Exploring Protein Amino Acid Sequence Analysis: From Sequence to Function

Protein amino acid sequence analysis is a key area in bioinformatics and molecular biology. By understanding the sequence of proteins, we can predict their three-dimensional structure, function, and interactions with other molecules. Below, we will delve into the protein amino acid sequence analysis: the whole process from sequence to function.

 

Acquisition of Protein Amino Acid Sequence

In the laboratory, various techniques such as mass spectrometry can be used to obtain the amino acid sequence of proteins from biological samples. In addition, with the advancement of genome sequencing technology, we can directly predict the amino acid sequence of proteins from DNA sequences.

 

1. Mass Spectrometry

Use peptide mass spectrometry and tandem mass spectrometry analysis to obtain sequence information of protein amino acids.

 

2. cDNA Sequencing

Obtain cDNA by transcribing from mRNA, then perform DNA sequencing to infer the amino acid sequence of the protein.

 

3. Synthetic Biology

Directly synthesize the gene of the target protein for subsequent expression and analysis.

 

Sequence Alignment and Homology Analysis

By comparing the protein sequences of different species or different family members, we can determine their similarities and differences. This helps to identify conservative regions (i.e., functionally important regions) and potential evolutionary relationships.

 

1. Alignment Tools

Use tools such as BLAST, ClustalW, etc., to compare the target sequence with known sequences.

 

2. Homology Analysis

Find sequences similar to known protein structures and functions to predict the potential properties of the target protein.

 

Structure Prediction and Analysis

1. Secondary Structure Prediction

Prediction of α-helices, β-folds, and random curls: Use tools such as PsiPred, DSSP, etc., to predict the secondary structure elements of proteins.

 

2. Tertiary Structure Prediction

(1) Homology Modeling: If a homologous protein with known structure is found, the tertiary structure of the target protein can be predicted by template-guided methods.

(2) Abstract Modeling: If no homologous template is available, methods such as Rosetta are used for de novo prediction.

 

Function Annotation and Analysis

1. Domain Analysis

Identification and annotation of functional domains: Use tools such as Pfam, InterProScan to find known functional domains and motifs.

 

2. Active Site Prediction

Identification of key residues and active sites: Resources like the Catalytic Site Atlas are used to identify and analyze potential catalytic residues.

 

Protein-Protein Interaction Analysis

1. Subcomplex Identification

Interface Residue Analysis: Analyze protein-protein interaction interfaces with prediction tools (such as PPCheck).

 

2. Network Analysis

Construct and analyze PPI networks: Construct protein interaction networks through databases and experimental data to further insight into biological processes.

 

Function and Pathway Analysis

1. Gene Ontology (GO) Annotation

Use tools like DAVID, PANTHER for functional annotation of proteins.

 

2. Metabolic and Signal Pathway Analysis

Use databases such as KEGG, Reactome for analyzing biological pathways that proteins are involved in.