Smith chart forbidden region6/4/2023 ![]() ![]() One of these is an elongated version of the β P region of the generic Ramachandran plot. Along the horizontal strip ψ' ~ 180°, there are three separate regions. With the shifted glycine Ramachandran plot (Figure (Figure3A), 3A), we can clearly identify the different regions. ![]() In order to display the observed density in one continuous region, we shift the coordinates from φ-ψ to φ'-ψ' where φ': 0° < φ' < 360°, and ψ': -90° < ψ' < 270°. The observed glycine map has 5 regions of density. The absence of the C β atom allows the glycine Ramachandran plot to run over the borders at -180° and 180° (Figure (Figure1A 1A). We call the hydrogen atom that replaces the C β atom, the H α2 atom. We call the hydrogen atom that is shared with the other amino acids, the H α1 atom. In particular, glycine does not have the C β atom, which induces many steric clashes in the generic Ramachandran plot. Glycine is fundamentally different to the other amino acids in that it lacks a sidechain. In this study, we focus on the physical origin of the ζ region. More recent calculations using standard molecular mechanics force-fields reproduced the energy surface of the original Flory calculation but not the ζ region. However, the statistical analysis also revealed the existence of a little leg of density poking out below the β-region (Figure (Figure1B 1B purple in Figure Figure2C), 2C), which Karplus called the ζ region. This was later confirmed in a statistical analysis of the protein database. The basic shape of pre-proline was predicted by Flory using steric interactions. See text for explanation of the regions.Īlthough the overall shape of the pre-proline Ramachandran plot (Figure (Figure1B) 1B) is well understood, there exists a region unique to pre-proline that remains unexplained. The clustered regions are: grey – sterically allowed red – α and α L yellow – β S blue – β P and β PR purple – ζ. (A) original steric map of glycine, in standard (left) and shifted (right) coordinates (B) revised schematic of glycine, in standard (left) and shifted (right) coordinates (C) pre-proline. We test these interactions with a simple model based on electrostatics and Lennard-Jones potentials. In this study, we identify the specific interactions that define the observed glycine Ramachandran plot by studying the conformations of glycine in the structural database. They calculated a somewhat better result with a quantum-mechanics/molecular-mechanics model, which reproduced the observed clustering along ψ, but not the partitioning into the 5 clusters. Using a molecular-dynamics simulation of Ace-Gly-Nme, Hu and co-workers found that the glycine Ramachandran plot generated by standard force-fields reproduced the original steric map but not the observed Ramachandran plot. It does not explain the observed clustering at ψ = 180° and ψ = 0°, nor the clustering into 5 distinct regions. An early attempt to explain the observed Ramachandran plot in terms of a steric map of glycine (Figure (Figure2A) 2A) fails to account for the observed distribution. The observed glycine Ramachandran plot has a distinctive distribution (Figure (Figure1A) 1A) quite different to the generic Ramachandran plot. The proline Ramachandran plot is severely restricted by the pyrrolidine ring, where the flexibility in the pyrrolidine ring couples to the backbone. The proline Ramachandran plot has been reproduced in a calculation. These clusters have now been explained in terms of backbone dipole-dipole interactions. The second discrepancy is that the Ramachandran plot cluster into distinct regions within the sterically-allowed regions of the Ramachandran plot. By removing these steric clashes, a better steric map can be constructed. ♼ steric clashes in the classic steric map have no effect in the observed Ramachandran plot.These discrepancies have now been resolved. However, recent studies found significant discrepancies between the classic steric map and the Ramachandran plot of high-resolution protein structures. This has become the standard explanation for the observed regions in the Ramachandran plot. The generic Ramachandran plot was first explained by Ramachandran and co-workers in terms of steric clashes. The generic and proline Ramachandran plots are now well understood but the glycine and pre-proline Ramachandran plots are not. There are four basic types of Ramachandran plots, depending on the stereo-chemistry of the amino acid: generic (which refers to the 18 non-glycine non-proline amino acids), glycine, proline, and pre-proline (which refers to residues preceding a proline ). The φ-ψ angles cluster into distinct regions in the Ramachandran plot where each region corresponds to a particular secondary structure. It provides a simple view of the conformation of a protein. The Ramachandran plot is the 2d plot of the φ-ψ torsion angles of the protein backbone. ![]()
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