I. Introduction to Conformation Searching

3Figure 4. Contours of alanine dipeptide potential energy surface (from Molecular Modelling:Principles and Applications, A. R. Leach, Addison Wesley Longman Limited, Essex,England, 1996.)In Figure 4, the angle Φ is plotted on the x-axis and the angle Ψ is shown on the y-axis. This plot shows thedifferent energy minima of alanine dipeptide. For a polypeptide with a geometry described by many more torsionalangles it is computationally difficult to map the full potential energy surface, and a systematic conformer search isnot feasible. For larger systems, other conformational searching techniques will be necessary.For a wide variety of known systems, it has been shown that the different Φ and Ψ angles in each protein fall inspecific ranges. When the different Φ and Ψ angle pairs found in many proteins are plotted, the graph produced iscalled a Ramachandran plot (Figure 5). Note that there are two major basins in which most of the Φ and Ψ anglepairs fall: one centered around Φ = –120º, Ψ = 135º and a second basin centered at about Φ = –90º, Ψ = –30º.There is also a much smaller minor basin centered at about Φ = 70º, Ψ = 45º.Figure 5. Ramachandran plot of Φ and Ψ angles from crystal structures of a variety ofproteins (from Molecular Modeling and Simulation, T. Schlick, Springer, New York, 2002.).