Affinity prediction and analysis method for human amphiphysin-1 Src homology-3 domain binding peptide

Abstract

The invention discloses an affinity prediction and analysis method for a human amphiphysin-1 Src homology-3 domain binding peptide. The method comprises the following steps of: selecting an electrical property parameter, a three-dimensional property parameter, a hydrophobicity parameter and hydrogen bond property parameter of an amino acid, establishing physicochemical property classification scores of the amino acid by adopting a principal component analysis method, representing each amino acid residue in a peptide sequence by using the scores to realize the parameter-based description of a peptide sequence structure, selecting characteristic parameters closely related to affinity from parameters of the peptide sequence structure by using a genetic algorithm, establishing a relational model, namely an affinity prediction and analysis model between the characteristic parameters and the affinity by using a Gaussian process, obtaining structural factors influencing the affinity of the peptide by analyzing hyper-parameters of the model, and performing prediction by using the model to obtain an affinity value of the peptide. By the method, a powerful tool can be provided for the high-throughput screening of high-affinity human amphiphysin-1 Src homology-3 domain binding peptides, and development and researches on human amphiphysin-1 Src homology-3 domain binding peptide inhibitors are further prompted.

Description

technical field [0001] The invention belongs to the field of computer chemistry and relates to a method for predicting and analyzing the affinity between polypeptide ligands and protein receptors by applying a calculation model. Background technique [0002] As one of the important components of biological systems, proteins play an irreplaceable role in the operation of life and perform a variety of biological functions, such as tissue construction, material transport, reaction catalysis, and immune regulation. Protein-protein interaction (PPI) also plays an extremely important role in signal transduction and other important biological processes. Typically, PPIs are mediated by domains. Src homology domain 3 (Src homology domain, SH3) is the most abundant domain in the human proteome, widely exists in various proteins such as protein kinases, lipases, GTPases and regulatory proteins and guides a variety of cellular biochemical processes . The Src homology domain 3 consist...

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Problems solved by technology

However, it is extremely time-consuming and labor-intensive to synthesize all possible peptide motifs (generally 10 amino acid residues) encoded by the human genome one by one based on experimental approaches and to test their affinity to the Src homology domain 3 of human biporin one by one. work; and the prediction methods reported in previous literature, such as the use of free energy analysis to study the binding thermodynamic behavior of Src homology domain 3 and different peptide ligands, are not suitable for the high binding peptide of Src homology domain 3 due to their low efficiency. Throughput screening

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