region of the S5a/Rpn10 unit. Lysine 63-linked chains are not associated with proteasomal degradation of the substrate protein. Instead, they allow the coordination of other processes such as endocytic trafficking , inflammation , translation , and DNA repair . In cells, lysine 63-linked chains are bound by

2968-517: Is a former protein crystallographer now professional sculptor in metal of proteins, nucleic acids, and drug molecules – many of which featuring α-helices, such as subtilisin , human growth hormone , and phospholipase A2 . Mike Tyka is a computational biochemist at the University of Washington working with David Baker . Tyka has been making sculptures of protein molecules since 2010 from copper and steel, including ubiquitin and

3074-409: Is a general term for any microscopically visible collection of abnormal material in a cell). Examples include: Post-translational modification of proteins is a generally used mechanism in eukaryotic cell signaling. Ubiquitylation, ubiquitin conjugation to proteins , is a crucial process for cell cycle progression and cell proliferation and development. Although ubiquitylation usually serves as

3180-462: Is a primary immune system sensor for viral and other invasive RNA in human cells. The RIG-I-like receptor ( RLR ) immune signaling pathway is one of the most extensively studied in terms of the role of ubiquitin in immune regulation. Immunohistochemistry using antibodies to ubiquitin can identify abnormal accumulations of this protein inside cells, indicating a disease process. These protein accumulations are referred to as inclusion bodies (which

3286-514: Is a protein involved in DNA synthesis . Under normal physiological conditions PCNA is sumoylated (a similar post-translational modification to ubiquitylation). When DNA is damaged by ultra-violet radiation or chemicals, the SUMO molecule that is attached to a lysine residue is replaced by ubiquitin. Monoubiquitylated PCNA recruits polymerases that can carry out DNA synthesis with damaged DNA; but this

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3392-504: Is a small protein that exists in all eukaryotic cells . It performs its myriad functions through conjugation to a large range of target proteins. A variety of different modifications can occur. The ubiquitin protein itself consists of 76 amino acids and has a molecular mass of about 8.6 kDa. Key features include its C-terminal tail and the 7 lysine residues. It is highly conserved throughout eukaryote evolution; human and yeast ubiquitin share 96% sequence identity . Ubiquitin

3498-542: Is a small (8.6  kDa ) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ubiquitously . It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Four genes in the human genome code for ubiquitin: UBB , UBC , UBA52 and RPS27A . The addition of ubiquitin to a substrate protein is called ubiquitylation (or ubiquitination or ubiquitinylation ). Ubiquitylation affects proteins in many ways: it can mark them for degradation via

3604-617: Is also increasing evidence for nonlysine residues as ubiquitylation targets using non-amine groups, such as the sulfhydryl group on cysteine, and the hydroxyl group on threonine and serine. The end result of this process is the addition of one ubiquitin molecule (monoubiquitylation) or a chain of ubiquitin molecules (polyubiquitination) to the substrate protein. Ubiquitination requires three types of enzyme: ubiquitin-activating enzymes , ubiquitin-conjugating enzymes , and ubiquitin ligases , known as E1s, E2s, and E3s, respectively. The process consists of three main steps: In

3710-495: Is because of the convenient structural fact that the diameter of an α-helix is about 12 Å (1.2 nm) including an average set of sidechains, about the same as the width of the major groove in B-form DNA , and also because coiled-coil (or leucine zipper) dimers of helices can readily position a pair of interaction surfaces to contact the sort of symmetrical repeat common in double-helical DNA. An example of both aspects

3816-406: Is encoded in mammals by four different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a , respectively. The UBB and UBC genes code for polyubiquitin precursor proteins. Ubiquitylation (also known as ubiquitination or ubiquitinylation) is an enzymatic post-translational modification in which an ubiquitin protein is attached to

3922-479: Is misleading and it is more realistic to say that the hydrogen bond potential of the free NH groups at the N-terminus of an α-helix can be satisfied by hydrogen bonding; this can also be regarded as set of interactions between local microdipoles such as C=O···H−N . Coiled-coil α helices are highly stable forms in which two or more helices wrap around each other in a "supercoil" structure. Coiled coils contain

