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Summary

In molecular mechanics, the potential energy of a protein molecule is the sum of a number of components, which relate to the molecule's internal structure and its interaction with nearby molecules.

Intramolecular potential energy

Internal potential energy of a molecule is described by a system of functions known as force field. The potential energy usually includes several terms:

Etotal = Ebond+ Eangle+ Etorsion + Eelectro +Evdw

Contributions

Ebond, bond length contribution

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. This is similar to the concept of Hooke's Law, so the bond can be envisaged as a spring connecting the atoms together. Total potential energy based on bond length is over set Sbond set of pairs of atoms that are connected by chemical bond defined as:

Ebond = Σ (i,j) E Sbond kijbijij0)2

where:

kijb is the force constant

αij0 is the equilibrium length

αij is the current length

for the bond between ith and jth atoms.

Just as the potential energy can be written as a quadratic form in the internal coordinates, so it can also be written in terms of generalized forces. The resulting coefficients are termed compliance constants.

Eangle, bond angle contribution

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 over set Sangle the triplet of atoms that are connected by two chemical bonds:

Eangle = Σ (i,j,k) E Sanglekijkaijkijk0)2

where:

kijk is the force constant

αijk0 is the equilibrium angle

αijk is the bond angle

Etorsion, torsion angle contribution

The middle bond of three bonds formed by four atoms maintains a certain angle which is also known as torsion is defined over set Storsion the quartet of atoms that are connected by three chemical bonds, as follows:

Etorsion = Σ (i,j,k,l) E Storsionkijklt[1+cos(nαijkl- αijkl0 )]

where:

kijklt is the force constant

αijkl0 is the equilibrium angle

αijkl is the torsion angle

Eelectro, electrostatic contribution

Interaction between charged atoms adds potential energy to the protein based on the distance between pairs of atoms defined over Selectro, the set of pairs of atoms with electrostatic interactions, as follows:

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

where:

eij is a constant

qiqj are charges of atoms

rij is the distance between atoms

EvdW, Van der Waals contribution

Depending on van der Waals radii of atoms every atom of protein interacts with each other that are not far apart. The potential energy contribution of this interaction is defined over SvdW, set of atoms with van der Waals interaction, as:

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

where:

rij distance between atoms

σij distance at Van der Waals energy is minimum