The alpha helix (? - helix ) is a common motif in the secondary structure of proteins and is the right spiral conformation (ie helix) where each backbone of the NH group donates the hydrogen bond to the bone back C = O group of amino acids located three or four previous residues along the order of proteins.
The alpha helix is ​​also called the classic Pauling-Corey-Branson? -helix . The name 3,6 13 -helix is also used for this helical type, showing the average number of residuals per helical spin, with 13 atoms involved in rings formed by hydrogen bonds.
Among the types of local structures in proteins, "-most are the most ordered and most predictable of the order, as well as the most common.
Video Alpha helix
Discovery
In the early 1930s, William Astbury pointed out that there was a drastic change in X-ray fiber diffraction from moist wool or hair fiber at significant stretching. The data show that unreaten fiber has a circular molecular structure with repeatability of ~ 5.1 ÃÆ'  ¥ ngstrÃÆ'¶ms (0.51 nanometer) characteristics.
Astbury originally proposed a threaded-chain structure for fiber. He then joined other researchers (especially American chemist Maurice Huggins) in proposing that:
- stretched protein molecules form a helix (which he called? -form)
- The stretch causes the helix to be choppy, forming a long state (what it calls? -form).
Though not true in the details, the Astbury model of these forms is essentially correct and conforms to the modern elements of the secondary structure, '-most and' -strand (Astbury nomenclature stored), developed by Linus Pauling, Robert Corey and Herman Branson in 1951 (see below); the paper shows the right and left helices, although in 1960 the crystalline structure of myoglobin showed that the shape of the right hand was common. Hans Neurath is the first to show that Astbury models can not be true in detail, because they involve atomic clashes. Neurath paper and Astbury data inspired H. S. Taylor, Maurice Huggins and Bragg and collaborators to propose a somewhat similar model of modern-hipelin keratin.
Two key developments in modern-helix modeling are: true bonding geometry, thanks to the determination of the crystalline structure of amino acids and peptides and Pauling's prediction of the planar peptide bonds ; and it releases the assumption of the number of integral residues per helical turn. An important moment came in the early spring of 1948, when Pauling got cold and went to bed. Boredom, he drew a polypeptide chain of the correct size on a piece of paper and folded it into a helix, carefully guarding the planar peptide bond. After several tries, he produced a model with a physically reasonable hydrogen bond. Pauling then worked with Corey and Branson to confirm the model before it was published. In 1954, Pauling was awarded his first Nobel Prize "for his research on the nature of chemical bonding and its application to the explanation of the structure of complex substances" (such as proteins), prominently including the structure of the -helix.
Maps Alpha helix
Structure
Geometry and hydrogen bond
The in-helix amino acids are arranged in a right-handed helical structure where each amino acid residue corresponds to a 100 Â ° curve in the helix (ie, the helix has 3.6 residues per turn), and the translations of 1.5 ((0, 15 nm) along the helical axis. Dunitz describes how Pauling's first article on the theme actually shows the left-handed helical, enantiomer of the actual structure. Pieces of left-handed helix occasionally occur with a large content of the amino acid glycine achiral, but not favorable to other normal acids, L -amino biologics. The pitch of the alpha-helix (the vertical distance between successive helices in succession) is 5.4 ÃÆ'... (0.54 m), which is a product of 1.5 and 3.6. What is most important is that the N-H group of an amino acid forms a hydrogen bond with the C = O group of the amino acid four of the previous residue; is this repeated i 4 -> i hydrogen bond is the most prominent characteristic of? -helix. The official international nomenclature [3] sets two ways to define? -helices, rule 6.2 in repeating ? , ? torsion angle (see below) and rule 6.3 in terms of the combined pattern of pitch and hydrogen bonding. The-aid can be identified in protein structures using several computational methods, one of which is the DSSP (Dictionary of Protein Secondary Structure).
Similar structures include 3 helix 10 ( i <3 -> i hydrogen bonds) and "-helix" Ã, Ã, 5 -> i hydrogen bonds). The helix can be described as a helix 3,6 13 , because i <α, α, 4 spaces add three more atoms to the H-bound loop compared to the more strict 3 < sub> 10 helix, and on average, 3.6 amino acids involved in one ring? -helix. The subscript refers to the number of atoms (including hydrogen) in closed loops formed by hydrogen bonds.
