User:Resathakan

= Potential Energy of Protein = A protein folds into the state of lowest potential energy. Potential energy of a protein can be evaluated with quantum chemistry. However required computation is to much. Another approach is to evaluate major terms that contribute to potential energy and sum them up to find an approximate potential energy.

Etotal = Ebond+ Eangle+ Etorsion + Eelectro +Evdw

Ebond, Bond Length Potential
When two atoms are connected by a chemical bond, they tend to maintain a fixed distance. The fixed distance depends on the atoms that forms the bond. Any variation from this fixed distance which is the equilibrium point adds additional potential energy to the protein. Total potential energy based on bond length is defined as;

Ebond = Σ(i,j) E S bond kijb(αijk-αijk0)2

where

kijb is the force constant rij0 is the equilibrium length rij is the current length

for the bond between ith and jth atoms.

E angle
Like bond length, when three atoms are connected with two chemical bonds, the two bonds tend to form a fixed angle. Any variation from this fixed equilibrium angle contributes to protein potential energy. Total potential energy based on angle is defined as;

Eangle = Σ(i,j,k) E S angle kijka(αij-rij0)2

E,torsion Torsion Angle Potential
The middle bond of three bonds formed by four atom maintains a certain angle which is also known as torsion is defined as follows;

Eelectro, Electrostatic Potential
Interaction between charged atoms adds potential energy to the protein based on distance of the distance between pairs of atoms defined as follows

Eelectro =  Σ(i,j) E S electro ( qiqj)/(eijrij)

Evdw van der Waals Potential
Depending on van der Waals radii of atoms every atom of protein interacts with each others that are not far apart. The potential energy contribution of this interaction is defined as:

Evdw = Σ(i,j) E S vdw εij [ (σij/rij)12 - 2(σij/rij)6]