Ramachandran diagram, protein

Figure 8.2 Ramachandran diagram for nonglycine amino-acid residues in proteins. Angles and are as defined in Fig. 8.1.

Figure 3.31. Raniachandran Diagram for Helices. Both right- and left-handed helices lie in regions of allowed conformations in the Ramachandran diagram. However, essentially all a helices in proteins are right-handed.

Only certain , y conformation pairs are observed. This is usually described in terms of the Ramachandran diagram, as shown in Figure 5.8, with as the horizontal axis and y as the vertical axis. In Figure 5.8, the experimentally determined backbone dihedral angles for the alanine, glycine, and proline residues of 699 proteins are depicted. There are three basic... 

The values of the two angles are illustrated in the Ramachandran diagram wiiich defines the limits of conformaUrmal freedom for each peptide bond unit and hence (or the entire polypeptide chain. However, even if limited confcamailons are allowed for each amino acid, the number of possible conformations for the polypeptide Is high. Fresidue protein with three confbrmaitons for each amino acid would have 3 " possible conformations. Therefore, the number of conformal ion.s that a protein can possess is very important... 

The first principle, which governs the amino acids packing in the whole protein, is presented in more detail in Section 2.7. The second principle relies on the observation that quite all the torsion angles and in proteins are located in the allowed region of the Ramachandran diagram. Based on these principles, models for describing the packing of a helices, pleated sheets, and the interactions between helices and pleated sheets have been presented. 

The location on the Ramachandran diagram of all observed conformations in proteins whose structure is known from high-resolution X-ray crystallography, clearly indicates the preference for the allowed regions of... 

Unless otherwise stated, for each individual protein crystal structure, an analysis of its secondary structure (helix, P-strand and coil), solvent accessibility and the placement of residues in the Ramachandran diagram [63R1] is provided in Fig. Where more than one polypeptide chain is... 

Ramachandran s stereochemical plot diagram) of dipeptides has been widely used to predict the secondary structures of proteins [306-309]. It is well known that the calculations on the polypeptides are limited by the number of atoms and hence high level ab initio and DFT calculations have been possible recently only. Several theoretical calculations with different levels of accuracy have been made on the polypeptides to study the < )- 1> plot distribution, H-bonding interactions, and stability [1-4, 308-322]. In the stability of polypeptides and proteins, H-bond plays an important role in the formation of the secondary structures such as the a-helix, (3-sheet, etc., and higher-order structures [1-4]. Quantum chemical calculations on some of the secondary structures in peptides and proteins ((3-sheets, (3-turns, and y-turns) at the HF and MP2 levels have been performed with special emphasis to the H-bonded structures... 

The term conformational map has been applied to two-dimensional energy diagrams or scatter plots describing the expected or actual distribution of torsion angles 0(C NC C ) and i/ (NC C N) in polypeptide chains. See Ramachandran, G.N., Sasikharan, V., Adv. Protein Chem. 1968, 23, 284-437... 

Fig. 4 Ramachandran plot, (a) Diagram showing regions with high energy due to steric hindrance between specified atoms on neighboring amino acid residues, (b) An example of dihedral angle plotting of for proteins from PDB data. (Reproduced from [37] with pemussion)...

---