Ramachandran diagrams

A chain of L-amino acids can form either a right-handed or a left-handed helix. From the Ramachandran diagram in Fig. 2-9, can you say anything about the relative stabilities of right and left-handed helices What do you predict for polyglycine ... 

Figure 1.11 Ramachandran diagrams illustrating the preferred conformations of the polypeptide chain, (a) The allowed regions and their relationship to different types of secondary structure, (b) The different conformational restrictions for the different amino acids. Note the high conformational freedom for glycine (G) and the restrictions on isoleucine (I) and valine (V).

A simple model for the kinetics of helix formation invokes as the rate-determining step the formation of a nucleus of neighboring residues with and iff angles in the a-helical region of the Ramachandran diagram (Chapter 1, section Cl and Figure 1.11).5 The nucleuses so improbable that there is only a single one... 

Model studies show that, for each amino acid, the pair of angles and P is greatly restricted by steric repulsion. The allowed pairs of values are depicted on a Ramachandran diagram (Fig. 8.2). A point (dT P) on the diagram represents the conformational angles d> and P on either side of the alpha carbon of one residue. 

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

Finally, the structure of the thermodynamically favored isomer of [l2(OCH3)2Ti2]2- was deduced from conformational analysis of X-ray structural data of some of the complexes using Ramachandrarfs method. The dihedral angles and T of the amino acid residues observed in the X-ray structures were determined and were correlated in a Ramachandran diagram. 

Are all combinations of ([) and / possible G. N. Ramachandran recognized that many combinations are forbidden because of steric collisions between atoms. The allowed values can be visualized on a two-dimensional plot called a Ramachandran diagram (Figure 3,28). Three-quarters of the possible (([), X /) comhinations are excluded simply by local steric clashes. Steric exclusion, the fact that two atoms cannot be in the same place at the same time, can be a powerful organizing principle. 

Figure 3.28. A Ramachandran Diagram Showing the Values of ( ) and ]/. Not all ([) and / values are possible without collisions between atoms. The most favorable regions are shown in dark green borderline regions are shown in light green. The structure on the right is disfavored because of steric clashes.

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.

Figure 2.34 Ramachandran diagram for 3 strands. The red area shows the sterically allowed conformatioris of extended, p-strand-like structures.

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... 

NAD+-pyruvate is shown in Fig. 8. The enzyme has an extensive amount of secondary structure. Ramachandran diagrams are shown in Fig. 9. Estimates of the proportion of amino acid residues located in the helices depend on the precise definition of secondary structure and vary around 40%. Three different p structures are found in LDH and account for around 23% of all residues. The amino terminal half of the molecule contains a six-stranded parallel sheet whereas the carboxy terminal half of the subunit has two three-stranded antiparallel p structures. The parallel sheet which is mainly in the interior of the molecule, exposes two edges to the solvent and one to a subunit interface. Thus, most of the residues in this structure are hydrophobic. The high concentration of / -branched residues such as valine, isoleucine, and threonine as well as the twist present in all observed p structures 143) can be seen in Fig. 

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... 

Two simple shape descriptors use local properties of special bonds to characterize a macromolecular structure. These are the helical content and the distribution of peptidic dihedral angles (the Ramachandran diagram). 

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