The Ramachandran plots of glycine and pre-proline Abstract Background: The Ramachandran plot is a fundamental tool in the analysis of protein structures. Of the 4 basic types of Ramachandran plots, the interactions that determine the generic and proline Ramachandran plots are well understood.
How do you find glycine in Ramachandran plots?
You often find glycine in highly flexible regions (like immunoglobulin hinge regions) or proteins that coil very tightly (like collagen). Collagen also involves proline, more on that in the next paragraph. In the third and fourth panel, you see the Ramachandran plots for Pro-Pro dipeptides and proline on its own in a backbone.
What is Ramachandran plot in biochemistry?
In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure.
What is the difference between glycine and pre-proline Ramachandran plots?
The interactions of the glycine and pre-proline Ramachandran plots are not. In glycine, the ψ angle is typically clustered at ψ = 180° and ψ = 0°.
Why is glycine the least restricted amino acid in Ramachandran plot?
Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH 3, CH 2, or CH group that starts the side chain of all other amino acids. Hence it is least restricted, and this is apparent in the Ramachandran plot for glycine (see Gly plot in gallery) for which the allowable area is considerably larger.
Why are glycine and proline commonly excluded from Ramachandran plots?
The quick answer I always give is that they exist at the two extreme ends of the spectrum in terms of phi/psi rotation (which is what the Ramachandran plot shows). Gly is the least restricted, Pro is the most restricted. Thus Gly can appear anywhere & Pro only in certain places.
Why is glycine special in Ramachandran plot?
Regions in the glycine Ramachandran plot. Glycine is fundamentally different to the other amino acids in that it lacks a sidechain. In particular, glycine does not have the Cβ atom, which induces many steric clashes in the generic Ramachandran plot.
Which amino acids are not placed in Ramachandran plot?
Glycine, Proline, etc. The tripeptide Glu-Gly-Ala with Gly having φ and ψ values of +55o and -116o respectively, does not show the steric hindrance that the Glu-Ser-Ala had. For that reason Gly will frequently plot in the disallowed region of a general-case Ramachandran plot.
What does Ramachandran plot show?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
Why is glycine found in loops?
This conformational flexibility is why you'll find glycine residues in loop regions of the protein structure, where the polypeptide chain has to make sharp turns. Proline residues also have a "weird" side chain.
Why are proline and glycine common in beta turns?
Proline and glycine residues are statistically preferred at several β-turn positions, presumably because their unique side chains contribute favorably to conformational stability in certain β-turn positions.
Where is glycine and proline found?
Abstract. Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding.
Does glycine have a side chain?
Glycine is the simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain.
What is L glycine used for?
Glycine is used for treating schizophrenia, stroke, benign prostatic hyperplasia (BPH), and some rare inherited metabolic disorders. It is also used to protect kidneys from the harmful side effects of certain drugs used after organ transplantation as well as the liver from harmful effects of alcohol.
What is the principle of Ramachandran diagram?
The Ramachandran Principle says that alpha helices, beta strands, and turns are the most likely conformations for a polypeptide chain to adopt, because most other conformations are impossible due to steric collisions between atoms.
Which is correct regarding the peptides in the Ramachandran plot?
Peptides that are unstructured will have all the backbone dihedral angles in the. disallowed regions.
What is the angle of a Ramachandran plot?
All three angles are at 180° in the conformation shown. In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot ), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ ...
When was the Ramachandran plot first calculated?
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined ( myoglobin, in 1960 ), although the conclusions were based on small-molecule crystallography of short peptides.
Drug Discovery Technologies
R.A. Laskowski, G.J. Swaminathan, in Comprehensive Medicinal Chemistry II, 2007
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M. Wetzer, ... A.E. Barron, in Polymer Science: A Comprehensive Reference, 2012
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Marco Wiltgen, in Encyclopedia of Bioinformatics and Computational Biology, 2019
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Om Silakari, Pankaj Kumar Singh, in Concepts and Experimental Protocols of Modelling and Informatics in Drug Design, 2021
Applied Mycology and Biotechnology
In evaluating the model there are many different aspects to consider; the residue placement, the interaction of neighbouring residues and the atoms within the residues.
Biotechnology-based therapeutics
In silico drug design plays a vital role in target identification and designing novel drugs in the field of biotechnology. They mainly used to inspect the expression of genes, sequence analysis, molecular modeling, and their 3D structure ( Wadood et al., 2013 ).
G Protein Coupled Receptors
This first stage generates an initial set of loop conformations via a dihedral angle search. Residues are added sequentially from both loop stems, and the process terminates at the middle (closure) residue. Thousands of loop halves are generated, and if two meet at the closure residue, these two comprise a loop candidate.
Overview
Amino-acid preferences
One might expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot, but the effect of side chains is small. In practice, the major effect seen is that of the presence or absence of the methylene group at Cβ. Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH3, CH2, or CH group that starts the side chain of all other amino acids. Hence it is least re…
Uses
A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein (as at top right). A second is to show the empirical distribution of datapoints observed in a single structure (as at right, here) in usage for structure validation, or else in a database of many structures (as in the lower 3 plots at left). Either case is usually shown against outlines for the th…
More recent updates
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined (myoglobin, in 1960 ), although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB). Many studies have taken advantage of this data to produce more detai…
Related conventions
One can also plot the dihedral angles in polysaccharides (e.g. with CARP).
Gallery
• Ramachandran plot for the general case; data from Lovell 2003
• Ramachandran plot for Glycine
• Ramachandran plot for Proline
• Ramachandran plot for pre-Proline
Software
• Web-based Structural Analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB
• Web-based tool showing Ramachandran plot of any PDB entry
• MolProbity web service that produces Ramachandran plots and other validation of any PDB-format file
Further reading
• Richardson, J.S. (1981). "The Anatomy and Taxonomy of Protein Structure". Anatomy and Taxonomy of Protein Structures. Advances in Protein Chemistry. Vol. 34. pp. 167–339. doi:10.1016/S0065-3233(08)60520-3. ISBN 9780120342341. PMID 7020376., available on-line at Anatax
• Branden, C.-I.; Tooze, J. (1991), Introduction to Protein Structure, Garland Publishing, NY, ISBN 0-8153-0344-0