Method for determining and predicting protein autonomous folding

Abstract

Techniques for determining an equilibrium structure of a protein in a predetermined environment, the protein having Ramachandran angles and a known denatured structure, are disclosed. In a preferred embodiment, a method is presented which involves determining a maximum RMS volume of the known denatured structure of the protein and calculating at least one force on the protein in its current structure in the predetermined environment. The net torque resulting from the at least one force for each of the Ramachandran angles of the protein is then determined. Then at least one section of the protein structure on a side of a Ramachandran angle with greatest torque is rotated to form a new structure. A new RMS volume for the new structure is then calculated, and the method is repeated using the new structure. The method ceases when the new RMS volume of the new protein structure is not less than the RMS volume of the starting structure.

1 - 11 . (canceled) 
     
     
         12 . A synthetic protein, the synthetic protein having a predetermined equilibrium structure in a predetermined environment, wherein an amino acid composition of the synthetic protein is determined using the method of claim  1 . 
     
     
         13 . The synthetic protein of  claim 12 , wherein said synthetic protein configured to move an ionic species against a concentration gradient. 
     
     
         14 . The synthetic protein of  claim 13 , wherein the ionic species is sodium, and the concentration gradient is that encountered during the desalination of water. 
     
     
         15 . The synthetic protein of  claim 13 , wherein a structure of the synthetic protein is based upon to a naturally occurring neural channel structure. 
     
     
         16 . The synthetic protein of  claim 13 , wherein the synthetic protein may be stacked to move the ionic species against a larger concentration gradient. 
     
     
         17 . A synthetic protein, the synthetic protein having a predetermined structure change in response to a predetermined environmental change, wherein an amino acid composition of the synthetic protein is determined using the method of claim  1 . 
     
     
         18 . A method of determining a global energy change upon folding of a protein having Ramachandran angles and a known denatured structure and a known equilibrium structure, comprising:
 (a) determining a maximum RMS volume of the known denatured structure of the protein;   (b) calculating at least one force on the protein in its current structure in the predetermined environment;   (c) determining a net torque resulting from the at least one force for each of the Ramachandran angles of the protein;   (d) rotating at least one section of the protein structure on a side of a Ramachandran angle with greatest torque as determined in (c) to form a new structure;   (e) determining a new RMS volume for the new structure;   (f) repeating (b) to (e) using different values for the global energy change upon folding until the new protein structure at (e) approximates the known equilibrium structure.