Ramachandran Plot PDF

Ramachandran Plot 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 favourable and he...

Ramachandran Plot 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 favourable and help check and improve the accuracy and quality of three-dimensional representations of proteins. It is a valuable tool for understanding the structural accuracy of protein conformations. What is a Ramachandran Plot? A Ramachandran plot, also known as a Ramachandran diagram or a Rama plot in the field of biochemistry, was initially developed by Viswanathan Sasisekharan, C. Ramakrishnan and Gopalasamudram Narayana Ramachandran. Ramachandran plot is the plot of angles called phi (φ) and psi (ψ) of the residues (commonly known as amino acids) present in a peptide. It assesses 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°). Figure 1. A Ramachandran plot showing the values of phi (φ) and psi (ψ). Not all phi (φ) and psi (ψ) values are possible without collisions between atoms. The most favourable regions are shown in dark green; borderline areas are shown in light green. The structure on the right is disfavoured because of steric clashes. Ramachandran Plot Quadrants The determination of the secondary structure of proteins can be done using a Ramachandran plot. Ramachandran's plot consists of four quadrants. 1. Quadrant-I: Quadrant-I contains the area where all the conformations are allowed. In this region, we can find left-handed alpha helices. 2. Quadrant-II: Quadrant-II is the biggest region in the whole graph. This region mainly has most of the allowed values of the dihedral angles for the conformation of atoms. 3. Quadrant-III: Quadrant-III is the second largest region after Quadrant-II. In this region, we can find right-handed alpha helices. 4. Quadrant-IV: Quadrant-IV has practically no framed locale. This conformation (ψ around – 180 to 0 degrees, φ around 0–180 degrees) is disfavoured due to steric hindrances. Figure 2. Ramachandran plots showing a variety of structures. (a) The values of ϕ and ψ for various allowed secondary structures. Although left-handed α helices extending over several amino acid residues are theoretically possible, they have not been observed in proteins. 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. We can see that the secondary structures are different by checking these angles on the Ramachandran plot. 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 usually a right-handed helical coil. 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 neighbouring 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 for 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 than other amino acids, leading to a less restricted conformational space, as evident in its Ramachandran plot. In contrast, with its 5-membered-ring side chain connecting Cα to backbone N, proline exhibits a limited number of potential combinations of φ and ψ in its Ramachandran plot. The residues preceding proline ("pre-proline") also show constrained combinations compared to the general case. Figure 3. Ramachandran plots for the amino acids Glycine (left) and Proline (right) showing greater than regular availability (glycine) and unavailability (proline) within accessible regions. Figure 4. Trans and cis isomers of a peptide bond involving the imino nitrogen of proline. Of the peptide bonds between amino acid residues other than Pro, more than 99.95% are in the trans configuration. For peptide bonds involving the imino nitrogen of proline, however, about 6% are in the cis configuration; many of these occur at β turns. Ramachandran Plot Uses The Ramachandran plot is important because: It helps researchers understand how protein molecules fold and move and helps analyze 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 modelling and structure prediction, vital for designing new drugs.  It helps identify experimental or computational protein structure errors, ensuring that structural biology research is accurate. The plot is 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 helpful 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 the 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 unfavourable conformations. It represents a static view and does not fully capture dynamic protein behaviour. Conclusion In conclusion, the Ramachandran Plot is used to confirm the structure of proteins. It helps us 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 modelling and drug design. Despite many Ramachandran Plot uses, it has some limitations and highlights the need for careful interpretation in structural biology research.