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Download BIOINFORMATICS PROBLEM 1 Goal: Describe secondary structure
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BIOINFORMATICS PROBLEM 1 Goal: Describe secondary structure of a synthetic protein (2i7u) focusing on the type of bonding that stabilizes it. Directions: Click HERE to see the 3D view for entry 2i7u. 1. Click on the 3D tab on the top menu to see representation of the structure in the Jmol window. Use your mouse to rotate the molecule once it appears. 2. Click on the "Custom View" button and select the "Rainbow" option under "Color" in the custom view options. N-‐terminal residues in the protein chain are colored blue, whereas the C-‐terminal residues are red. 3. Turn off the black background by clicking on the checkbox. Now turn on the H-‐bonds to see magenta dashed lines. QUESTIONS 1. What is the predominant secondary structural element seen in this structure? Alpha helix Beta sheet Beta helix Pi helix 2. How many polymer chains do you see in this visualization? One Two Three Four 3. Locate the first H-‐bond (denoted as magenta dashed lines) at the blue end of the polymer. Mouse over the ends of the dashed line to identify the residues involved in making this bond. Select "Backbone" under "Style" in the custom view options for easier identification of the amino acids. If one end of the H-‐bond is at Leu 4, the other end is at: Met 1 Glu 7 Ala 8 Lys 10 Color the molecule by Hydrophobicity -‐ amino acid residues with hydrophobic side chains are colored red while those with hydrophilic side chains are colored blue. Rotate the molecule in the graphics window to explore the distribution of these residues. 4. Where are the hydrophilic residues located in the helix? Towards the core of the 4-‐helix bundle Away from the core of the 4-‐helix bundle In the core of each helix There is no pattern in their distribution Goal: Describe secondary structure of concanavalin focusing on the type of bonding that stabilizes it. Directions: Click HERE to see the 3D view for entry 2cna. 4. Click on the 3D tab on the top menu to see representation of the structure in the Jmol window. Use your mouse to rotate the molecule once it appears. 5. Click on the "Custom View" button and select (1) secondary structure and then (2) the the "Rainbow" option under "Color" and cartoon under Style in the custom view options. N-‐terminal residues in the protein chain are colored blue, whereas the C-‐ terminal residues are red. N 6. Select hydrophobicity under color (red is nonpolar and blue is polar) 7. Turn off the black background by clicking on the checkbox. Now turn on the H-‐bonds to see magenta dashed lines. Questions 1. What is the predominant secondary structural element seen in this structure? Alpha helix Beta sheet Beta helix Pi helix 2. How many polymer chains do you see in this visualization 1 2 3 4 Hydrophobicity -‐ amino acid residues with hydrophobic side chains are colored red while those with hydrophilic side chains are colored blue. Rotate the molecule in the graphics window to explore the distribution of these residues. 3. Where are type of residues located in the sheets? Mostly non polar Mostly polar Mixed 4. Describe how the H-‐bonds are linked
