Ramachandran plot torsion angles

Click For Summary
SUMMARY

The discussion centers on the influence of amino acid interactions on torsion angles in protein structures, specifically addressing repulsive effects and hydrophilic/hydrophobic interactions. It is established that torsion angles, represented by the dihedral angles φ and ψ, are significantly affected by the strength of interactions between side chains. The Ramachandran plot serves as a visualization tool for energetically allowed regions of these angles, indicating that the stability of sidechain dihedral angles is contingent upon the values of φ and ψ. The conversation also highlights the dependency of torsion angles on the solution environment.

PREREQUISITES
  • Understanding of Ramachandran plots in protein structure analysis
  • Knowledge of dihedral angles in molecular geometry
  • Familiarity with amino acid interactions, specifically hydrophilic and hydrophobic interactions
  • Basic principles of protein chemistry and stability
NEXT STEPS
  • Research the application of Ramachandran plots in protein modeling
  • Explore the role of sidechain interactions in protein folding
  • Learn about computational methods for predicting dihedral angles
  • Investigate the effects of solvent conditions on protein structure stability
USEFUL FOR

Biochemists, molecular biologists, and computational chemists interested in protein structure and dynamics, as well as researchers focusing on the effects of amino acid interactions on protein stability.

MrGenetic
Messages
10
Reaction score
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
 
Biology news on Phys.org
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.
 
Last edited:
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
 

Similar threads

  • · Replies 11 ·
Replies
11
Views
2K
  • · Replies 2 ·
Replies
2
Views
2K
  • · Replies 21 ·
Replies
21
Views
2K
  • · Replies 12 ·
Replies
12
Views
2K
  • · Replies 8 ·
Replies
8
Views
3K
  • · Replies 7 ·
Replies
7
Views
5K
  • · Replies 14 ·
Replies
14
Views
2K
  • · Replies 4 ·
Replies
4
Views
2K
  • · Replies 1 ·
Replies
1
Views
5K
  • · Replies 6 ·
Replies
6
Views
8K