4028-406: Is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid that is four residues earlier in the protein sequence. The alpha helix is also commonly called a: In the early 1930s, William Astbury showed that there were drastic changes in

4134-412: Is related to degradation by the proteasome (referred to as the "molecular kiss of death"), while other polyubiquitylations (e.g. on K63, K11, K6 and M1) and monoubiquitylations may regulate processes such as endocytic trafficking , inflammation , translation and DNA repair . The discovery that ubiquitin chains target proteins to the proteasome, which degrades and recycles proteins, was honored with

4240-410: Is starting to suggest roles for these chains. There is evidence that atypical chains linked by lysine 6, 11, 27, 29 and methionine 1 can induce proteasomal degradation. Branched ubiquitin chains containing multiple linkage types can be formed. The function of these chains is unknown. Differently linked chains have specific effects on the protein to which they are attached, caused by differences in

4346-451: Is that the hydrophobic face of the antimicrobial peptide forms pores in the plasma membrane after associating with the fatty chains at the membrane core. Myoglobin and hemoglobin , the first two proteins whose structures were solved by X-ray crystallography , have very similar folds made up of about 70% α-helix, with the rest being non-repetitive regions, or "loops" that connect the helices. In classifying proteins by their dominant fold,

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4452-446: Is the lysine conjugated to SUMO, x is any amino acid (aa), D or E is an acidic residue. Substrate specificity appears to be derived directly from Ubc9 and the respective substrate motif. Currently available prediction programs are: SUMO attachment to its target is similar to that of ubiquitin (as it is for the other ubiquitin-like proteins such as NEDD 8). The SUMO precursor has some extra amino acids that need to be removed, therefore

4558-507: Is the transcription factor Max (see image at left), which uses a helical coiled coil to dimerize, positioning another pair of helices for interaction in two successive turns of the DNA major groove. α-Helices are also the most common protein structure element that crosses biological membranes ( transmembrane protein ), it is presumed because the helical structure can satisfy all backbone hydrogen-bonds internally, leaving no polar groups exposed to

4664-519: Is used to identify the site of ubiquitylation. Ubiquitin can also be bound to other sites in a protein which are electron-rich nucleophiles , termed "non-canonical ubiquitylation". This was first observed with the amine group of a protein's N-terminus being used for ubiquitylation, rather than a lysine residue, in the protein MyoD and has been observed since in 22 other proteins in multiple species, including ubiquitin itself. There

4770-541: Is very error-prone, possibly resulting in the synthesis of mutated DNA. Lysine 63-linked polyubiquitylation of PCNA allows it to perform a less error-prone mutation bypass known by the template switching pathway. Ubiquitylation of histone H2AX is involved in DNA damage recognition of DNA double-strand breaks. Lysine 63-linked polyubiquitin chains are formed on H2AX histone by the E2/E3 ligase pair , Ubc13-Mms2/RNF168. This K63 chain appears to recruit RAP80, which contains

4876-495: The ESCRT-0 complex, which prevents their binding to the proteasome. This complex contains two proteins, Hrs and STAM1, that contain a UIM, which allows it to bind to lysine 63-linked chains. Methionine 1-linked (or linear) polyubiquitin chains are another type of non-degradative ubiquitin chains. In this case, ubiquitin is linked in a head-to-tail manner, meaning that the C-terminus of the last ubiquitin molecule binds directly to

4982-623: The Nobel Prize in Chemistry in 2004. Ubiquitin (originally, ubiquitous immunopoietic polypeptide ) was first identified in 1975 as an 8.6 kDa protein expressed in all eukaryotic cells. The basic functions of ubiquitin and the components of the ubiquitylation pathway were elucidated in the early 1980s at the Technion by Aaron Ciechanover , Avram Hershko , and Irwin Rose for which

