Ramachandran plot torsion angles

In summary, the stability of torsion angles in protein structure is affected by repulsive effects of amino acid interactions between side chains, specifically through their hydrophobic or hydrophilic interactions. This can be visualized through a plot of energetically allowed regions for backbone dihedral angles. The ability to predict these angles and their effects is an ongoing area of research.
  • #1
MrGenetic
10
0
Can torsion angles were affected by repulsive effect of aminoacid interactions between side chains?
Can torsion angles were affected by hydrophilic or hydrophilic interactions between side chains?
I know that protein levels were affected by them but torsion angles is suspicious for me
 
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  • #2
MrGenetic said:
Can torsion angles were affected by repulsive effect of aminoacid interactions between side chains?
Can torsion angles were affected by hydrophilic or hydrophilic interactions between side chains?
Yes, of course, they are more affected with stronger interactions.
On a single chain there are more interaction between the polar or non polar groups.
Two single chain that are close can interact, and exercise a repulsive effect on each other, if there are polar groups.

You wrote twice hydrophilic, but I suppose you wanted to say hydrophobic or hydrophilic.
Anyway, an aminoacid, in a solution can have different reactions, it depend on how the solution is.
In any case, they solution can affect the torsion angles.
 
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  • #3
The plot is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The stability of some sidechain dihedral angles are affected by the values φ and ψ. Not all.

From wikipedia
When the two intersecting planes are described in terms of Cartesian coordinates by the two equations:
643b42eaa74a2227e2553755864d2b99daf5b9b3

602aef36c9617f4947bad06846f6cfcd1784b311

the dihedral angle, φ between them is given by:

$$cos ⁡ φ = | a 1 a 2 + b 1 b 2 + c 1 c 2 | a 1 2 + b 1 2 + c 1 2 a 2 2 + b 2 2 + c 2 2 . {\displaystyle \cos \varphi ={\frac {\left\vert a_{1}a_{2}+b_{1}b_{2}+c_{1}c_{2}\right\vert }{{\sqrt {a_{1}^{2}+b_{1}^{2}+c_{1}^{2}}}{\sqrt {a_{2}^{2}+b_{2}^{2}+c_{2}^{2}}}}}.} $$

Here is a link about the ability to predict those dihedral angles and a library of functions to do so. Best I can do:
http://www.sciencedirect.com/science/article/pii/S0022283683711708?via=ihub
 

1. What is a Ramachandran plot torsion angle?

A Ramachandran plot torsion angle is a graphical representation of the allowed values for the dihedral angles of a protein backbone. It shows the relationship between the phi and psi angles of amino acid residues in a protein, which determines the overall shape and stability of the protein.

2. How is a Ramachandran plot torsion angle calculated?

A Ramachandran plot torsion angle is calculated using the coordinates of the atoms in a protein's backbone. The phi angle is determined by the rotation around the bond between the nitrogen and the alpha carbon atoms, while the psi angle is determined by the rotation around the bond between the alpha carbon and carbonyl carbon atoms.

3. What can a Ramachandran plot torsion angle tell us about a protein?

The Ramachandran plot torsion angle can provide information about the conformation and stability of a protein. It can show if there are any steric clashes or strained conformations in the protein structure, which can affect its function. It can also help identify secondary structures, such as alpha helices and beta sheets, within the protein.

4. How is a Ramachandran plot torsion angle useful in protein structure prediction?

A Ramachandran plot torsion angle is useful in protein structure prediction because it can help identify possible conformations that a protein may adopt. By comparing the predicted torsion angles to the allowed values on the plot, researchers can narrow down the potential structures of a protein and improve the accuracy of their predictions.

5. Are there any limitations to using a Ramachandran plot torsion angle?

There are some limitations to using a Ramachandran plot torsion angle. It assumes that the protein is in a stable, folded conformation, so it may not accurately represent the conformation of unfolded or denatured proteins. Additionally, the plot is based on empirical data and may not account for rare or unusual amino acid conformations. It is also important to note that the plot may look different for proteins with non-standard amino acids or modifications.

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