Tertiary Structure of Proteins. II. Freedom of Dihedral Angles and Energy Calculation

By using the procedure described in a preceding paper, several sets of ϕ and ψ are obtained which reproduced similar conformations to the native structure of lysozyme or myoglobin. Contrary to the expectation, the value of f has no maximum along a line connected any two of the minima in the 2 n -dimensional phase space. This result shows the existence of many solutions for ϕ and ψ which generate the native conformation under restricted condition of fixed geometry in the main chain. Energy calculation is performed on the conformations obtained above to examine atomic collisions along the main chain. After refinement to remove the collisions, a conformation is finally obtained for lysozyme which has a total energy of -270 kcal/mol and still has an low value of f . Similarly a conformation can be found for myoglobin having an energy of -580 kcal/mol in total.