Determination of an empirical energy function for protein conformational analysis by energy embedding

✍ Scribed by Gordon M. Crippen; P. K. Ponnuswamy

• Publisher: John Wiley and Sons
• Year: 1987
• Tongue: English
• Weight: 956 KB
• Volume: 8
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.540080707

✦ Synopsis

It is quite easy to propose an empirical potential for conformational analysis such that given crystal structures lie near local minima. What is much more difficult, is to devise a function such that the native structure lies near a relatively deep local minimum, at least in some neighborhood of the native in conformation space. An algorithm is presented for finding such a potential acting on proteins where each amino acid residue is represented by a single point. When the given structure is either an a-helical, p-strand, or hairpin bend segment of pancreatic trypsin inhibitor, the resulting potential function in each case possesses a deep minimum within 0.10 A of the native conformation. The improved energy embedding algorithm locates a marginally better minimum in each case only 0.1-1.3 away from the respective native state. In other words, this potential function guides a conformational search toward structures very close to the native over a wide range of conformation space.