2. 5 Some amino acid residues are accommodated in the different types of secondary structure better than others 2.5.1 The probability is calculated from known protein structures. It is used in predicting secondary structures. 2.5.2 Some bias or propensities can be explained easily. 2.5.3 Others are not yet understood
2.5 Some amino acid residues are accommodated in the different types of secondary structure better than others. 2.5.1 The probability is calculated from known protein structures. It is used in predicting secondary structures. 2.5.2 Some bias or propensities can be explained easily. 2.5.3 Others are not yet understood
Collagen triple helix Antiparallel β sheets Parallel B sheets Right-twisted B sheets +180 Left-handed a helix 120 Right-handed -60 a heli 120 180 180 +18 φ( degrees) a Ramachandran plots for a variety of structures
Ramachandran plots for a variety of structures
c helixβ ConformationβTurn Glu Met Ala eu ys Phe GIn Trp e Val As His Arg Thr Ser ys Asn T yr ro Gly Relative probabilities that a given amino acid will occur in the three common types of secondary structure
Relative probabilities that a given amino acid will occur in the three common types of secondary structure
table 6-2 Approximate Amounts of a Helix and B Conformation in some single-Chain proteins Residues (% Protein (total residues) a helix β Conformation Chymotrypsin (247) 14 Ribonuclease(124) 26 35 Carboxypeptidase(307) 38 17 Cytochrome c(104) 39 0 Lysozyme (129) 12 Myoglobin (153) 0 Source: Data from Cantor, C.R.& Schimmel, P.R.(1980)Biophysical Chemistry, Part I: The Conformation of Biological Macromolecules, p. 100, W.H. Freeman and Company, New York Portions of the polypeptide chains that are not accounted for by a helix or B conformation consist of bends and irregularly coiled or extended stretches. Segments of a helix and B conformation sometimes deviate slightly from their normal dimensions and geometry
2.6 Supersecondary structures and domains 2.6.1 The supersecondary structures, also called motifs or simply folds, refers to clusters of secondary structures that repeatedly appear. 2.6.2 The already identified supersecondary structures include main!yβaβ motif, Greek key motif.,βB- hairpin loop, four-helix-bundle..etc. 2.6.3 Supersecondary structure motifs are usually also folding motifs of proteins.(a conjecture, Not completely established experimentally). 26. 4 A compact region(usually including less than 200-400 residues) that is a distinct structural unit within a larger polypeptide chain is called a domain. 2.6.5 Many domains fold independently into thermodynamically stable structures, and sometimes, have separate functions
2.6.1 The supersecondary structures, also called motifs or simply folds, refers to clusters of secondary structures that repeatedly appear. 2.6.2 The already identified supersecondary structures include mainly bab motif, Greek key motif, b-hairpin loop, four-helix-bundle, …etc. 2.6.3 Supersecondary structure motifs are usually also folding motifs of proteins. (a conjecture, Not completely established experimentally). 2.6.4 A compact region (usually including less than 200~400 residues) that is a distinct structural unit within a larger polypeptide chain is called a domain. 2.6.5 Many domains fold independently into thermodynamically stable structures, and sometimes, have separate functions. 2.6 Supersecondary structures and domains