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 is a PCNA Ramachandran plot?
A Ramachandran plot generated from human PCNA, a trimeric DNA clamp protein that contains both β-sheet and α-helix ( PDB ID 1AXC). The red, brown, and yellow regions represent the favored, allowed, and "generously allowed" regions as defined by ProCheck A Ramachandran plot can be used in two somewhat different ways.
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).
What is the shape of pre-proline Ramachandran plot (Figure 1b)?
Although the overall shape of the pre-proline Ramachandran plot (Figure 1B) is well understood, there exists a region unique to pre-proline that remains unexplained. The basic shape of pre-proline was predicted by Flory using steric interactions [ 17 ]. This was later confirmed in a statistical analysis of the protein database [ 2 ].
What is Z score in Ramachandran z score?
Two numbers (bottom right) indicate percentage of residues in favored (top) and outlier (bottom) regions. Fortuitously, Hooft et al. (1997) proposed a numerical metric, called the Ramachandran Z score (Rama-Z), which characterizes the shape of the (ϕ, ψ) angle distribution in the Ramachandran plot.
What does a Ramachandran plot tell you?
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).
How do you plot a Ramachandran plot?
Instructions:Select a protein structure file in PDB format from your hard disk.Select Amino Acid type to show.Check the boxes for Glycine, Verbosity, and Labels as desired.Click the GO! button.
When would you use a Ramachandran plot?
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).
What are the principles underlying the formation of the Ramachandran plot?
Answer : 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 the first quadrant in Ramachandran plot?
The Ramachandran Plot helps with determination of secondary structures of proteins. Quadrant I shows a region where some conformations are allowed. This is where rare left-handed alpha helices lie.
What is phi and psi angles in Ramachandran plot?
The Ramachandran Plot In a polypeptide the main chain N-Calpha and Calpha-C bonds relatively are free to rotate. These rotations are represented by the torsion angles phi and psi, respectively.
What do the shaded regions of the Ramachandran plot represent?
The colouring/shading on the plot represents the different regions described in Morris et al. (1992): the darkest areas (here shown in red) correspond to the "core" regions representing the most favourable combinations of phi-psi values. Ideally, one would hope to have over 90% of the residues in these "core" regions.
What is Ramachandran plot PDF?
Ramachandran plot provides a simple two-dimensional graphical representation of all possible protein structures in terms of torsion angles. Polypeptide conformations are defined by the values of phi and psi. Most values of phi and psi are not allowed due to steric interference between non-bonded atoms.
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.
What is Ramachandran plot?
The Ramachandran plot visualizes energetically allowed and forbidden regions for the dihedral angles. For poor quality homology models, many dihedral angles are found in the forbidden regions of the Ramachandran plot. Such deviations usually indicate problems with the structure.
What is the validation process of a protein model?
The validation process includes manual inspection of the protein model to ensure that the model supports any experimental data. This often entails superimposing the model with the template structures for comparison. Software such as the SUPERPOSE module of the CCP4 ( Collaborative Computational Project 1994) suite of crystallography programs, and Swiss-PDB Viewer perform structural alignments of the model with other similar structures, such as the templates. Commercial homology modelling programs often include their own model evaluation software i.e. ProTable in SYBYL (Clark et al. 1989). The quality of the superposition process is generally measured by a root mean square deviation (RMSD) value, which is the sum of the squared distance between each corresponding Cα atom position in the two structures following superposition. The core Cα atoms of protein models which share 35-50% sequence identity with their templates, will generally deviate by 1.0-1.5 Å from their experimental counter parts ( Chothia and Lesk 1986; Peitsch 2002). Manual inspection and manipulation of the model can be performed using molecular graphics software such as O (Jones et al 1999), Swiss-PDB Viewer ( Guex and Peitsch 1997) and Pymol ( DeLano 2002 ). Manual manipulation and visualisation are one of the most important steps to determine the accuracy of the model and to check if the model matches observed experimental data. This process may include altering side-chain rotamers to match a template structure or employing docking programs such as AUTODOCK ( Morris et al, 1998 ), ICM-Dock ( Abagyan et al. 1997) or GOLD ( Verdonk et al. 2003) to dock known substrates into the active site or known protein-binding molecules to the surface of the model.