5088-445: The Nobel Prize in Chemistry was awarded in 2004. The ubiquitylation system was initially characterised as an ATP -dependent proteolytic system present in cellular extracts. A heat-stable polypeptide present in these extracts, ATP-dependent proteolysis factor 1 (APF-1), was found to become covalently attached to the model protein substrate lysozyme in an ATP - and Mg -dependent process. Multiple APF-1 molecules were linked to

5194-673: The X-ray fiber diffraction of moist wool or hair fibers upon significant stretching. The data suggested that the unstretched fibers had a coiled molecular structure with a characteristic repeat of ≈5.1 ångströms (0.51 nanometres ). Astbury initially proposed a linked-chain structure for the fibers. He later joined other researchers (notably the American chemist Maurice Huggins ) in proposing that: Although incorrect in their details, Astbury's models of these forms were correct in essence and correspond to modern elements of secondary structure ,

5300-460: The centrosome to the nucleus . In many cases, SUMO modification of transcriptional regulators correlates with inhibition of transcription. One can refer to the GeneRIFs of the SUMO proteins, e.g. human SUMO-1, to find out more. There are 4 confirmed SUMO isoforms in humans; SUMO-1 , SUMO-2 , SUMO-3 and SUMO-4 . At the amino acid level, SUMO1 is about 50% identical to SUMO2. SUMO-2/3 show

5406-546: The diffusion constant . In stricter terms, these methods detect only the characteristic prolate (long cigar-like) hydrodynamic shape of a helix, or its large dipole moment . Different amino-acid sequences have different propensities for forming α-helical structure. Methionine , alanine , leucine , glutamate , and lysine uncharged ("MALEK" in the amino-acid 1-letter codes) all have especially high helix-forming propensities, whereas proline and glycine have poor helix-forming propensities. Proline either breaks or kinks

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5512-401: The entropic cost associated with the folding of the polypeptide chain is not compensated for by a sufficient amount of stabilizing interactions. In general, the backbone hydrogen bonds of α-helices are considered slightly weaker than those found in β-sheets , and are readily attacked by the ambient water molecules. However, in more hydrophobic environments such as the plasma membrane , or in

5618-475: The i  + 4 spacing adds three more atoms to the H-bonded loop compared to the tighter 3 10 helix, and on average, 3.6 amino acids are involved in one ring of α-helix. The subscripts refer to the number of atoms (including the hydrogen) in the closed loop formed by the hydrogen bond. Residues in α-helices typically adopt backbone ( φ ,  ψ ) dihedral angles around (−60°, −45°), as shown in

5724-422: The proteasome , alter their cellular location , affect their activity, and promote or prevent protein interactions . Ubiquitylation involves three main steps: activation, conjugation, and ligation, performed by ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s), respectively. The result of this sequential cascade is to bind ubiquitin to lysine residues on

5830-462: The Alpha Helix" (2003) features human figures arranged in an α helical arrangement. According to the artist, "the flowers reflect the various types of sidechains that each amino acid holds out to the world". This same metaphor is also echoed from the scientist's side: "β sheets do not show a stiff repetitious regularity but flow in graceful, twisting curves, and even the α-helix is regular more in

5936-503: The C-terminal glycine residue of SUMO and an acceptor lysine on the target protein. SUMO family members often have dissimilar names; the SUMO homologue in yeast , for example, is called SMT3 (suppressor of mif two 3). Several pseudogenes have been reported for SUMO genes in the human genome . SUMO modification of proteins has many functions. Among the most frequent and best studied are protein stability, nuclear - cytosolic transport, and transcriptional regulation. Typically, only

6042-739: The E3 ligases). SUMOylation is reversible and is removed from targets by specific SUMO proteases. In budding yeast, the Ulp1 SUMO protease is found bound at the nuclear pore, whereas Ulp2 is nucleoplasmic. The distinct subnuclear localisation of deSUMOylating enzymes is conserved in higher eukaryotes. SUMO can be removed from its substrate, which is called deSUMOylation. Specific proteases mediate this procedure (SENP in human or Ulp1 and Ulp2 in yeast). Recombinant proteins expressed in E. coli may fail to fold properly, instead forming aggregates and precipitating as inclusion bodies . This insolubility may be due to