Residue in? -the selection usually adopts the spine (? , Ã, ? ) around dihedral angle (-60 Â °, -45 Â °), as shown in the picture on the right. In more general terms, they adopt a dihedral angle such that ? the dihedral angle of one residue and ? the dihedral angle of the next residual to about -105 Â °. Consequently, the diaphrally-angled corners, in general, fall on the diagonal line on the Ramachandran diagram (from slope -1), ranging from (-90 Â °, -15 Â °) to (-35 Â °, -70 Â °). For comparison, the number of dihedral angles for helix 3 10 is approximately -75 Â °, while for -most approximately -130 Â °. The general formula for the rotation angle ? per residual helix polypeptide with trans-isomer is given by the equation
The -helix is ​​very solid; hardly any empty space inside the helix. The amino acid side chains are located on the outside of the helix, and pointing about "down" (that is, toward the N-terminus), like the branches of a pine tree (the effect of a Christmas tree). This directionality is sometimes used in low-density initial electron density maps to determine the direction of the protein backbone.
2D (2-dimensional ) diagram to represent? -helet
Three different diagram styles of 2D â € <â €
The helical wheel represents the helix with the projection of the C spine structure? under the helical axis, whereas the wenxiang diagram represents the more abstract as a fine spiral circular on the page field. Both label the sequence with a single-letter amino code (see amino acids) at each position C ? , using different colors or symbols to encode the properties of amino acids. Hydrophobic vs. hydrophilic amino acids are always distinguished, as the most important property that governs helical interactions. Sometimes hydrophilic positively vs negative is different, and sometimes ambiguous amino acids such as glycine (G) are distinguished. Color coded conventions vary. The helical wheel does not alter the representation along the helix, whereas the wenxiang diagram is able to show the relative location of the amino acid in "-helix" regardless of how long.
Either the circular style of the diagram can provide an intuitive and easily visualized 2D image that characterizes the hydrophobic disposition and the hydrophilic residue in the selection, and can be used to study the interactions of the helices, the interaction of helices as quantified by helical hydrophobic moments, or protein- protein. A variety of utilities and websites are available to produce helical wheels, such as pages by Kael Fischer.
The third style 2D diagram is called "helical net". This is produced by opening the cylindrical surface of each helix along the line parallel to the axis and placing the result vertically. The helix network is not suitable for studying helix-helix interactions, but has become the dominant way to represent sequence arrangements for integral membrane proteins because it shows an important relationship of the helical sequence to the vertical position within the membrane even without the knowledge of how the helix is ​​arranged in 3D.
Stability
The helices observed in proteins can range from four to more than forty lengths, but a typical helix contains about ten amino acids (about three revolutions). In general, short polypeptides do not show many of the hell-structures in solution, since the entropic costs associated with polypeptide chain folding are not compensated with sufficient stabilization interactions. In general, the backbone of hydrogen bonds from? -relections are considered slightly weaker than those found in? -sets, and easily attacked by ambient water molecules. However, in more hydrophobic environments such as plasma membranes, or in the presence of co-solvents such as trifluoroethanol (TFE), or isolated from solvents in the gas phase, oligopeptides easily adopt a stability -helix structure. Furthermore, crosslinking may be incorporated into the peptide to adjust the helical folds. The cross link stabilizes the helical state by entropically destabilizing the folded state and by removing stable stable "feed" folds that compete with the full helical state. It has been shown that? - the selection is more stable, stronger for mutation and can be design rather than? natural protein structures, as well as in artificial proteins that are designed.
Experimental determination
Because "-was almost defined by the hydrogen bond and spinal conformation, the most detailed experimental evidence for" aid-structure is derived from crystallographic resolution of X-ray atoms such as the example shown on the right. It is obvious that all of the carbonyl oxygen backbones point downward (toward C-terminus) but spewed out a bit, and the H-bond is roughly parallel to the helical axis. The protein structure of NMR spectroscopy also shows a good helix, with characteristic observations of the nuclear Overhauser effect (NOE) coupling between atoms at adjacent helical spins. In some cases, individual hydrogen bonds can be observed directly as small scalar scalars in NMR.
There are several low-resolution methods to establish common helix structures. The NMR chemistry shifts (specifically from C ? , C ? and C?) And the residual dipolar coupling are often helical characteristics. The UV-far circular helical dichroism spectrum (170-250 Â · nm) is also idiosyncratic, showing a double minimum of about 208 and 222 nm. Infrared spectroscopy is rarely used, since the spectrums resemble random coils (though this can be seen by, for example, hydrogen-deuterium exchange). Finally, cryo electron microscopes are now able to distinguish individual-aid in proteins, although their assignment to residues is still an active research area.
