Analysis of protein native structure stability according to a thermodynamic energy assay containing environmental parameters

摘要

PURPOSE: An analytical method of protein natural structure stability according to thermodynamic energy assay of protein containing environmental parameters is provided, thereby stabilizing the natural structure of protein, and easily determining whether the protein structure to be analyzed is natural structure. CONSTITUTION: The analytical method of protein natural structure stability according to thermodynamic energy assay of protein containing environmental parameters comprises judging whether decoy structure score of the new protein/protein group is larger than its natural structure score using energy parameters calculated by using groups, and calculating one or more of unfolded fraction, specific heat and internal energy defined in an approximate partition function, wherein the groups comprise a plurality of training protein group showing the natural structure extracted from the protein data of which amino acid sequence and tertiary structure via X-ray determination are known; a training decoy structure protein group which is formed by corresponding the amino acid sequence of protein A having length of NA to from a first amino acid to NA amino acid of protein B having the same or longer length of NB than NA, and repeating the correspondence with increasing one amino acid position of protein B; energy parameters containing all kinds of amino acids and one local environment selected from (1) three two-dimensional structures of amino acids and three hydrophobic classifications, (2) pairwise contact of two amino acids, (3) three two-dimensional structures of amino acids, three hydrophobic classifications and pairwise contact of two amino acids, (4) Ramachandran angle of amino acids, and (5) Ramachandran angle of amino acids and pairwise contact of two amino acids, and calculated by using the energy equation showing energy level when a sequence s has a structure of letter "L" and using a condition when the decoy structure score - natural structure score 0; new protein/protein group which does not belong to the training protein group; and new decoy structure protein group which is formed by the same method of the training protein group using the training protein group.