Thermodynamic propensities of amino acids in the native state ensemble: implications for fold recognition
First Claim
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1. A protein database comprising nonhomologus proteins having known residue-specific free energies of folding.
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Abstract
The present invention relates to a system and computer-based method that is used to determine thermodynamic environment differences within a protein. This method is used to construct a database of proteins, wherein the database can be used to identify correct sequences that correspond to a particular target fold.
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38 Claims
- 1. A protein database comprising nonhomologus proteins having known residue-specific free energies of folding.
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13. A method of developing a protein database comprising the steps of:
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inputting high resolution structures of proteins;
generating an ensemble of incrementally different conformational states by combinatorial unfolding of a set of predefined folding units in all possible combinations of each protein;
determining the probability of each said conformational state;
calculating a residue-specific free energy of each said conformational state; and
classifying a stability constant into a thermodynamic classification group.
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19. A method of identifying a protein fold comprising determining the distribution of amino acid residues in different thermodynamic environments corresponding to a known protein structure.
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23. A system for developing a protein database and for identifying a protein fold comprising:
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a protein database having a data structure for protein data, said data structure including data fields for thermodynamic classifications for amino acids of a protein; and
a computer-based program for identifying protein fold data for said database, said program having an input module for receiving high resolution structure data for one or more proteins, and a processing module for determining amino acid thermodynamic classifications for said one or more proteins and storing said amino acid thermodynamic classifications into said data fields of said protein database.
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36. A database having a data structure which stores information defining thermodynamic classification groups, said database comprising:
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a field for storing a value of an amino acid name or amino acid abbreviation; and
one or more classification fields for storing a value representing a numerical value for a thermodynamic classification for a particular amino acid.
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Specification