Long homopolymers of amino acids often form helices if dissolved. This long and isolated helix can also be detected by other methods, such as dielectric relaxation, birefringence flow, and diffusion constant measurement. In strict terms, this method only detects a typical hydrodynamic shape (length like a cigar) of a helix, or a large dipole moment.
Amino-acid propensities
Different amino acid sequences have different tendencies to form the hell-structure. Methionine, alanine, leucine, glutamate, and lysine uncharged ("MALEK" in the 1-letter amino acid code) all have a tendency to form very high helices, while proline and glycine have a tendency to form a bad helix. The proline either breaks or tangles the helix, either because it can not donate the amide hydrogen bond (lacking hydrogen amide), and also because its sidechain interferes sterically with the backbone of the previous bend - inside the helix, this forces a bend of about 30 ° on the helix axis. However, proline is often seen as the first residue of helices, this is presumably due to its structural rigidity. At the other extreme, glycine also tends to disrupt the helix because of its high conformability flexibility making it extremely costly to adopt a relatively limited structure.
Table of alpha-helical amino acid predictive tendencies
Estimated difference in free energy ,? ( G ), estimated in kcal/mol per residue in configuration? -heliks, relative to arbitrary alanine set as zero. A higher number (more positive free energy) is less favorable. A significant deviation from these figures is possible, depending on the identity of the neighboring residue.
When Dipol
The helix has overall dipole moment due to the aggregate effect of the individual microdipol of the peptide bonding carbonyl group pointing along the helical axis. The effect of macrodipole is a matter of controversy. ? -the selection often occurs with the N-terminal ends bound by negatively charged groups, sometimes amino acid side chains such as glutamate or aspartate, or sometimes phosphate ions. Some consider macrodipole helical to interact electrostatically with such groups. Others feel that it is misleading and more realistic to say that the hydrogen bond potential of the NH group is free on N-terminus of? - can almost be met by hydrogen bonds; this can also be considered as a set of interactions between local microdipoles such as C = O Ã, Â · Ã, Â · H-N .
The circular winding
Coiled-coil? A helix is ​​a very stable form in which two or more helices enclose one another in a "supercoil" structure. The circular winding contains a very distinctive sequence motif known as heptad replication , in which the motif repeats itself every seven residues along the sequence ( amino acid residue, not the base pairs of DNA.). The first and foremost fourth residues (known as positions a and d ) are almost always hydrophobic; the fourth residue is usually leucine - this gives rise to the name of a structural motif called leucine zipper , which is a coil-type coil. This hydrophobic residue is packed together on the inside of the helix bundle. In general, the fifth and seventh residues (positions e and g ) have opposite charges and form salt bridges stabilized by electrostatic interactions. Fiber proteins such as keratin or "stalk" of myosin or kinesin often adopt a coil-coiled structure, as do some protein dimerizing. A pair of circular coils - bundles of four helices - is a very common structural motif in proteins. For example, it occurs in human growth hormone and some cytochrome varieties. Rop protein, which promotes plasmid replication in bacteria, is an interesting case where a single polypeptide forms a circular coil and two monomers converge to form a four-helix bundle.
Face Settings
Amino acids that make up certain helices can be plotted on helical wheels, representations depicting the orientation of the constituent amino acids (see article for leucine zippers for such diagrams). Often in globular proteins, as well as in special structures such as circular coils and leucine zippers, an? will almost show two "faces" - one containing mainly hydrophobic amino acids oriented toward the inner part of the protein, in the hydrophobic nucleus, and containing polar dominated amino acids oriented to the soluble surface of the protein dissolved by the solvent.
Changes in binding orientation also occur for randomly organized oligopeptides. This pattern is very common in antimicrobial peptides, and many models have been designed to illustrate how this relates to their function. Common to many of them is that hydrophobic faces of antimicrobial peptides form pores in the plasma membrane after connecting with the fat chain in the membrane core.
Large-scale assembly
Myoglobin and hemoglobin, the first two proteins whose structures are solved by X-ray crystallography, have very similar creases composed of about 70%? -helix, with the rest being non-repetitive areas, or "loops" connecting the helices. In classifying proteins with their dominant folds, the Structural Classification of the Protein database maintains a large category specifically for all-? protein.
Hemoglobin then has a larger-scale quaternary structure, where the functional oxygen-binding molecule consists of four subunits.
