Protein sequence analysis and structure prediction experiments

Summary

Source of content: Guangdong Pharmaceutical University Laboratory Instruction Manual.

Operation method

Protein sequence analysis and structure prediction experiments

Move

1. Search for human lipocalin protein sequences

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

(2) Select protein in the selection field after Search;

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

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

(5) Click sequence acceptor number NP_004788 (adiponectin precursor; adipose most abundant gene transcript 1 [Homo sapiens]) to display sequence details;

(6) Save the sequence in FASTA format (refer to the above steps to retrieve the human adiponectin protein sequence using the SRS information query system);

2. use BioEdit software to analyze the basic properties of the human lipocalin protein sequence, such as molecular mass, amino acid composition and hydrophobicity.

Open BioEdit software → input the FASTA format sequence of human lipocalin protein sequence into the analysis box → click on the sequence description in the sequence description box on the left → click on the sequence column → select protein → click on Amino Acid Composition → view the molecular mass and amino acid composition of the protein.

Alternatively, after selecting the protein, click Kyte & Doolittle Mean Hydrophobicity Profile→ to view the hydrophobicity level of the protein molecule.

3. Protein homology analysis of human lipocalin protein sequence

(1) Go to the NCBI/Blast webpage;

(2) Select Protein-protein BLAST (blastp);

(3) Paste the FASTA format sequence into the input field;

(4) Click BLAST;

(5) View proteins with which it is homologous.

4. Motif structure analysis of human lipocalin protein sequence

(1) The link in expasy-tools (http://cn.expasy.org/tools/) was accessed, or the URL (http://myhits.isb-sib.ch/cgi-bin/motif_scan) was entered directly into the web page;

(2) Paste the FASTA format sequence of the human lipocalin protein sequence into the input field;

(3) Click Scan;

(4) View the analysis results (note the motif information in Prosite Profile).

5. Secondary structure prediction of human lipocalin protein sequence

(1) Can be accessed by the link in expasy-tools (http://cn.expasy.org/tools/) or by directly entering the URL (http://www.predictprotein.org/);

(2) After entering the predictprotein page, register first;

(3) Then Paste the FASTA format sequence of human lipocalin protein sequence into the input field. (4) Paste the FASTA format sequence of the human lipocalin protein sequence into the input field, and submit the protein sequence to be analyzed;

(4) View the results of the analysis from the email box.

PHD predictions results

PROF predictions results

6. 3D structure prediction of human lipocalin protein sequence

(1) Go to http//www.expasy.org/swissmod/SWISS-MODEL.html (SwissModel First Approach Mode) web page;

(2) Select Automated mode;

(3) After entering the Automated mode interface, enter the E-Mail address and sequence name, paste the FASTA format sequence of human lipocalin protein sequence into the input field, click "submit modeling request" and wait for the result.

(4) Check the analysis results from the e-mail address.

Caveat

1.Need to download the software into rasmol to view the 3D image.

2.Sometimes the result is faster, the result will be sent to E-Mail immediately, and the result page will be displayed through the E-Mail link. But sometimes it is slow.

Common Problems

I. Homework

1. Submit the results of basic property analysis, homology analysis, motif structure analysis, and secondary and 3D structure prediction of the human lipocalin protein sequence using the above software.

2. Compare the results with each other, explain the reasons for the different results, and summarize the key points to note in conducting the above analyses.

For more product details, please visit Aladdin Scientific website.

https://www.aladdinsci.com/