6148-523: The Glycine-xxx-Glycine (or small-xxx-small) motif. α-Helices under axial tensile deformation, a characteristic loading condition that appears in many alpha-helix-rich filaments and tissues, results in a characteristic three-phase behavior of stiff-soft-stiff tangent modulus. Phase I corresponds to the small-deformation regime during which the helix is stretched homogeneously, followed by phase II, in which alpha-helical turns break mediated by

6254-421: The N-terminus of the next one. Although initially believed to target proteins for proteasomal degradation, linear ubiquitin later proved to be indispensable for NF-kB signaling. Currently, there is only one known E3 ubiquitin ligase generating M1-linked polyubiquitin chains - linear ubiquitin chain assembly complex (LUBAC). Less is understood about atypical (non-lysine 48-linked) ubiquitin chains but research

6360-514: The Smc5/6 complex) and Pias-gamma and HECT proteins. On Chromosome 17 of the human genome, SUMO2 is near SUMO1+E1/E2 and SUMO2+E1/E2, among various others. Some E3's, such as RanBP2, however, are neither. Recent evidence has shown that PIAS-gamma is required for the SUMOylation of the transcription factor yy1 but it is independent of the zinc-RING finger (identified as the functional domain of

6466-491: The Structural Classification of Proteins database maintains a large category specifically for all-α proteins. Hemoglobin then has an even larger-scale quaternary structure , in which the functional oxygen-binding molecule is made up of four subunits. α-Helices have particular significance in DNA binding motifs, including helix-turn-helix motifs, leucine zipper motifs and zinc finger motifs. This

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6572-414: The addition of a single ubiquitin molecule (monoubiquitylation) or different types of ubiquitin chains (polyubiquitylation). Monoubiquitylation is the addition of one ubiquitin molecule to one substrate protein residue. Multi-monoubiquitylation is the addition of one ubiquitin molecule to multiple substrate residues. The monoubiquitylation of a protein can have different effects to the polyubiquitylation of

6678-548: The aggregate effect of the individual microdipoles from the carbonyl groups of the peptide bond pointing along the helix axis. The effects of this macrodipole are a matter of some controversy. α-helices often occur with the N-terminal end bound by a negatively charged group, sometimes an amino acid side chain such as glutamate or aspartate , or sometimes a phosphate ion. Some regard the helix macrodipole as interacting electrostatically with such groups. Others feel that this

6784-910: The brain have been shown to decrease malformation of amyloid precursor protein (APP) , which plays a key role in triggering Alzheimer's disease. Conversely, lower levels of ubiquilin-1 in the brain have been associated with increased malformation of APP. A frameshift mutation in ubiquitin B can result in a truncated peptide missing the C-terminal glycine . This abnormal peptide, known as UBB+1 , has been shown to accumulate selectively in Alzheimer's disease and other tauopathies . Ubiquitin and ubiquitin-like molecules extensively regulate immune signal transduction pathways at virtually all stages, including steady-state repression, activation during infection, and attenuation upon clearance. Without this regulation, immune activation against pathogens may be defective, resulting in chronic disease or death. Alternatively,

6890-448: The branches of an evergreen tree ( Christmas tree effect). This directionality is sometimes used in preliminary, low-resolution electron-density maps to determine the direction of the protein backbone. Helices observed in proteins can range from four to over forty residues long, but a typical helix contains about ten amino acids (about three turns). In general, short polypeptides do not exhibit much α-helical structure in solution, since

6996-752: The chain conformations exposes and conceals different parts of the ubiquitin protein, and the different linkages are recognized by proteins that are specific for the unique topologies that are intrinsic to the linkage. Proteins can specifically bind to ubiquitin via ubiquitin-binding domains (UBDs). The distances between individual ubiquitin units in chains differ between lysine 63- and 48-linked chains. The UBDs exploit this by having small spacers between ubiquitin-interacting motifs that bind lysine 48-linked chains (compact ubiquitin chains) and larger spacers for lysine 63-linked chains. The machinery involved in recognising polyubiquitin chains can also differentiate between K63-linked chains and M1-linked chains, demonstrated by

