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ramachandran plot notes

by Ali Keebler Published 3 years ago Updated 2 years ago

The Ramachandran plot shows the distribution of the torsion angles of a protein within certain regions. The horizontal axis on the plot shows φ values, while the vertical shows ψ values. Both horizontal and vertical axes start from -180 and extend to +180.

The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide. In sequence order, φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and ψ is the C(i),Ca(i),N(i),C(i+1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran, et.

Full Answer

What is Ramachandran plot in biology?

Ramachandran Plot : Polypeptide chain conformation. Ramachandran plot is a plot of the torsional angles – phi (φ)and psi (ψ) – of the residues (amino acids) contained in a peptide.

What do the dots in the Ramachandran plot represent?

Each dot in the plot corresponds to an amino acid, with its φ and ψ angles. On the left is a structure at low resolution and on the right is a high-resolution structure. The Ramachandran plot shows the distribution of the torsion angles of a protein within certain regions.

What do the allowed regions of the Ramachandran plot show?

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). In practice, the distribution of the Phi/Psi values observed in a protein structure can be used for structure validation (Ramakrishnan et al., 2007).

Is Ramachandran plot subject to copyright?

… Content may be subject to copyright. Content may be subject to copyright. Ramachandran, C. Ramakrishnan and V. Sasisekharan. Ramachandran plot provides a simple two-dimensional graphic representation of all possible protein structures in terms of torsion angles. Although the plot was developed using theoretical of plot was realized.

What is Ramachandran plot and its significance?

The Ramachandran plot provides a way to view the distribution of torsion angles in a protein structure and shows that the torsion angles corresponding to the two major secondary structure elements (α-helices and β-sheets) are clearly clustered within separate regions.

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.

What is Ramachandran plot biology discussion?

Plots of phi versus psi dihedral angles for amino acid residues are called Ramachandran plots. One can tell if the backbone is following a helical or an extended beta strand structure based on the values of the phi-psi angles over a length of backbone (usually 3-4 residues is sufficient).

What is Ramachandran plot Slideshare?

The Ramachandran Plot • The two torsion angles of the polypeptide chain, describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ) • It provides an easy way to view the distribution of torsion angles of a protein structure.

How many quadrants are present in Ramachandran plot?

Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot.

Who discovered Ramachandran plot?

Gopalasamudram Narayanan RamachandranGopalasamudram Narayanan Ramachandran, or G.N. Ramachandran, FRS (8 October 1922 – 7 April 2001) was an Indian physicist who was known for his work that led to his creation of the Ramachandran plot for understanding peptide structure. He was the first to propose a triple-helical model for the structure of collagen.

What is a Ramachandran outlier?

Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing.

What is Ramachandran plot PDF?

Ramachandran plot provides a simple two-dimensional graphic. representation of all possible protein structures in terms of torsion angles. Although the plot was developed using theoretical. methods, mathematical calculations and models building, once the protein structure began to discover, the importance.Dec 31, 2018

Why Proline is called Helix breaker?

Proline also destabilizes α-helices because of its irregular geometry; its R-group bonds back to the nitrogen of the amide group, which causes steric hindrance. In addition, the lack of a hydrogen on Proline's nitrogen prevents it from participating in hydrogen bonding.Aug 10, 2020

What are torsion angles in proteins?

A torsion angle, also known as a dihedral angle, is formed by three consecutive bonds in a molecule and defined by the angle created between the two outer bonds. The backbone of a protein has three different torsion angles.Feb 1, 2020

How does protein fold?

Folded proteins are held together by various molecular interactions. During translation, each protein is synthesized as a linear chain of amino acids or a random coil which does not have a stable 3D structure. The amino acids in the chain eventually interact with each other to form a well-defined, folded protein.Feb 26, 2019

Why are glycine and proline commonly excluded from Ramachandran plots?

Its van der Waals radius is smaller and is thus less restricted. Proline, on the other hand has a 5-membered ring as a side chain. Therefore it is much more restricted than the other amino acids and allows for only a limited number of ψ and φ. Gly is the only amino acid that has no chiral center.

