Archive for category Structural Biology #2

Caroline and Raphael Protein Image

2HSJ Protein Visualization: Platelet Activating Factor from Streptococcus pneumonia

We examined protein 2HSJ, a probable platelet activating factor from S. pneumonia using PyMOL visualization tools. 2HSJ is a little studied protein that functions in lipid metabolism and hydrolysis. Our measurements show protein dimensions of 104.4 Å by  66.3 Å  by 52.5 Å (as seen in Image 1). This protein has known ligand binding between amino acid residues ALA 161 and VAL 167 (shown hot pink in Image 2).   A Consurf homology comparison using BLAST shows conserved areas in the central parts of each chain. However, much of the external surface, including the known ligand binding area, is categorized as having “insufficient data.” Thus, no conclusions about active site location based on Consurf conserved regions can be draw.

Platelet Activating Factor

Measurements shown on the structure of a probable platelet activating factor of S. pneumonia.

Platelet Activating Factor

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Lipase Consurf

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ConSurf Imaging

We used Consurf to visually analyze the structural basis for our enzyme Integrase. Since Integrase is found in viruses and functions to cleave and repackage the viral DNA we were expecting much of it to be conserved, especially near the active site. Looking at both the A and B chains we found it was most conserved on the A- chain and our guess of the active site was right on key. This was a very useful tool. In the end we found that we can actually compare both the A and B chains and check out the structural basis as a whole which was highly conserved as we expected it to be.

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Aldo-keto reductase

So here is con surf run of aldo keto reductase, it looks pretty conserved.

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ConSurf

Using ConSurf we analyzed both A and B chains of integrase. Both chains showed significant amounts of conservation but there was one specific area on the A chain that was incredibly highly conserved.  Even though an integrase can act upon viruses, which change frequently and rapidly, it is able to achieve its desired result while, itself, maintaining relatively stable.

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Protein Images for Joanna and Maurico

The protein we chose to look at was insulin.  Insulin is a signalling hormone that indicates levels of sugar in the blood.  It is synthesized in the pancreas, and the distributed through the body to have an effect on  many systems.  Insulin is a relatively small molecule, measuring aproximately 25x16x18 angstroms.  As such, cells actually synthesized as a larger molecule, and 2 chains are cut off.  Insulin is a great molecule to use to study protein structure, because it has multiple chains held together by disulfide bonds.  This image shows an insulin monomer, the A and B chains are in different colors, and the three disulfide bonds are shown with yellow sticks.

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