7102-416: The combined pattern of pitch and hydrogen bonding. The α-helices can be identified in protein structure using several computational methods, such as DSSP (Define  Secondary Structure of Protein). Similar structures include the 3 10 helix ( i  + 3 → i hydrogen bonding) and the π-helix ( i  + 5 → i hydrogen bonding). The α-helix can be described as a 3.6 13 helix, since

7208-465: The conformations of the protein chains. K29-, K33-, K63- and M1-linked chains have a fairly linear conformation; they are known as open-conformation chains. K6-, K11-, and K48-linked chains form closed conformations. The ubiquitin molecules in open-conformation chains do not interact with each other, except for the covalent isopeptide bonds linking them together. In contrast, the closed conformation chains have interfaces with interacting residues. Altering

7314-409: The ends. Homopolymers of amino acids (such as polylysine ) can adopt α-helical structure at low temperature that is "melted out" at high temperatures. This helix–coil transition was once thought to be analogous to protein denaturation . The statistical mechanics of this transition can be modeled using an elegant transfer matrix method, characterized by two parameters: the propensity to initiate

7420-521: The example shown at right. It is clear that all the backbone carbonyl oxygens point downward (toward the C-terminus) but splay out slightly, and the H-bonds are approximately parallel to the helix axis. Protein structures from NMR spectroscopy also show helices well, with characteristic observations of nuclear Overhauser effect (NOE) couplings between atoms on adjacent helical turns. In some cases,

7526-428: The fact that the latter can induce proteasomal degradation of the substrate. The ubiquitylation system functions in a wide variety of cellular processes, including: Multi-monoubiquitylation can mark transmembrane proteins (for example, receptors ) for removal from membranes (internalisation) and fulfil several signalling roles within the cell. When cell-surface transmembrane molecules are tagged with ubiquitin,

7632-408: The first identified and are the best-characterised type of ubiquitin chain. K63 chains have also been well-characterised, whereas the function of other lysine chains, mixed chains, branched chains, M1-linked linear chains, and heterologous chains (mixtures of ubiquitin and other ubiquitin-like proteins) remains more unclear. Lysine 48-linked polyubiquitin chains target proteins for destruction, by

7738-504: The formation of hypervascular lesions and renal tumors. The BRCA1 gene is another tumor suppressor gene in humans which encodes the BRCA1 protein that is involved in response to DNA damage. The protein contains a RING motif with E3 Ubiquitin Ligase activity. BRCA1 could form dimer with other molecules, such as BARD1 and BAP1 , for its ubiquitylation activity. Mutations that affect

7844-466: The fully helical state. It has been shown that α-helices are more stable, robust to mutations and designable than β-strands in natural proteins, and also in artificially designed proteins. The 3 most popular ways of visualizing the alpha-helical secondary structure of oligopeptide sequences are (1) a helical wheel , (2) a wenxiang diagram, and (3) a helical net. Each of these can be visualized with various software packages and web servers. To generate

7950-407: The helical axis. Dunitz describes how Pauling's first article on the theme in fact shows a left-handed helix, the enantiomer of the true structure. Short pieces of left-handed helix sometimes occur with a large content of achiral glycine amino acids, but are unfavorable for the other normal, biological L -amino acids . The pitch of the alpha-helix (the vertical distance between consecutive turns of

8056-607: The helix) is 5.4 Å (0.54 nm), which is the product of 1.5 and 3.6. The most important thing is that the N-H group of one amino acid forms a hydrogen bond with the C=O group of the amino acid four residues earlier; this repeated i  + 4 → i hydrogen bonding is the most prominent characteristic of an α-helix. Official international nomenclature specifies two ways of defining α-helices, rule 6.2 in terms of repeating φ , ψ torsion angles (see below) and rule 6.3 in terms of

