Protein Structure Physics

Each conformation potential energy can be calculated by looking at various measures

Bond Length

This is the distance between two atoms. Also known as inter-nuclear separation.

The energy depends on whether they are bonding or anti-bonding.

If the two atoms are anti-bonding energy doesn't go negative, but if they are too close there is higher energy as they want to separate.

If the two atoms are bonding, then use the morse potential. There is a negative energy when the are just the correct length away. Very high energy when the are too close, and close to 0 when they are far away.

$$ V(r) = D_e ( 1-e^{-a(r-r_0)} )^2 $$

where De is the well depth (or greatest negative energy). This depends on the bond type.

r0 is the optimum bond length.

a is a constant for the width. This depends on the bond type.

and r is the bond length.

Bond Angle

The angle is determined by three atoms, ABC. The energy for this angle is

$$ V_{angle}(\theta) = k_{\theta}(\theta - \theta_0)^2 $$

where θ0 is the optimum bond angle

and kθ is a constant around 100kJ/mol/radian2