Visualizing Molecules and Proteins There are many different computer programs one can use to view molecules in 3D, and t

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Visualizing Molecules And Proteins There Are Many Different Computer Programs One Can Use To View Molecules In 3d And T 1 (89.07 KiB) Viewed 46 times

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Visualizing Molecules and Proteins There are many different computer programs one can use to view molecules in 3D, and the best one depends on your field of science and what information you are interested in obtaining. The options to view molecules in 3D are RasMol, JMol, PyMol, PC3D, Protein Explorer, and the list goes on. In this assignment we are going to view two proteins utilizing the 3D viewer through the protein data bank. The Protein Data Bank is a database with information about over 100 million proteins and small molecules. It is useful for researches to understand all aspects of biomedicine from protein synthesis to health and disease. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. Assignment: The follow questions in blue and italic should be answered in a WORD document and then uploaded once you have completed the assignment. 1. Find a structure of cholesterol and place it in a MS Word document. 2. Then find a "spacefill 3D cholesterol structure" via Goggle Images and paste in MS word document. 3. Compare the two structures by answering the following questions: a. how does the structure compare with the 3Dmodel of cholesterol? For example, that double bond: it's much easier to spot in the standard line structure (those two lines are a dead giveaway). b. What in the 3D structure might clue you in that a double bond is there? c. Briefly describe the overall shape of the cholesterol molecule. Is is flat? Curved? Is it spherical or cylindrical? Is this overall shape obvious from the traditional line structure? So far you have not used any "viewing program" only images from the internet. The real power of the programs mentioned is apparent when you examine large molecules, those that are too big to draw by conventional means.
Let's look at a small protein molecule. Insulin is one of the smallest proteins found in the human body. Do a little research on insulin. 4. What does insulin do in the body? 5. Proteins are long chains of amino acids. How many amino acids make up insulin? Now go to the protein data bank (http://www.rcsb.org/). In the search box, type "human insulin". When you do this, you will access several pages of insulin structures. To make this easier for you I have selected one particular structure to view. Now type in "4A7E", at the top of the screen in the search field. Then at the left side of the screen under a 3D picture of insulin, click on the "3D View: Structure". make sure you are viewing the model in "secondary structure" mode. Then explore the structure using the cartoon, spacefill, backbone, etc. and then answer the following questions. 6. Do you see a-helix or B-sheet secondary protein structure? If you are unfamiliar with these terms, please view the youtube video that discusses the four levels of protein structure. In the boxes on the right you can change your view of the molecule to cartoon, spacefill, etc. For the questions below, change the style to "Spacefill" and change the color to "hydrophobicity". This will indicate different colors for polar amino acids, polar charged amino acids, and nonpolar amino acids. Red/beige/orange are polar and polar charged while shades of green are non-polar amino acids. If you hover your mouse over an amino acid residue, the program will give you its name and position. For example: [GLU 17] which means that particular amino acid is glutamic acid in position number 17 of the chain. You can use the chart at the end of this document to see the full names of the amino acids by their 3 letter code. 7. Does the molecule have polar or nonpolar amino acid residues? 8. Choose 4 different amino acids in this structure and indicate their name and position in the chain. 9. Looking at the information under the "447E", what technique was used to determine this structure and what does the term "porcine" mean about this version of insulin.
Now let's view a larger protein that you should also be familiar with, hemoglobin. Finally, look at the file 2HHD, which (for some reason) is the filename for hemoglobin, the oxygen carrying protein in the blood. This is a huge protein. As many of you may know, iron is the key to its functioning. 9. What about the 2nd structure of this protein? a-helix or b-sheet? Using the box on the left, view the ligands in this molecule in any form you like to view easily. Then rotate the structure, so the ligand or ligands are easily viewable. Then take a screenshot and add it to your document. Then answer the questions below. 10. Does this protein have ligands? How many? What are the ligands? As usual, save your answers in a MS Word document, upload to your folio dropbox by the due date and time.