Drug Discovery Technologies

R.A. Laskowski, G.J. Swaminathan, in Comprehensive Medicinal Chemistry II, 2007

Polymers in Biology and Medicine

M. Wetzer, ... A.E. Barron, in Polymer Science: A Comprehensive Reference, 2012

Algorithms for Structure Comparison and Analysis: Homology Modelling of Proteins

Marco Wiltgen, in Encyclopedia of Bioinformatics and Computational Biology, 2019

Homology modeling: Developing 3D structures of target proteins missing in databases

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.

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.

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 ...

What is the Ramachandran plot?

The Ramachandran plot is among the most central concepts in structural biology , seen in publications and textbooks alike. However, with the increasing numbers of known protein-structures and greater accuracy of ultra-high resolution protein structures, we are still learning more about the basic principles of protein structure. Here we use high fidelity conformational information to explore novel ways, such a geo-style and wrapped Ramachandran plots, to convey some of the basic aspects of the Ramachandran plot and of protein conformation. We point out the pressing need for a standard nomenclature for peptide conformation and propose such a nomenclature. Finally, we summarize some recent conceptual advances related to the building blocks of protein structure. The results for linear groups imply the need for substantive revisions in how the basics of protein structure are handled.

When was Ramachandran plot developed?

Ramachandran plot also known as a Ramachandran diagram or [, ] plot was originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan and V. Sasisekharan. Ramachandran plot provides a simple two-dimensional graphic. representation of all possible protein structures in terms of torsion angles.

Who Is G N Ramachandran?

Image
Gopalasamudram Narayana Ramachandran(8 October 1922 – 7 April 2001) is an Indian biophysicist and crystallographer who, along with Gopinath Kartha, worked out the triple helical structure of collagen. G N Ramachandran is an Indian biophysicist who was known for his work that led to his creation of the Ramachan…
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Ramachandran Plot and Peptide Torsion Angles

  • The figure below shows the three main chain torsion angles of a polypeptide. These are phi (ψ), psi (φ), and omega (w).
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Secondary Structure Plot Regions

  • Secondary structures of a peptide are segments of the peptide that have ordered and repetitive structure, and the repetitive structure is due to a repetitive confirmation of the residues and, ultimately, repetitive values of ψ and φ. The different secondary structures can be distinguished by their range of ψ and φ values with the values of different secondary structures mapping to dif…
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Plot Regions Limited by Steric Hindrance

  • Most combinations of ψ and φ are sterically forbidden, as illustrated in the tripeptide, Glu-Ser-Ala. With Ser having values of ψ = -116o and φ = 55othe Ser side chain is in contact with Ala, colored blue. In plots of native peptides, the data points will form clusters in the several areas in which steric hindrance does not occur. 1. Mechanism of Eukaryotic DNA Replication 2. DNA Replicatio…
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Final Words

  • The nature of the covalent bonds in the polypeptide chain places constraints on the structure. The peptide bond exhibits partial double bond character that keeps the entire peptide group in a rigid planar configuration. The N-Cα and Cα-C bonds can rotate with bond angles Φ and Ψ, respectively. Secondary structure can be defined completely if the Φ and Ψ angles are known fo…
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Overview

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. The figure on the left illustrates the definitio…

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…

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…

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

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      • 17. /vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 18. /vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:45
      • 19. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:261
      • 20. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:205
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      Metadata
      Bindings
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      Backtrace
      • 19. /vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35
      • 20. /vendor/outl1ne/nova-menu-builder/src/helpers.php:33
      • 22. /vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 23. /vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:45
      • 24. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:261
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      Metadata
      Backtrace
      • 24. /vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35
      • 25. /vendor/outl1ne/nova-menu-builder/src/helpers.php:33
      • 27. /vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 28. /vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:45
      • 29. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:261
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      Metadata
      Bindings
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      Backtrace
      • 14. /app/View/Composers/SidebarView.php:22
      • 15. /app/View/Composers/SidebarView.php:12
      • 16. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:124
      • 17. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:162
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      850μsview::2dd102cf0462e89a4d4d8bc77355d767652bf9aa:15receivinghelpdeskask
      Metadata
      Bindings
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      Backtrace
      • 21. view::2dd102cf0462e89a4d4d8bc77355d767652bf9aa:15
      • 23. /vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:108
      • 24. /vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 25. /vendor/livewire/livewire/src/ComponentConcerns/RendersLivewireComponents.php:69
      • 26. /vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:61
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