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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 ...
Three-dimensional structure 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 the ...
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 and radiation, or heat. [3]
Of the numerous protein secondary structures present, the 3 10-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 3 10-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini.
Helix–coil transition models are formalized techniques in statistical mechanics developed to describe conformations of linear polymers in solution. The models are usually but not exclusively applied to polypeptides as a measure of the relative fraction of the molecule in an alpha helix conformation versus turn or random coil .
Hydrophobicity scales can also be obtained by calculating the solvent accessible surface areas for amino acid residues in the expended polypeptide chain [22] or in alpha-helix and multiplying the surface areas by the empirical solvation parameters for the corresponding types of atoms. [3]
In polymer science, the Lifson–Roig model [1] is a helix-coil transition model applied to the alpha helix-random coil transition of polypeptides; [2] it is a refinement of the Zimm–Bragg model that recognizes that a polypeptide alpha helix is only stabilized by a hydrogen bond only once three consecutive residues have adopted the helical conformation.
The probability thresholds for helix and strand nucleations are constant but not necessarily equal; originally 1.03 was set as the helix cutoff and 1.00 for the strand cutoff. Turns are also evaluated in four-residue windows, but are calculated using a multi-step procedure because many turn regions contain amino acids that could also appear in ...