User:Gilad Parann-Nissany/Sandbox 1

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Current revision (06:35, 30 July 2009) (edit) (undo)
 
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A first attempt to create a Proteopedia page. I am going to try for some 3D protein stuff. Let's see if I succeed.
A first attempt to create a Proteopedia page. I am going to try for some 3D protein stuff. Let's see if I succeed.
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<applet load='2QG6' size='300' frame='true' align='right' caption='Human Nicotine-related protein with an unusual name - Nicotine Riboside Kinase (Nrk1; PDB: 2QG6)' />
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<applet load='2QG6' size='300' frame='true' align='right' caption='Human Nicotine-related protein with an unusual name - Nicotinamide Riboside Kinase (Nrk1; PDB: 2QG6) - in complex with Nicotinamide Mononucleotide (Nmn)' />
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So we start with <scene name='User:Gilad_Parann-Nissany/Sandbox_1/The_basic_nrk1/1'>Nicotine</scene>. Last time I smoked a cigar was at my brother's wedding. This is unquestionably related to <scene name='User:Gilad_Parann-Nissany/Sandbox_1/Measured_distance_1/1'>this distance</scene> between these two Oxygen groups on our Riboside. If it was larger I would obviously smoke more often.
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So we start with <scene name='User:Gilad_Parann-Nissany/Sandbox_1/The_basic_nrk1/1'>Nicotinamide Riboside Kinase</scene>.
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(Last time I smoked a cigar was at my brother's wedding)
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So lets see what happens if we enlarge this distance.
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<scene name='User:Gilad_Parann-Nissany/Sandbox_1/Measured_distance_1/1'>This is a distance</scene> between two Oxygen atoms on our Riboside.
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Surprisingly this attempt does not change the distance by a single Angstrom - apparently quite strong forces hold this protein together. But under strong tension, the protein does show signs of stress and develops a <scene name='User:Gilad_Parann-Nissany/Sandbox_1/Frothy_residue_1/2'>frothiness</scene> in its residues.
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Now here are some yellow <scene name='User:Gilad_Parann-Nissany/Sandbox_1/Frothy_residue_1/2'>frothy</scene> residues.
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This makes sense. I do like - in the rare cases when I smoke a cigar - to drink a glass of frothy beer!
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Now we move on to the next step of this advanced research. The protein must have some <scene name='User:Gilad_Parann-Nissany/Sandbox_1/Potential_binding_sites_1/1'>binding sites</scene>. Right? Right! The ProMate tool allows us to identify these immediately.
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Science is wonderful.
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Now lets try for some <scene name='User:Gilad_Parann-Nissany/Sandbox_1/The_basic_nrk1/2'>evolutionary conservation</scene> levels: you will notice that the sections that attach to the nucleotide are more strongly conserved (more purple).
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Now we move on to the next step of this advanced research. Obviously if a person can both smoke a cigar and drink beer at the same time, the responsible protein must have some <scene name='User:Gilad_Parann-Nissany/Sandbox_1/Potential_binding_sites_1/1'>binding sites</scene>. Right? Right! The ProMate tool allows us to identify these immediately, proving that the theory does have practical use.
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Finally - smoking cigars and drinking beer are habits that die hard. Therefore the sites responsible for this behavior must have formidable evolutionary conservation levels. This theory is now to be tested.
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Current revision

A first attempt to create a Proteopedia page. I am going to try for some 3D protein stuff. Let's see if I succeed.

Human Nicotine-related protein with an unusual name - Nicotinamide Riboside Kinase (Nrk1; PDB: 2QG6) - in complex with Nicotinamide Mononucleotide (Nmn)

Drag the structure with the mouse to rotate

So we start with . (Last time I smoked a cigar was at my brother's wedding)

between two Oxygen atoms on our Riboside.

Now here are some yellow residues.

Now we move on to the next step of this advanced research. The protein must have some . Right? Right! The ProMate tool allows us to identify these immediately.

Now lets try for some levels: you will notice that the sections that attach to the nucleotide are more strongly conserved (more purple).

Proteopedia Page Contributors and Editors (what is this?)

Gilad Parann-Nissany

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