8162-480: The image at right. In more general terms, they adopt dihedral angles such that the ψ dihedral angle of one residue and the φ dihedral angle of the next residue sum to roughly −105°. As a consequence, α-helical dihedral angles, in general, fall on a diagonal stripe on the Ramachandran diagram (of slope −1), ranging from (−90°, −15°) to (−70°, −35°). For comparison, the sum of the dihedral angles for

8268-588: The immune system may become hyperactivated and organs and tissues may be subjected to autoimmune damage . On the other hand, viruses must block or redirect host cell processes including immunity to effectively replicate, yet many viruses relevant to disease have informationally limited genomes . Because of its very large number of roles in the cell, manipulating the ubiquitin system represents an efficient way for such viruses to block, subvert or redirect critical host cell processes to support their own replication. The retinoic acid-inducible gene I ( RIG-I ) protein

8374-463: The individual hydrogen bonds can be observed directly as a small scalar coupling in NMR. There are several lower-resolution methods for assigning general helical structure. The NMR chemical shifts (in particular of the C , C and C′) and residual dipolar couplings are often characteristic of helices. The far-UV (170–250 nm) circular dichroism spectrum of helices is also idiosyncratic, exhibiting

8480-420: The interior of the protein, in the hydrophobic core , and one containing predominantly polar amino acids oriented toward the solvent -exposed surface of the protein. Changes in binding orientation also occur for facially-organized oligopeptides. This pattern is especially common in antimicrobial peptides , and many models have been devised to describe how this relates to their function. Common to many of them

8586-518: The internal SUMO consensus sites found in SUMO-2/3, it is thought to terminate these poly-SUMO chains. Serine 2 of SUMO-1 is phosphorylated, raising the concept of a 'modified modifier'. Cellular DNA is regularly exposed to DNA damaging agents. A DNA damage response (DDR) that is well regulated and intricate is usually employed to deal with the potential deleterious effects of the damage. When DNA damage occurs, SUMO protein has been shown to act as

8692-405: The ligase function are often found and associated with various cancers. Alpha helix An alpha helix (or α-helix ) is a sequence of amino acids in a protein that are twisted into a coil (a helix ). The alpha helix is the most common structural arrangement in the secondary structure of proteins . It is also the most extreme type of local structure, and it is the local structure that

8798-569: The manner of a flower stem, whose branching nodes show the influence of environment, developmental history, and the evolution of each part to match its own idiosyncratic function." Julian Voss-Andreae is a German-born sculptor with degrees in experimental physics and sculpture. Since 2001 Voss-Andreae creates "protein sculptures" based on protein structure with the α-helix being one of his preferred objects. Voss-Andreae has made α-helix sculptures from diverse materials including bamboo and whole trees. A monument Voss-Andreae created in 2004 to celebrate

8904-485: The membrane if the sidechains are hydrophobic. Proteins are sometimes anchored by a single membrane-spanning helix, sometimes by a pair, and sometimes by a helix bundle, most classically consisting of seven helices arranged up-and-down in a ring such as for rhodopsins (see image at right) and other G protein–coupled receptors (GPCRs). The structural stability between pairs of α-Helical transmembrane domains rely on conserved membrane interhelical packing motifs, for example,

9010-549: The memory of Linus Pauling , the discoverer of the α-helix, is fashioned from a large steel beam rearranged in the structure of the α-helix. The 10-foot-tall (3 m), bright-red sculpture stands in front of Pauling's childhood home in Portland, Oregon . Ribbon diagrams of α-helices are a prominent element in the laser-etched crystal sculptures of protein structures created by artist Bathsheba Grossman , such as those of insulin , hemoglobin , and DNA polymerase . Byron Rubin

9116-480: The mitotic spindle and spindle midzone, indicating that SUMO paralogs regulate distinct mitotic processes in mammalian cells. One of the major SUMO conjugation products associated with mitotic chromosomes arose from SUMO-2/3 conjugation of topoisomerase II, which is modified exclusively by SUMO-2/3 during mitosis. SUMO-2/3 modifications seem to be involved specifically in the stress response. SUMO-1 and SUMO-2/3 can form mixed chains, however, because SUMO-1 does not contain