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 ...
How to read Ramachandran plot?
How to read Ramachandran plot? A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. 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. A second is to show the empirical distribution of data points observed in a single structure .
Who is G N Ramachandran?
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 Ramachandran plot for understanding peptide ...
When was the torsional angle plot developed?
The plot was developed in 1963 by G. N. Ramachandran, by plotting the φ values on the x-axis and the ψ values on the y-axis, as for the image at left. Plotting the torsional angles in this way graphically shows which combination of angles is possible. What Is Peptide Linkage?
How to get Ramachandran in JSmol?
Right-click on an empty space of the JSmol panel showing the 3D structure on the page, or click on the JSmol logo (or frank) in the bottom right corner. When the menu comes up, select Console. Click in the lower text panel of the console that comes up and type the command Ramachandran, followed by the return key.
When was the torsional angle plot developed?
The plot was developed in 1963 by G. N. Ramachandran, et. al. by plotting the φ values on the x-axis and the ψ values on the y-axis, as for the image at left. Plotting the torsional angles in this way graphically shows which combination of angles are possible. The torsional angles of each residue in a peptide define the geometry ...
What is a Ramachandran plot?
The Ramachandran plot [ 1] is the 2d plot of the φ-ψ torsion angles of the protein backbone. It provides a simple view of the conformation of a protein. The φ-ψ angles cluster into distinct regions in the Ramachandran plot where each region corresponds to a particular secondary structure. 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 [ 2 ]). The generic and proline Ramachandran plots are now well understood [ 3] but the glycine and pre-proline Ramachandran plots are not.
How many types of Ramachandran plots are there?
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 [ 2 ]).
What is the Ramachandran validation of protein structures?
Ramachandran validation of protein structures is commonly performed using developments, such as MolProbity. We suggest tailoring such analyses by position-wise, geometry-specific steric-maps, which show (φ,ψ) regions with steric-clash at every residue position. These maps are different from the classical steric-map because they are highly sensitive to bond length and angle values that are used, in our steric-maps, as observed in the residue positions in super-high-resolution peptide and protein structures. (φ,ψ) outliers observed in such structures seldom have steric-clash. Therefore, we propose that a (φ,ψ) outlier is unacceptable if it is located within the steric-clash region of a bond geometry-specific steric-map for a residue position. These steric-maps also suggest position-specific accessible (φ,ψ) space. The PARAMA web resource performs in-depth position-wise analysis of protein structures using bond geometry-specific steric-maps.
Who is the Indian soldier of science?
An Indian soldier of science who had implanted deep foot prints in the biophysical world of peptides, proteins and imaging is none other than G.N. Ramachandran. Hardly has another Indian biophysicist received such world wide acclaim. The year 2013 marked the 50th year of his much lauded and used Ramachandran map and has been celebrated in India with gusto, worthy of his remarkable contribution. As the year passed by, it is imperative that we salute the great soul yet again. It is no mere coincidence with respect to G.N. Ramachandran that after the year long celebrations of 2013, the year 2014 will be celebrated world-wide as the International Year of Crystallography. It is essential to emphasize that any celebration with respect to crystallography is incomplete without remembering Ramachandran. His life and contributions are now widely known, but a recount of the tales will always remain relevant, and the budding generation of young scientists must realize his value over and over again.
Gene Regulation
As members of the ENCODE and psychENCODE consortia, we study the molecular mechanism of gene regulation by integrating genomic, epigenomic, and transcriptomic data. Furthermore, we study how genetic variations in the human population affect gene regulation and susceptibility for diseases.
Protein Docking
We develop methods to compute binding affinities between protein molecules. Combining this ability with a fast Fourier transform-based search algorithm, we develop computational methods for predicting protein-complex structures.
Small Silencing RNAs
We develop computational methods to understand the biogenesis and regulatory mechanisms of small silencing RNAs (microRNAs or miRNAs, small silencing RNAs or siRNAs, and PIWI-interacting RNAs or piRNAs).
Who Is G N Ramachandran?
Ramachandran Plot and Peptide Torsion Angles
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Ramachandran Plot Explanation
- (Smart Notes Description) How to read Ramachandran plot? A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. 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...
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