| Abstract: | A quantitative conformational theory of proteins is developed that enables one to predict the native structure of a protein from its amino acid sequence. The theory is based on the following principles: (1) the spatial structure and conformational properties of a protein are predetermined by its amino acid sequence; (2) the native conformation of a protein corresponds to the free energy minimum; (3) all interactions within a protein molecule are specified as short-, mediumy-, and long-range types, interactions of different types being consistent with each other. The role of the short-, medium-, and long-range interactions in the spatial organization of a protein globule is discussed, and a step-by-step analysis of amino acid sequences with gradually increasing lengths is presented. The proposed theory is based on a semiempirical computational method that involves quantitative evaluation of all pairwise atomic interactions within a protein molecule in an aqueous medium. Examples illustrating the suggested approach are presented. |
