What does Ramachandran Plot tell us?

Ramachandran Plot is a graphical representation of the dihedral angles (ϕ and ψ) of amino acid residues in protein structures. Ramachandran Plot is used to confirm the structure of proteins. Regions in the plot indicate whether a protein structure is energetically favorable or not and help in checking and improving the accuracy and quality of three-dimensional representations of proteins. It is a valuable tool for understanding the structural accuracy of protein conformations. In this article, we will cover Ramachandran Plot notes, uses, and limitations of Ramachandran Plot.

What is a Ramachandran Plot?

A Ramachandran plot, also known as a Ramachandran diagram or a Rama plot in the field of biochemistry, was originally developed by Viswanathan Sasisekharan (born in 1993), C. Ramakrishnan and Gopalasamudram Narayana Ramachandran. Ramachandran plot is the plot of angles called psi (ψ) and phi (φ) of the residues (commonly known as amino acids) present in a peptide.

It assess the stereochemical quality of protein structures by plotting the phi (ϕ) and psi (ψ) dihedral angles of amino acid residues.  As the partial-double-bond keeps the peptide bond planar, the ω angle at that particular peptide bond is always 180 degrees (180°). 

Ramachandran Plot Quadrants

Determination of the secondary structure of proteins can be done by Ramachandran plot. Ramachandran’s plot consists of four quadrants.

1. Quadrant-I: Quadrant-I is the area of confirmations, where all the confirmations are allowed. In this region, we can find left-handed alpha.
2. Quadrant-II: Quadrant-II is the biggest region in the whole graph. Particularly, this region has better conditions for the confirmation of atoms.
3. Quadrant-III: Quadrant-III is the biggest region after Quadrant-II. In this region, we can find right-handed alpha.
4. Quadrant-IV: Quadrant-IV has practically no framed locale. This conformation(ψ around—180 to 0 degrees, φ around 0-180 degrees) is disfavored due to steric conflict.

Secondary Structure Plot

The secondary structures of a peptide are small, repeating building blocks. They look the same because the amino acid building blocks have similar angles. By checking these angles on the Ramachandran plot, we can tell different secondary structures apart. This plot helps us see patterns in how the peptide is put together. The two most common examples of secondary structures in the Ramachandran plot are α-helix and β-sheets, which are discussed in detail below.

α-helix

An alpha helix is right-handed helical coiled. The polypeptide chain coils tightly around a central axis and is stabilized by hydrogen bonds between specific amino acid residues. This secondary structure imparts stability to proteins and is crucial for their proper folding and function.

In a Ramachandran plot, the alpha helix is represented by a distinct region characterized by specific angles (phi and psi) corresponding to the repeating pattern of hydrogen bonds in the alpha helix structure. This region typically falls within a narrow range of phi and psi angles, reflecting the regular backbone conformation of the alpha helix.

β-sheets

Beta sheets are secondary structures in proteins where neighboring strands of the polypeptide chain are aligned side by side and stabilized by hydrogen bonds between the backbone atoms of adjacent strands.

In a Ramachandran plot, beta sheets are represented by specific regions corresponding to the characteristic phi and psi angles associated with the regular arrangement of amino acid residues in beta strands.

Preferences of Amino Acids

The larger side chains would impose more constraints and result in a limited allowed region in the Ramachandran plot, but their impact is relatively small. Instead, the most significant influence is observed with the presence or absence of the methylene group at Cβ.

Glycine, with only a hydrogen atom in its side chain, has a smaller van der Waals radius compared to other amino acids, leading to a less restricted conformational space, as evident in its Ramachandran plot. In contrast, proline, with its 5-membered-ring side chain connecting Cα to backbone N, exhibits a limited number of potential combinations of ψ and φ in its Ramachandran plot. The residues preceding proline (“pre-proline”) also show constrained combinations compared to the general case.

Ramachandran Plot Uses

The Ramachandran plot is important because:

• It helps scientists understand how protein molecules fold and move, and help in analysis of protein structure.
• It helps check the protein structures by identifying sterically allowed and disallowed regions of phi (ϕ) and psi (ψ) dihedral angles.
• Understanding Ramachandran plots helps in protein modeling, and structure prediction, which is improtant for designing new drugs
• It helps in identifying errors in experimental or computational protein structures, ensuring the structural biology research is accurate.
• The plot serves as a fundamental tool for researchers in structural biology, bioinformatics, and drug discovery, facilitating the study of protein folding, dynamics, and interactions.

Limitations of Ramachandran Plot

The Ramachandran plot is a useful tool for overall structural assessment. However it has certain limitations such as:

• The plot simplifies complex protein conformational space into a two-dimensional representation.
• It relies on averaged data and may not capture specificities of individual protein families.
• Quality depends on resolution, with lower resolutions potentially leading to inaccuracies.
• Crystal packing effects can distort dihedral angles in the plot.
• Inadequate representation for protein families with limited structural data.
• Allowed regions may still include energetically unfavorable conformations.
• Represents a static view, not fully capturing dynamic protein behavior.

Conclusion – Ramachandran Plot

In conclusion, the Ramachandran Plot is used to confirm the structure of proteins. It helps us to understand protein structure by analyzing the allowed and disallowed regions of phi (ϕ) and psi (ψ) angles. Ramachandran Plot helps scientists confirm protein structures, improve accuracy, and identify errors, thus playing a crucial role in protein modeling and drug design. Despite many Ramachandran Plot uses, it also has some limitations as well highlighting the need for careful interpretation in structural biology research.

FAQs on Ramachandran Plot

What does Ramachandran Plot Tell You?

The Ramachandran plot tells you whether the angles of amino acid residues in a protein structure are in allowed or disallowed regions, helping assess the quality of the protein model and identify potential errors..

What Information does a Ramachandran Plot Provide?

A Ramachandran plot shows if a protein’s shape is correct by checking specific angles, helping scientists validate protein structures.

How to Interpret a Ramachandran Plot?

Interpreting a Ramachandran plot involves checking if data points fall within allowed regions, indicating correct protein backbone conformations, and identifying points falling in disallowed regions suggesting unusual structural features.

What is the Principle of Ramachandran Plot?

The Ramachandran plot assesses the sterically allowed and disallowed conformations of a protein’s backbone by plotting the phi (ϕ) and psi (ψ) dihedral angles. It tells the regions of energetically favorable protein folding.

Can a Ramachandran Plot Predict Protein Function?

A Ramachandran plot cannot directly predict protein function. However, it can provide insights into protein structure, which is crucial for understanding function.

Why is Ramachandran Plot Important in Protein Folding?

The Ramachandran plot is important in protein folding because it identifies the allowed backbone conformations, helping proteins achieve stable three-dimensional structures necessary for proper folding and function.

What is the phi and psi Angle?

The phi (ϕ) and psi (ψ) angles are specific measurements used in protein structure to describe the rotation of peptide bonds along the backbone. They determine the orientation of adjacent amino acid residues in a protein chain.

What is the Ramachandran Plot in Protein Modeling?

The Ramachandran plot in protein modeling helps analyze allowed and disallowed phi (ϕ) and psi (ψ) angles, ensuring protein structure quality and detecting errors.