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Practical

The document describes how to view 3D protein structures using software like RASMOL and SWISSPDBVIEWER. It provides steps to download protein data files from online databases, open them in the software, and view the structures from different angles and colors. As an exercise, students identified a lung cancer protein, viewed its structure, and also viewed the structure of a drug protein used to treat it. The results demonstrated that 3D protein structures can be determined and analyzed using these visualization software tools.

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Nurul Faizaah
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224 views

Practical

The document describes how to view 3D protein structures using software like RASMOL and SWISSPDBVIEWER. It provides steps to download protein data files from online databases, open them in the software, and view the structures from different angles and colors. As an exercise, students identified a lung cancer protein, viewed its structure, and also viewed the structure of a drug protein used to treat it. The results demonstrated that 3D protein structures can be determined and analyzed using these visualization software tools.

Uploaded by

Nurul Faizaah
Copyright
© Attribution Non-Commercial (BY-NC)
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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PRACTICAL 3

PROTEIN THREE DIMENSIONAL STRUCTURE VIEWING

TITLE: THREE DIMENSIONAL PROTEIN STRUCTURE VIEWING. AIM: To view a protein in 3D Dimensional structure Style OBJECTIVE: To study and learn about the 3 dimensional protein structure by using few softwares To identify cancer causing protein and view 3D protein in rasmol To identify study and learn the cure for the cancer causing protein.

INTRODUCTION: RASMOL RasMol is a program for molecular graphics visualization originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol SWISSPDBVIEWER Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

PROCEDURE: 1. The three dimensional viewing software RASMOL was downloaded and installed. 2. 3. 4. A protein database bank (PDB) file was downloaded from the pdb site The PDB file was opened in the RASMOL software Protein three dimensional structures was viewed in different angles, color, shapes in RASMOl. The results were saved. The same process was repeated for other software like SWISSPDBVIEWER.

5. 6.

LAB EXERCISE:

1) A lung cancer causing protein was identified. The protein structure was then viewed by downloading the pdb file and viewed using rasmol software. 2) The result was copied

3) The treatment for the same disease causing protein was identified.The drug structure which is also a protein was then viewed from downloaded pdb file using rasmol software. 4) The result was copied.

RESULTS:

Title : LUNG SURFACTANT PROTEIN D (SP-D) (FRAGMENT)

Title : STRUCTURAL BASIS FOR THE DEFECTS OF HUMAN LUNG CANCER SOMATIC MUTATION IN THE REPRESSION ACTIVITY OF KEAP1 ON NRF2

Title: Crystal structure of a methotrexate-resistant mutant of human dihydrofolate reductase

CONCLUSION: Three dimensional protein structures can be determined by using the above softwares.

REFFERENCE:

WEBSITE:
http://www.openrasmol.org/ http://www.pdb.org/pdb/home/home.do www.sciencedaily.com/releases/2011/03/110302121706.htm lungcancer.about.com ... Lung Cancer Lung Cancer Treatment

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