Functional roles
DNA binding
-Helices have a special meaning in DNA binding motifs, including helix-turn-helix motifs, leucine zipper motifs and zinc finger motifs. It is due to the convenient structural fact that a diameter? -helix is ​​about 12 ÃÆ'... (1,2Ã, nm) including an average set of sidechains, almost equal to the main strand width in B-form DNA, and also because the coiled (or leucine ripper) helix dimer can easily positioned a pair of interaction surfaces to contact the common symmetrical type of repetition in double-helix DNA. An example of both aspects is the Max transcription factor (see figure on the left), which uses a helical coiled coil for dimerize, positioning another pair of helices for interaction in two consecutive rounds of the DNA mainline.
Limiting the membrane
? -Helices are also the most common element of the protein structure that passes through the biological membrane (transmembrane protein) this is thought to be because the helical structure can satisfy all internal hydrogen-backbone bonds, leaving no polar groups exposed to the membrane if sidechains are hydrophobic. Proteins are sometimes anchored by a single-stranded membrane strand, sometimes by a pair, and sometimes by a helix bundle, the most classical composed of seven helices arranged up and down in rings like for rhodopsin (see picture on right) or for protein-coupled G receptors (GPCRs).
Mechanical properties
-Helices under axial axial deformations, characteristic loading conditions that appear in many filaments and alpha-helix networks, result in a three-phase characteristic of rigid-soft-rigid modulus tangent behavior. Phase I corresponds to a small deformation regime in which the helix is ​​stretched homogeneously, followed by phase II, in which alpha-helices are broken breaks mediated by the breakup of the H-bond group. Phase III is usually associated with large covalent deformation bond stretching.
Dynamic features
The alpha-helices in proteins may have motions such as low frequency acordions as observed by Raman spectroscopy and are analyzed through a quasi-continuum model. The helices are not stabilized by tertiary interactions exhibiting dynamic behavior, which can mainly be attributed to a frayed helix from its tip.
Helix-coil transition
Homopolymer of amino acids (such as polylysine) can adopt? The low-melt-at-temperature molecular structure at high temperatures. This helix-coil transition was once considered analogous to protein denaturation. The statistical mechanics of this transition can be modeled using an elegant transfer matrix method, characterized by two parameters: the tendency to start the helix and the tendency to extend the helix.
In art
At least five artists have explicitly referred to "-helix" in their work: Julie Newdoll in the paintings and Julian Voss-Andreae, Bathsheba Grossman, Byron Rubin, and Mike Tyka in sculpture.
San Francisco regional artist Julie Newdoll, who has a degree in Microbiology with a minor in the arts, specializes in paintings inspired by microscopic and molecular images since 1990. His painting "Rise of Alpha Helix" (2003) features human figures arranged in a? helical settings. According to artists, "the flowers reflect the different types of sidechains that each of the amino acids hold onto the world". It is interesting to note that this same metaphor also echoes from the scientist's side: "The sheets do not show rigid repetitive regularity but flow in elegant, twisted, and even-almost overly regular curves by the flowering of the stem, environment, historical development, and evolution of each passage to match its own idiosyncratic function. "
Julian Voss-Andreae is a German-born sculptor with a degree in physics and an experimental sculpture. Since 2001 Voss-Andreae created "protein sculptures" based on protein structure with "e-stop" being one of the preferred objects. Voss-Andreae has made sculptures of various materials including bamboo and whole trees. A Voss-Andreae monument made in 2004 to celebrate the memory of Linus Pauling, the inventor of "-helix", is made of large steel beams rearranged in "-helix" structures. A 10 foot (3 m) tall, bright red statue stands in front of Pauling's childhood home in Portland, Oregon.
The ribbon diagram of "-electricity is a prominent element in laser carved crystal statues of protein structures created by Bathsheba Grossman artists, such as insulin, hemoglobin, and DNA polymerases.Byron Rubin is a former protein crystallographer who is now a professional sculptor in the field of metals proteins, nucleic acids, and drug molecules - many of which feature? -telections, such as subtilisin, human growth hormone, and phospholipase A2.
Mike Tyka is a computational biochemist at the University of Washington who works with David Baker. Tyka has made sculptures of protein molecules since 2010 from copper and steel, including ubiquitin and tetramer potasium channels.
See also
- 3 10 helix
- Helical pi
- Beta sheet
- Davydov soliton
- Fold (chemical)
- Push into the packing hole
- Proteopedia Helices_in_Proteins
References
Further reading
External links
- Ver NetSurfP. 1.1 - Accessibility of Protein Surface and Secondary Structure Prediction
- ? - helix rotation angle calculator
- Artist Julie Newdoll's website
- Artist Julian Voss-Andreae website
Source of the article : Wikipedia
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