Conformational energy of amino-acids in proteins: a comparison with theoretical energy maps

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Introduction It has been demonstrated that peptides can adopt only some conformations due to steric hindrances between main chain and side chain atoms. Subsequently, energy calculation have allowed to obtain plots of preferred regions for  and  in a few residues. Recently, a new geometric approach has allowed to calculate the steric energy maps for each amino-acids. The present work analizes the spatial conformation of complex chains of amino-acids, and assesses the correspondence of the  and  angles of each amino-acid in a chain with the conformational energy maps which have been determined on a theoretical basis. Materials and Methods A statistical evaluation has been carried out on the amino-acids of proteins of known 3D structure, obtained from the Brookhaven Data Bank (PDB). A software has been set up, within the Mathematica environment, which consists of three modules. The first module extract relevant data from the PDB file and stores it into one Mathematica file. The second module carries out the comparison with the conformational energy maps either of one specific amino-acid or of all amino-acids of the protein. The third module carries out the statistical evaluations. Results Two proteins have been considered so far: proteinase inhibitor (9PTI) and lyzozyme (7LYZ). Selecting a threshold at 3Kcal it has been found that 58% of the amino-acids (of both proteins) have conformations within the regions of the steric maps with energy below threshold. Selecting a threshold at 10 Kcal 73 % of the amino-acids were in the low energy regions. This finding indicates that the adoption of a criteria of loose agreement with the steric maps may increase the efficiency of computer protein folding simulation

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