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The Ramachandran Plot Constructing Interpretation Applications amp Limitations of Ramachandran Plot
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A Ramachandran plot is a graphical representation used in structural biology and biochemistry to analyze the dihedral angles of a protein's backbone. It is named after its creator, G. N. Ramachandran, who introduced this tool in the 1960s. Understanding dihedral angles is crucial for studying the conformation and stability of protein structures. • In this lecture, we will cover • • The basics of Ramachandran Plot • • Building the Ramachandran Plot • • Interpretation and Significance • • Limitations and Applications • What is Ramachandran Plot and what is importance? • The Ramachandran plot is a two-dimensional graph that shows the allowed and disallowed regions of conformational space for the two dihedral angles in the protein backbone, Phi and Psi. • It was developed by Indian physicist G. N. Ramachandran in 1963. • The Ramachandran plot is important because it can be used to validate the quality of protein structure models and to identify regions of a protein that are likely to be disordered. It can also be used to study protein folding and dynamics, and to design new proteins with desired properties. • Torison Angles • In a protein, the backbone is composed of a series of amino acids linked by peptide bonds. The dihedral angles describe the rotation of atoms along these bonds, specifically the phi (ϕ) and psi (ψ) angles: • 1. Phi (ϕ) angle: It measures the rotation about the bond between the nitrogen atom (N) and the alpha carbon (Cα) of one amino acid and the carbon atom (C) and nitrogen atom (N) of the next amino acid. • 2. Psi (ψ) angle: It measures the rotation about the bond between the alpha carbon (Cα) of one amino acid and the carbon atom (C) and nitrogen atom (N) of the next amino acid. • Construction of Ramachandran Plot • The Ramachandran plot is a scatter plot where each point represents a specific pair of phi and psi dihedral angles for a particular amino acid residue in a protein structure. The x-axis corresponds to the phi angle, while the y-axis represents the psi angle. The plot is typically created using crystallographic or NMR data. • Interpretation of Ramachandran Plot • The Ramachandran plot is divided into two main regions: allowed and disallowed. The allowed regions are those regions where the protein backbone can adopt stable conformations. The disallowed regions are those regions where the protein backbone would be sterically hindered. • The most common secondary structural elements in proteins, alpha helices and beta sheets, have characteristic regions in the Ramachandran plot. • 00:00 Introduction • 00:24 Topic COvered • 00:34 What is Ramachandran Plot? • 01:15 Torison Angles • 01:48 Constructing Ramachandran Plot • 02:09 Interpreting Ramachandran Plot • 03:45 Significance of Ramachandran Plot • 05:08 Limitations of Ramachandran Plot • 06:00 Applications of Ramachandran Plot • 07:30 Conclusion • For Queries: [email protected] • Twitter:Me@BioResource • Related Videos: • --------------------------------------------------------------------------------------------------------------- • Plotting Bacterial Growth Curve: • Plotting Bacterial Growth Curve in Excel • Colony Forming Units: • CFU: Colony Forming Unit cfu/ml cal... • Serial Dilution Methods: • Serial Dilution Methods Calaculations • Copy Number Calculation for qPCR: • Copy Number Calculation for qPCR • How to analyze Primer Sequence or Oligonucleotide sequence designed for PCR / qPCR: • How to analyze Primer Sequence or Oli... • How to generate qPCR standard curve in excel and calculate PCR efficiency: • How to generate qPCR standard curve i... • Real Time qPCR optimization, Calculating PCR Efficiency: • Real Time qPCR optimization, Calcula... • Taqman Assay Vs SYBR Green Assay: • Real Time PCR Assays- Taqman Assay Vs... • Resolving poor PCR efficiency: • Resolving Poor PCR assay Efficiency i... • Calculating molecular weight of Unknown protein • How to calculate molecular weight of ... • Designing qPCR Primers • • Primer designing for real time PCR us... • Oligonucleotide Preparation Purification • Oligonucleotide Preparation and Purif... • How to check Oligo Concentration • • How to check the Oligo concentration ...
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