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62-465: ISWI ( I mitation SWI tch) is one of the five major DNA chromatin remodeling complex types, or subfamilies, found in most eukaryotic organisms. ISWI remodeling complexes place nucleosomes along segments of DNA at regular intervals. The placement of nucleosomes by ISWI protein complexes typically results in the silencing of the DNA because the nucleosome placement prevents transcription of the DNA. ISWI, like

124-483: 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 –

186-468: A Beta sheet -turn- Alpha helix that is self-organized as a Nest (protein structural motif) . This is thought to be because modern ATPases evolved from small NTP-binding peptides that had to be self-organized. Protein design has been able to replicate the ATPase function (weakly) without using natural ATPase sequences or structures. Importantly, while all natural ATPases have some beta-sheet structure,

248-476: 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

310-437: 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

372-470: A fixed number of solute molecules are transported for each ATP molecule hydrolyzed; for the Na /K exchanger, this is three Na ions out of the cell and two K+ ions inside per ATP molecule hydrolyzed. Transmembrane ATPases make use of ATP's chemical potential energy by performing mechanical work: they transport solutes in the opposite direction of their thermodynamically preferred direction of movement—that is, from

434-400: 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

496-452: 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

558-532: 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

620-425: 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

682-432: 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

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744-625: 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

806-508: 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

868-436: A specific type of ion. P-ATPases may be composed of one or two polypeptides, and can usually take two main conformations, E1 and E2. 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

930-517: 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

992-739: Is an anabolic enzyme that harnesses the energy of a transmembrane proton gradient as an energy source for adding an inorganic phosphate group to a molecule of adenosine diphosphate (ADP) to form a molecule of adenosine triphosphate (ATP). This enzyme works when a proton moves down the concentration gradient, giving the enzyme a spinning motion. This unique spinning motion bonds ADP and P together to create ATP. ATP synthase can also function in reverse, that is, use energy released by ATP hydrolysis to pump protons against their electrochemical gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in

1054-495: 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

1116-402: Is close to the subunit b 2 and makes up the stalk that connects the transmembrane subunits to the α3β3 and δ subunits. F-ATP synthases are identical in appearance and function except for the mitochondrial F 0 F 1 -ATP synthase, which contains 7-9 additional subunits. The electrochemical potential is what causes the c-ring to rotate in a clockwise direction for ATP synthesis. This causes

1178-413: Is involved in the movement of ions across the membrane. The bacterial F 0 F 1 -ATPase consists of the soluble F 1 domain and the transmembrane F 0 domain, which is composed of several subunits with varying stoichiometry. There are two subunits, γ, and ε, that form the central stalk and they are linked to F 0 . F 0 contains a c-subunit oligomer in the shape of a ring (c-ring). The α subunit

1240-479: 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

1302-451: 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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1364-589: Is the sodium-potassium pump (Na /K ATPase) that maintains the cell membrane potential . Another example is the hydrogen potassium ATPase (H /K ATPase or gastric proton pump) that acidifies the contents of the stomach. ATPase is genetically conserved in animals; therefore, cardenolides which are toxic steroids produced by plants that act on ATPases, make general and effective animal toxins that act dose dependently. Besides exchangers, other categories of transmembrane ATPase include co-transporters and pumps (however, some exchangers are also pumps). Some of these, like

1426-458: 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

1488-434: Is the local structure that 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

1550-737: The SWI/SNF chromatin remodeling family in the ATPase domain. Outside the ATPase domain ISWI loses the similarity with the member of the SWI/SNF family, possessing a SANT domain instead of the bromodomain . The protein ISWI can interact with several proteins giving three different chromatin-remodeling complexes in Drosophila melanogaster : NURF ( nucleosome remodeling factor), CHRAC (chromatin remodeling and assembly complex) and ACF (ATP-utilising chromatin remodeling and assembly factor). In vitro ,

1612-673: 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 ,

1674-546: 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

1736-401: 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

1798-475: 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

1860-462: 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

1922-523: 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

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1984-455: The ISWI protein alone can assemble nucleosomes on linear DNA and it can move nucleosomes on linear DNA from the center to the extremities. Inside the CHRAC complex, ISWI catalyzes the inverse reaction, moving nucleosomes from the extremities to the center. A single molecule study using atomic force microscopy (AFM) and tethered particle motion (TPM) has observed that ISWI can bind naked DNA in

