Polypeptide research Protein sequence analysis and structure prediction

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Key words: sequence protein structure

Key words: sequence protein structure protein sequence analysis structure prediction

[purpose]

1. Master the operation method of protein sequence retrieval;
2. Familiar with basic property analysis of protein;
3. Familiar with the prediction of protein function based on sequence homology analysis, and understand the prediction of protein function based on motif, structural site and structural functional domain database;
4. Understand protein structure prediction.

[experiment content]

1. Using Entrez or SRS information query system to retrieve the sequence of human adiponectin;
2. Bioedit software was used to analyze the molecular weight, amino acid composition, hydrophobicity and other basic properties of these protein sequences;
3. The homology of human adiponectin was analyzed based on NCBI / blast software;
4. The motif structure of human adiponectin was analyzed;
5. The secondary structure and three-dimensional structure of human adiponectin were predicted.

[experimental method]

1. Retrieval of human adiponectin protein sequence:

(1) Call your Internet browser and enter the Entrez web address in its address bar（ http://www.ncbi.nlm.nih.gov/Entrez )；

(2) Select protein in the selection column after search;

(3) Enter home sapiens adiponectin in the input field;

(4) Click go to display the serial acceptance number and serial name;

(5) Click on the serial acceptance number NP_ 004788 (adponectin precursor; adpose most assistant gene script 1 [Homo sapiens]), then display the sequence details;

(6) Transfer the sequence to FASTA format for preservation (refer to the above steps to use SRS information query system to retrieve the human adiponectin protein sequence);

1. Using bioedit software to analyze the molecular weight, amino acid composition and hydrophobicity of human adiponectin protein sequence

Open the bioedit software → input the FASTA format sequence of human adiponectin protein into the analysis box → click the sequence description in the left sequence description box → click the sequence column → select protein → click amino acid composition → view the molecular weight and amino acid composition of the protein;

Or select protein, click Kyte & Doolittle mean hydrophobicity profile → check the hydrophobicity level of the protein;

1. Homology analysis of human adiponectin protein sequence:

(1) Enter NCBI / blast web page;

(2) Select protein protein blast (blast P);

(3) Paste FASTA format sequence into input field;

(4) Click blast;

(5) Check the homologous protein;

1. Motif structure analysis of human adiponectin protein sequence:

(1) Access http://hits.isb-sib.ch/cgi-bin/PFSCAN Webpage;

(2) The FASTA format sequence of human adiponectin protein sequence was pasted into the input field;

(3) Click Scan;

(4) View the analysis results (note the motif information in the PROSITE profile);

1. Prediction of secondary structure of human adiponectin protein sequence:

(1) Enter the following protein structure prediction server website:

http// www.embl-heidelberg.de/predictprotein//predictprotein.html (The PredictProtein Server)；

(2) Click Default in you can column;

(3) Fill in email address and sequence name;

（4） Paste the FASTA format sequence of human adiponectin protein sequence into the input column and click Submit;

(5) Check the analysis results from email;

1. Three dimensional structure prediction of human adiponectin protein sequence:

(1) Access

http// www.expasy.org/swissmod/SWISS-MODEL.html (swissmodel first approach mode) web page;

(2) Fill in email address, name and sequence name;

(3) The FASTA format sequence of human adiponectin protein sequence was pasted into the input field;

(4) Click send request;

(5) Check the analysis results from email (Note: download the software into Rasmol to view the three-dimensional image).

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