Method for protein structure determination, gene identification, mutational analysis, and protein design
AssigneeThe Research Foundation of State University of New York
InventorsCharles Michael Fortmann, Yeona Kang, David H. Coleman
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Abstract
An efficient computational method and system for predicting the folding regions and associated secondary and tertiary structures of a protein is disclosed. Methods and systems for sorting amino acid sequences based on predicted structures, as well as methods and systems for determining the presence or absence of genes in nucleic acid sequences or structural mutations in amino acid sequences are also disclosed. A method and system for the design of a protein is also disclosed.
Claims45
A method of predicting the presence or absence of a folded structure in an amino acid sequence, the method comprising:
- providing:
- an amino acid sequence,
- a pre-determined value of hydrophobicity of each amino acid residue on the sequence,
- and the charge of each amino acid residue on the sequence;
- identifying a first and a second amino acid residue on the amino acid sequence that are separated by a pre-determined number of intervening amino acid residues on the contour of the amino acid sequence;
- using the hydrophobicity of the first and the second amino acid residue and the sum of charges of the intervening amino acid residues to predict and/or denote the presence or absence of a folded structure.
A method for determining the presence or absence of a gene in a nucleic acid sequence, the method comprising:
- providing a nucleic acid sequence and a corresponding amino acid sequence, wherein the amino acid sequence is a translation of the nucleic acid sequence;
- applying a method of predicting protein structure to the amino acid sequence to determine the presence or absence of a folded region in the amino acid sequence;
- determining the presence or absence of a gene in the nucleic acid sequence based on the presence or absence of a folded region in the amino acid sequence.
A method for determining the presence or absence of a structural mutation in an amino acid sequence, the method comprising:
- providing a first amino acid sequence and a second amino acid sequence, wherein the second amino acid sequence is a natural variation of the first amino acid sequence;
- applying a method of predicting protein structure to the first and the second amino acid sequences to determine the presence or absence of a folded region in the first and the second amino acid sequences;
- comparing the presence or absence of the folded region in the first and the second amino acid sequence so as to correlate the presence or absence of a structural mutation due to the natural variation.
A method for selecting the design of a protein, comprising:
- (a) providing a first set of one or more amino acid sequences;
- (b) applying a method of predicting protein structure to the first set of one or more amino acid sequences to determine the presence or absence of a folded region in each of the first set of one or more amino acid sequences;
- (c) generating a second set of one of more amino acid sequences based on the predicted structure of the first set of one or more amino acid sequences;
- (d) selecting one or more amino acid sequences based on the type, order and/or number of secondary structures produced by the first and the second set of one or more amino acid sequences to design a protein.
Dependencies are inferred from the claim text.