What will the effect of Torsion angles Phi (Φ) and Psi (Ψ) in Ramachandran plot?
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The torsion angles Phi (Φ) and Psi (Ψ) in the Ramachandran plot play a crucial role in determining the conformational preferences and energy landscapes of protein structures. Studies have shown that unfavorable (Φ,Ψ) angles lead to higher energy conformers, suggesting increased dynamics and flexibility. The Ramachandran Z-score (Rama-Z) is a valuable metric for assessing the quality of protein structures based on these torsion angles. Intrinsic preferences of amino acids, particularly Gly, Val, and Ile, are influenced by electrostatic destabilization rather than steric hindrance, highlighting the significance of specific peptide group and sidechain atoms in determining energetically favored regions in the Ramachandran plot. Experimental methods like Raman optical activity (ROA) spectroscopy provide insights into the conformational distribution and potential energy surfaces of dipeptides, aiding in understanding protein structure dynamics. The Proteomic Φ-Ψ plot (PRplot) offers a comprehensive visualization of protein structures, clustering them based on their secondary structure elements along a sigmoidal curve in a bidimensional space.
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| Papers (5) | Insight |
|---|---|
| The torsion angles Phi (Φ) and Psi (Ψ) in the Ramachandran plot define protein structures, clustering proteins based on alpha-helices, beta-strands, or both, simplifying structural complexity. | |
| The torsion angles Phi (Φ) and Psi (Ψ) determine peptide main chain conformation on the Ramachandran plot, revealing favored conformers and the potential energy surface of the dipeptide. | |
| The high-energy regions in the Ramachandran plot are primarily caused by electrostatic destabilization, not steric hindrance, influenced by key peptide atoms and some sidechain hydrogen atoms. | |
| Torsion angles Φ and Ψ in the Ramachandran plot indicate protein backbone conformation quality, with deviations affecting the Ramachandran Z-score and overall stereochemistry assessment. | |
5 Citations | The study suggests that the relationship between conformational strain indicated by unfavorable (Φ,Ψ) angles in the Ramachandran plot and protein flexibility is weak or almost non-existent. |
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