Alpha helix
As α -helix in biochemistry a common secondary structure element of a protein is called. It is one of the most stable natural conformations of a peptide sequence and is nearly ubiquitous in the secondary structure. Of the secondary structure of a protein is understood without regard to the side groups of the three-dimensional structure of the amino acid chain. The secondary structure of a protein is shown ( amino acid sequence) in the primary structure. Parent structure levels are the tertiary structure and the quaternary structure. The three-dimensional structure of a protein is crucial for its selective function (see Protein Structure ).
- 3.1 helix prediction
- 3.2 Summary of the helix parameters
History
In the late 1930s began William Astbury crystal structure analyzes carried out on crystalline peptides. It was found that repeat certain spatial features on a regular basis, in which hydrogen bonds were assumed within the molecule. However, he was not yet known, the planarity of the peptide bond. The most common spatial structures were later called α -helix and β -sheet. Linus Pauling, Robert Corey and Herman Branson Brainard proposed in 1951 a model of the α - helix. The α in " α -helix " has no scientific value, but brings only expressed that the α -helix was found in front of the β -sheet. Developed by GN Ramachandran Ramachandran plot allowed their identification on the basis of the dihedral angles of the successive amino acids in the protein.
Structure
The α -helix is a right-handed twisted spiral ( preferably of L- amino acids) with an average of 3.6 amino acid side chains per revolution. A length of p = 0.54 nm ( 5.4 Å) is achieved per turn. This progress is called the pitch. It is the product of shift ( also called translation ) (0.15 nm) and residues per turn (3.6 ). This distance between residues is the reason that amino acids that are located in the primary structure of three or four points of each other, are located in the helical structure in the immediate vicinity. The α -helix is stabilized by a hydrogen bond between the carbonyl oxygen of the nth and the amide proton of the (n 4 ) th amino acid of the same molecule.
The CO and NH groups must lie close to each other to form the hydrogen bond. The narrowest configuration provides a coiled strand, in which the two groups lie above one another. The side chains face towards the outside. The amino acid proline ( " structure breakers " ) can not be easily fit into the helix ( only at positions 1-4, as seen from the amino terminus of this is possible ). Consequently, it comes to positions at which proline occurs, deviations from the regular structure. α -helices are very stable and can form a rigid cylinder a kind of skeleton of the protein. Therefore, they are often depicted in protein structures but not as helices as cylinders. A protein with a predominantly helical structure is myoglobin, a cognate with the hemoglobin muscle protein.
An α -helix is often stable only in the context of a protein, which is why the case of isolated α -helices often additional stabilizing bonds are introduced, eg by replacing the hydrogen bond by a CC bond by crosslinking of the amino acid side chains or by formation of disulfide bridges.
Other important structural elements
In addition to the α -helix and β -sheet secondary structure, there are other types of designs. The not belonging to a motive parts of the primary structure of a protein called random loops ( random coil structures). These structures are instrumental in the formation of the entire protein structure.
Other frequently occurring motifs are:
- π -helix
- 310- helix
- Left-handed helix of collagens
- β - loop
Geometry of the helix and the helix -helix interactions
α -helices are the basis of typical fibrous proteins ( α - keratin, the basic substance of the hair, myosin, a component of the muscle fibers, etc.) as well as introduced the example of myoglobin, structuring components of soluble, globular proteins. Individual helices can perform this task in general does not take over, but well-ordered aggregates of two, three, four or more Individualhelices. Figure 3 illustrates how two or three α -helices can assemble due to hydrophobic interactions to a " coiled coil " itself. This requires amphipathic helices, the helices of one side of which are hydrophilic ( water face ) and the other side is hydrophobic and thus capable of interactions. The geometry shown in Figure 1 has the effect that the " hydrophobic band" is not parallel to the helical axis, but the helix surrounds in the form of an elongated, left-handed spiral. When approaching the hydrophobic bands of two or more helices, arises as the " coiled-coil " designated superhelix.
Helix prediction
First efforts for the prediction of protein secondary structures date back to the 1960s and could be continually refined with the advent of modern X-ray structure analysis. A very helpful, rational approach for the prediction of α -helix connects with the name Marianne Schiffer and connects to the above considerations. As illustrated Figure 1, the n / -3.4 criterion that can mate with a balance of N residues, the three or four positions are removed. Thus, for example, residues 1, 4, and 5 hydrophobic so they can interact and thus stabilize a helical structure. The same applies to the remains of 6, 3 and 2, etc. This prediction scheme was initially for insulin and myoglobin its value.
With the release of further X-ray structural analyzes of the "helical -wheel " approach increasingly important statistical methods. An early approach of this kind is due to Chou and Fasman (1974, 1978). Subsequently, a table is shown, which reflects the helical potential of amino acid residues. As " helix formers ", is referred to an amino acid, provided that their potential ( Pα ) is significantly higher than 1 and as a " helix breaker ", when it is much smaller.
Is the helix represented.