2046-481: The Na /K ATPase, cause a net flow of charge, but others do not. These are called electrogenic transporters and electroneutral transporters, respectively. The Walker motifs are a telltale protein sequence motif for nucleotide binding and hydrolysis. Beyond this broad function, the Walker motifs can be found in almost all natural ATPases, with the notable exception of tyrosine kinases . The Walker motifs commonly form

2108-539: 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

2170-501: The absence of ATP , wrapping DNA around the protein. In presence of ATP , the protein generates DNA loops while simultaneously generating negative supercoils in the template. The first figure in this paper shows three AFM images from where single DNA interacting with ISWI was deposed on mica surfaces. On the center, a single ISWI is bound near the end of a dsDNA template. The right image shows two DNA loops generated by ISWI. These loops contains supercoils. The TPM study instead showed that

2232-548: 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

2294-448: 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

2356-542: The central stalk and the catalytic domain to change shape. Rotating the c-ring causes three ATP molecules to be made, which then causes H to move from the P-side of the membrane to the N-side of the membrane. The counterclockwise rotation of the c-ring is driven by ATP hydrolysis and ions move from the N-side to the P-side, which helps to build up electrochemical potential. The ATP synthase of mitochondria and chloroplasts

2418-488: The closely related SWI/SNF subfamily, is an ATP-dependent chromatin remodeler. However, the chromatin remodeling activities of ISWI and SWI/SNF are distinct and mediate the binding of non-overlapping sets of DNA transcription factors. The protein ISW1 is the first ATPase subunit which has been isolated in the ISWI chromatin remodeling family in the fruit fly Drosophila . This protein presents high level of similarity to

2480-416: 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

2542-416: The designed "Alternative ATPase" lacks beta sheet structure, demonstrating that this life-essential function is possible with sequences and structures not found in nature. ATPase (also called F 0 F 1 -ATP Synthase) is a charge-transferring complex that catalyzes ATP to perform ATP synthesis by moving ions through the membrane. The coupling of ATP hydrolysis and transport is a chemical reaction in which

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2604-467: The duration of loop formed by ISWI was ATP-dependent. ATPase Some such enzymes are integral membrane proteins (anchored within biological membranes ), and move solutes across the membrane, typically against their concentration gradient. These are called transmembrane ATPases. Transmembrane ATPases import metabolites necessary for cell metabolism and export toxins, wastes, and solutes that can hinder cellular processes. An important example

2666-409: 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

2728-521: 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,

2790-466: 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

2852-407: 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

2914-607: 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

2976-480: 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

3038-463: 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

3100-420: 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

3162-569: 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

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3224-485: 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,

3286-549: 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

3348-418: 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

3410-434: 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

3472-402: The other direction. One stalk is utilized to transmit torque. The number of peripheral stalks is dependent on the type of ATPase: F-ATPases have one, A-ATPases have two, and V-ATPases have three. The F 1 catalytic domain is located on the N-side of the membrane and is involved in the synthesis and degradation of ATP and is involved in oxidative phosphorylation . The F 0 transmembrane domain

3534-427: 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

3596-459: 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

3658-453: 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

3720-590: The side of the membrane with low concentration to the side with high concentration. This process is referred to as active transport . For instance, inhibiting vesicular H -ATPases would result in a rise in the pH within vesicles and a drop in the pH of the cytoplasm. All of the ATPases share a common basic structure. Each rotary ATPase is composed of two major components: F 0 /A 0 /V 0 and F 1 /A 1 /V 1 . They are connected by 1-3 stalks to maintain stability, control rotation, and prevent them from rotating in

3782-490: The type of ions they transport. P-ATPases (sometime known as E1-E2 ATPases) are found in bacteria and also in eukaryotic plasma membranes and organelles. Its name is due to short time attachment of inorganic phosphate at the aspartate residues at the time of activation. Function of P-ATPase is to transport a variety of different compounds, like ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transports

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3844-621: 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

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