9222-418: The modern α-helix. Two key developments in the modeling of the modern α-helix were: the correct bond geometry, thanks to the crystal structure determinations of amino acids and peptides and Pauling's prediction of planar peptide bonds ; and his relinquishing of the assumption of an integral number of residues per turn of the helix. The pivotal moment came in the early spring of 1948, when Pauling caught

9328-434: The nature of the chemical bond and its application to the elucidation of the structure of complex substances" (such as proteins), prominently including the structure of the α-helix. The amino acids in an α-helix are arranged in a right-handed helical structure where each amino acid residue corresponds to a 100° turn in the helix (i.e., the helix has 3.6 residues per turn), and a translation of 1.5 Å (0.15 nm) along

9434-427: The presence of co-solvents such as trifluoroethanol (TFE), or isolated from solvent in the gas phase, oligopeptides readily adopt stable α-helical structure. Furthermore, crosslinks can be incorporated into peptides to conformationally stabilize helical folds. Crosslinks stabilize the helical state by entropically destabilizing the unfolded state and by removing enthalpically stabilized "decoy" folds that compete with

9540-406: The presence of codons read inefficiently by E. coli , differences in eukaryotic and prokaryotic ribosomes, or lack of appropriate molecular chaperones for proper protein folding. In order to purify such proteins it may be necessary to fuse the protein of interest with a solubility tag such as SUMO or MBP ( maltose-binding protein ) to increase the protein's solubility. SUMO can later be cleaved from

9646-399: The protein comes from. Although SUMO has very little sequence identity with ubiquitin (less than 20%) at the amino acid level, it has a nearly identical structural fold. SUMO protein has a unique N-terminal extension of 10-25 amino acids which other ubiquitin-like proteins do not have. This N-terminal is found related to the formation of SUMO chains. The structure of human SUMO1 is depicted on

9752-502: The protein of interest using a SUMO-specific protease such as Ulp1 peptidase . SUMO protein is implicated in the etiology of many biomedical disease states not limited to: cancer, diabetes, chronic inflammatory tumors, neurodegenerative diseases, cardiovascular diseases, pulmonary diseases, atherosclerosis, liver diseases, infectious diseases, and intestinal disorders. Programs for prediction SUMOylation: Ubiquitin Ubiquitin

9858-422: The protein substrate via an isopeptide bond , cysteine residues through a thioester bond , serine and threonine residues through an ester bond , or the amino group of the protein's N-terminus via a peptide bond . The protein modifications can be either a single ubiquitin protein (monoubiquitylation) or a chain of ubiquitin (polyubiquitylation). Secondary ubiquitin molecules are always linked to one of

9964-565: The protein. In budding yeast, there are four SUMO E3 proteins, Cst9, Mms21, Siz1 and Siz2 . While in ubiquitination an E3 is essential to add ubiquitin to its target, evidence suggests that the E2 is sufficient in SUMOylation as long as the consensus sequence is present. It is thought that the E3 ligase promotes the efficiency of SUMOylation and in some cases has been shown to direct SUMO conjugation onto non-consensus motifs. E3 enzymes can be largely classed into PIAS proteins, such as Mms21 (a member of

10070-401: The proteins are rapidly degraded into small peptides (usually 3–25 amino acid residues in length). Ubiquitin molecules are cleaved off the protein immediately prior to destruction and are recycled for further use. Although the majority of protein substrates are ubiquitylated, there are examples of non-ubiquitylated proteins targeted to the proteasome. The polyubiquitin chains are recognised by

10176-459: The relatively constrained α-helical structure. Estimated differences in free energy change , Δ(Δ G ), estimated in kcal/mol per residue in an α-helical configuration, relative to alanine arbitrarily set as zero. Higher numbers (more positive free energy changes) are less favoured. Significant deviations from these average numbers are possible, depending on the identities of the neighbouring residues. A helix has an overall dipole moment due to

