Posts Tagged PyMol

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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Anna and Shalanda – PyMol Visualization of 1OAC

Using the Protein Data Bank, we located the protein 1OAC, otherwise known as copper amine oxidase of E. coli.  It is a dimer and has two active sites which are buried away from the solvent.  The enzyme has an inactive and an active form. 1OAC has a single copper ion and a covalently bonded cofactor.  The formation of this cofactor is done post-translationally by modifying a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). (Information taken from Proteopedia)  A great summary of the enzyme is available at PDBsum.  To access that information, input the PDB code for the enzyme (1OAC).

This gallery shows two images.  The first was generated in PyMol and shows the dimer chains in two different colors.  The second image, generated by Consurf, shows the conservation of the residues of chain a (purple being most conserved, blue being most variable, and yellow representing no data available).

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Jennifer Oden Pymol

Pymol was very useful and very eye catching. We looked at Apolipoprotein M. We were able to see the different alpha helices and the beta sheets. We were also able to easily see the binding site. This protein was a very large protein. We looked at the protein with the consurf software and found out that the protein had many places that had insufficient information. It was very helpful to use this program to visualize the protein. A picture of the protein that we researched is linked.

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kate rosendall pymol

We looked at a protien structure using pymol, this is a visual aid to that allows us to see the chemical make up of a protein as well as how it folds into it’s structure. It was very interesting to see the binding sites of a very familiar protein in a new way.

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PyMOL and Integrase-Jessica/Sara

Integrase is an enzyme that splices viral DNA; it is well known in studies of HIV. Four copies of integrase will attach to viral DNA and create a larger structure called an  intasome. This structure has 2 subunits toward the middle which will provide the active site where  the DNA is cut and attached together. This is important because it allows the viral genome to become part of the cell, furthermore propagating the virus. In the pyMOL image attached, you can see this active site mentioned.

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Leptin Protein Views (Steve and Ann)

We decided on Leptin, a hormone involed with appetite suppression, because obesity is an increasing problem in affluent countries and we are in one. There is one disulfide bridge within this protein, and 4 alpha helices adjacent to each other with multiple leucine residues that are highly conserved (as verified by Consurf). Also, there is a random chain that is not highly conserved except for a tail region, potentially meaning that this tail region is important for the protein’s function.

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Lipase visualization- Tara and Stefan

Lipase is an enzyme that hydrolyzes lipids. The structure we looked at came from Gibberella zeae and was obtained by xray diffraction. This enzyme is crucial to G. zeae pathogenicity. It contains 319 residues and measured 94 by 129 angstroms. We created an image of the electrostatics and of the atoms.

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Fun with Pymol

The combination of PDB and Pymol creates a great tool to visualize protein structures and manipulate them. The structure above is Aldo-Keto Reductase, which is a stress enzyme found in plants. In this view, you can see NADP bound to it in blue, with alpha helices in red and beta sheets in yellow.

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P53 Protein (Ben/Kyle)

This is a well known Tumor Suppressor protein. 3 are shown below near a DNA molecule.

Here is a consurf image of the same protein. (darker areas are more conserved)

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Protein visualization (Rachel / Thomas)

Solved crystal structure of BRCA1 BRCT (made in Jmol):

Electrostatic map of BRCA1 BRCT (made in Pymol):

Sequence of BRCA1 BRCT showing features such as beta strands and alpha helices:

The structure has a diameter of ~27 A.  ~55 A in length.

There are a variety of secondary structures including beta turns, beta strands and alpha helices.

BRCA1 is composed of 215 residues.

Conserf run (MSA):

Dark purple regions are conserved.  Notice ligands binding in that region.

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