Rotamer strain energy in protein helices quantification of a major force opposing protein folding

It is widely believed that the dominant force opposing protein folding is t he entropic cost of restricting internal rotations. The energetic changes f rom restricting side-chain torsional motion are more complex than simply a loss of conformational entropy, however. A second force opposing protein fo lding arises when a side-chain in the folded state is not in its lowest-ene rgy rotamer, giving rotameric strain. chi strain energy results from a dihe dral angle being shifted from the most stable conformation of a rotamer whe n a protein folds. We calculated the energy of a side-chain as a function o f its dihedral angles in a poly(Ala) helix. Using these energy profiles, we quantify conformational entropy, rotameric strain energy and chi strain en ergy for all 17 amino acid residues with sidechains in alpha -helices. We c an calculate these terms for any amino acid in a helix interior in a protei n, as a function of its side-chain dihedral angles, and have implemented th is algorithm on a web page. The mean change in rotameric strain energy on f olding is 0.42 kcal mol(-1) per residue and the mean chi strain energy is 0 .64 kcal mol(-1) per residue. Loss of conformational entropy opposes foldin g by a mean of 1.1 kcal mol(-1) per residue, and the mean total force oppos ing restricting a side-chain into a helix is 2.2 kcal mol(-1). Conformation al entropy estimates alone therefore greatly underestimate the forces oppos ing protein folding. The introduction of strain when a protein folds should not be neglected when attempting to quantify the balance of forces affecti ng protein stability. Consideration of rotameric strain energy may help the use of rotamer libraries in protein design and rationalise the effects of mutations where side-chain conformations change. (C) 2001 Academic Press.