10282-415: The right. It shows SUMO1 as a globular protein with both ends of the amino acid chain (shown in red and blue) sticking out of the protein's centre. The spherical core consists of an alpha helix and a beta sheet . The diagrams shown are based on an NMR analysis of the protein in solution. Most SUMO-modified proteins contain the tetrapeptide consensus motif Ψ-K-x-D/E where Ψ is a hydrophobic residue, K

10388-453: The rupture of groups of H-bonds. Phase III is typically associated with large-deformation covalent bond stretching. Alpha-helices in proteins may have low-frequency accordion-like motion as observed by the Raman spectroscopy and analyzed via the quasi-continuum model. Helices not stabilized by tertiary interactions show dynamic behavior, which can be mainly attributed to helix fraying from

10494-414: The same protein. The addition of a single ubiquitin molecule is thought to be required prior to the formation of polyubiquitin chains. Monoubiquitylation affects cellular processes such as membrane trafficking , endocytosis and viral budding . Polyubiquitylation is the formation of a ubiquitin chain on a single lysine residue on the substrate protein. Following addition of a single ubiquitin moiety to

10600-461: The seven lysine residues or the N-terminal methionine of the previous ubiquitin molecule. These 'linking' residues are represented by a "K" or "M" (the one-letter amino acid notation of lysine and methionine, respectively) and a number, referring to its position in the ubiquitin molecule as in K48, K29 or M1. The first ubiquitin molecule is covalently bound through its C-terminal carboxylate group to

10706-445: The subcellular localization of the protein is altered, often targeting the protein for destruction in lysosomes. This serves as a negative feedback mechanism, because often the stimulation of receptors by ligands increases their rate of ubiquitylation and internalisation. Like monoubiquitylation, lysine 63-linked polyubiquitin chains also has a role in the trafficking some membrane proteins. Proliferating cell nuclear antigen (PCNA)

10812-466: The tumor suppressor p53 by Mdm2 can be followed by addition of a polyubiquitin chain using p300 and CBP . Ubiquitylation affects cellular process by regulating the degradation of proteins (via the proteasome and lysosome ), coordinating the cellular localization of proteins, activating and inactivating proteins, and modulating protein–protein interactions . These effects are mediated by different types of substrate ubiquitylation, for example

10918-479: The two proteins. They are highly specific, as are the E3 ligases that attach the ubiquitin, with only a few substrates per enzyme. They can cleave both isopeptide (between ubiquitin and lysine) and peptide bonds (between ubiquitin and the N-terminus ). In addition to removing ubiquitin from substrate proteins, DUBs have many other roles within the cell. Ubiquitin is either expressed as multiple copies joined in

11024-559: The ubiquitylation cascade, E1 can bind with many E2s, which can bind with hundreds of E3s in a hierarchical way. Having levels within the cascade allows tight regulation of the ubiquitylation machinery. Other ubiquitin-like proteins (UBLs) are also modified via the E1–E2–E3 cascade, although variations in these systems do exist. E4 enzymes, or ubiquitin-chain elongation factors, are capable of adding pre-formed polyubiquitin chains to substrate proteins. For example, multiple monoubiquitylation of

11130-621: The α-helix and the β-strand (Astbury's nomenclature was kept), which were developed by Linus Pauling , Robert Corey and Herman Branson in 1951 (see below); that paper showed both right- and left-handed helices, although in 1960 the crystal structure of myoglobin showed that the right-handed form is the common one. Hans Neurath was the first to show that Astbury's models could not be correct in detail, because they involved clashes of atoms. Neurath's paper and Astbury's data inspired H. S. Taylor , Maurice Huggins and Bragg and collaborators to propose models of keratin that somewhat resemble

11236-503: Was observed due to the high antitumor activity of proteasome inhibitors. Various studies have shown that defects or alterations in ubiquitylation processes are commonly associated with or present in human carcinoma. Malignancies could be developed through loss of function mutation directly at the tumor suppressor gene , increased activity of ubiquitylation, and/or indirect attenuation of ubiquitylation due to mutation in related proteins. The VHL ( Von Hippel–Lindau ) gene encodes

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