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Three-dimensional structure [1] of an alpha helix in the protein crambin. 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 ...
In biochemistry, denaturation is a process in which proteins or nucleic acids lose folded structure present in their native state due to various factors, including application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), agitation, radiation, or heat. [3]
A typical example is gramicidin A, a peptide that forms a dimeric transmembrane β-helix. [8] This peptide is secreted by gram-positive bacteria as an antibiotic. A transmembrane polyproline-II helix has not been reported in natural proteins. Nonetheless, this structure was experimentally observed in specifically designed artificial peptides. [9]
A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins. The sequence of amino acids that make up a helical region of the protein's secondary structure are plotted in a rotating manner where the angle of rotation between consecutive amino acids is 100°, so that the final ...
In the less extensive technique of equilibrium unfolding, the fractions of folded and unfolded molecules (denoted as and , respectively) are measured as the solution conditions are gradually changed from those favoring the native state to those favoring the unfolded state, e.g., by adding a denaturant such as guanidinium hydrochloride or urea.
Amylose A is a parallel double-helix of linear chains of glucose. Amylose is made up of α(1→4) bound glucose molecules. The carbon atoms on glucose are numbered, starting at the aldehyde (C=O) carbon, so, in amylose, the 1-carbon on one glucose molecule is linked to the 4-carbon on the next glucose molecule (α(1→4) bonds). [3]
This exposes a single glucose residue joined to the glucose chain through an α-1,6 glycosidic linkage [10] Mechanism for cleaving of alpha-1,6 linkage. Amylo-α-1,6-glucosidase (EC 3.2.1.33), or glucosidase, cleaves the remaining alpha-1,6 linkage, producing glucose and a linear chain of glycogen. [10]
The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position based on 17-amino-acid sequence windows. The original description of the method included four scoring matrices of size 17×20, where the columns correspond to the log-odds score, which reflects the probability of finding a given amino acid at each position in the 17 ...