Method and electronic system for predicting at least one fitness value of protein, related computer program product

A fitness value, protein technology, applied in proteomics, computing, sequence analysis, etc., can solve problems such as insufficient identification of protein mutants

Pending Publication Date: 2022-08-09
PEACCEL
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0028] The information provided by these state-of-the-art methods is useful but insufficient to identify the most valuable protein mutants generated by directed evolution

Method used

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  • Method and electronic system for predicting at least one fitness value of protein, related computer program product
  • Method and electronic system for predicting at least one fitness value of protein, related computer program product
  • Method and electronic system for predicting at least one fitness value of protein, related computer program product

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0201] Example 1: Cytochrome P450 ( Figures 4 to 6 )

[0202] In this example, the amino acid sequence of cytochrome P450 was encoded as a numerical sequence using the following AAindex code: D-normalized frequency of extended structure (Maxfield and Scheraga, Biochemistry. 1976; 15(23):5138-53).

[0203] The first dataset (from Li et al., 2007: Nat Biotechnol 25(9): 1051-1056.; Romero et al., PNAS. 2013: January 15, Vol. 11, n°3: E193-E201) was derived from surrounding cytochromes A study of the sequence / stability-function relationship of the P450 family, particularly the cytochrome P450 BM3 A1, A2 and A3, aimed at improving the thermostability of cytochromes. The multifunctional cytochrome P450 family of heme-containing oxidoreductases hydroxylates a wide range of substrates to yield products of great medical and industrial importance. New chimeric proteins were constructed using eight contiguous fragments inherited from any of the three different parents. The measured a...

Embodiment 2

[0212] Example 2: Predicted analogs of human glucagon-like peptide-1 (GLP1) ( Figure 7 and 8 )

[0213] In this example, the amino acid sequence of GLP1 was encoded as a numerical sequence using the following AAindex code: D Electron-Ion Interaction Potential Value (Cosic, IEEE Trans Biomed Eng. 1994 Dec; 41(12): 1101-14.).

[0214] Taslutide and Extendin-4 are GLP1 analogs that act as peptide agonists of the glucagon-like peptide (GLP) receptor and are under clinical development for the treatment of type II diabetes (tasuglutide) middle.

[0215] hGLP1 HAEGTFTSDVSSYLEGQAAKEFIAWLVKGR (SEQ ID NO: 1) Tasglutide HAEGTFTSDVSSYLEGQAAKEFIAWLVK A R (SEQ ID NO: 2)

[0216] The methods of the invention have been carried out to provide GLP1 with increased binding affinity (interaction with receptor) and / or increased potency (activation of receptor-adenylate cyclase activity) relative to native human GLP1 and tasuglutide candidate agonists of the receptor....

Embodiment 3

[0233] Example 3: Evolution of the enantioselectivity of epoxide hydrolase ( Figure 14 and 15 )

[0234] In this example, the amino acid sequence of epoxide hydrolase was encoded as a numerical sequence using the following AAindex code: DSD of AA Composition of Total Protein (Nakashima et al. Proteins. 1990;8(2):173-8).

[0235] Enantioselectivity is the preferential formation of one stereoisomer over another in a chemical reaction. Enantioselectivity is important for the synthesis of many industrially relevant chemicals and is difficult to achieve. Green chemistry utilizes recombinant enzymes (because enzymes have high specificity) to synthesize target chemical products. Therefore, enzymes with increased efficiency are particularly sought in green chemistry.

[0236] Reetz, et al. (Ang 2006 Feb 13;45(8):1236-41) describe the kinetic resolution of enantioselective mutants of epoxide hydrolase from Aspergillusniger as glycidyl ether 1 ( Directed evolution of catalysts in ...

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Abstract

A method for predicting at least one fitness value of a protein is executed on a computer and comprises the steps of: encoding (100) an amino acid sequence of the protein into a numerical sequence according to a protein database, the numerical sequence comprising a value for each amino acid in the sequence; calculating (110) a protein profile from the sequence of values; and for each fitness: comparing (130) the calculated protein profile with protein profile values of a predetermined database containing protein profile values for different values of the fitness, predicting (130) the value of the fitness according to the comparing step.

Description

[0001] This application is a divisional application of CN201680027558.6. [0002] The present invention relates to a method and related electronic system for predicting at least one fitness value of a protein comprising an amino acid sequence. The invention also relates to a computer program product comprising software instructions, the program product being executed by a computer, which program product when executed by the computer performs such a method. [0003] Background of the Invention [0004] Proteins are biomolecules composed of chains of at least one amino acid sequence. Proteins differ from each other mainly by their amino acid sequences, and the differences between sequences are called "mutations". [0005] One of the ultimate goals of protein engineering is the design and construction of peptide, enzyme, protein or amino acid sequences with desired properties (collectively referred to as "fitness"). The construction of amino acid sequences (i.e., "mutants") mod...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/50G16B30/10G06F17/14G16B30/00G16B20/00
CPCG16B20/50G16B30/10G06F17/14G06F17/142G16B20/00G16B30/00C07K2/00C12N15/1089C40B40/10
Inventor N·冯塔因F·卡德特
Owner PEACCEL
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