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| - | {{Seed}}
| + | __NOTOC__ |
| - | [[Image:1zds.png|left|200px]] | + | [[Image:1n70.png|left|200px]] |
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| | <!-- | | <!-- |
| - | The line below this paragraph, containing "STRUCTURE_1zds", creates the "Structure Box" on the page. | + | The line below this paragraph, containing "STRUCTURE_1n70", creates the "Structure Box" on the page. |
| | You may change the PDB parameter (which sets the PDB file loaded into the applet) | | You may change the PDB parameter (which sets the PDB file loaded into the applet) |
| | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), |
| | or leave the SCENE parameter empty for the default display. | | or leave the SCENE parameter empty for the default display. |
| | --> | | --> |
| - | {{STRUCTURE_1zds| PDB=1zds | SCENE= }} | + | {{STRUCTURE_1n70| PDB=1n70 | SCENE= }} |
| | | | |
| - | ===Crystal Structure of Met150Gly AfNiR with Acetamide Bound=== | + | ===The Crystal Structure of Nitrite Reductase Mutant His287Ala from Rhodobacter Sphaeroides=== |
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| - | <!-- | |
| - | The line below this paragraph, {{ABSTRACT_PUBMED_16574144}}, adds the Publication Abstract to the page | |
| - | (as it appears on PubMed at http://www.pubmed.gov), where 16574144 is the PubMed ID number. | |
| - | --> | |
| - | {{ABSTRACT_PUBMED_16574144}} | |
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| | ==About this Structure== | | ==About this Structure== |
| - | 1ZDS is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDS OCA].
| + | 1N70 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N70 OCA]. |
| - | | + | [[Category: Rhodobacter sphaeroides]] |
| - | ==Reference==
| + | [[Category: Guo, H.]] |
| - | <ref group="xtra">PMID:16574144</ref><references group="xtra"/>
| + | [[Category: Olesen, K.]] |
| - | [[Category: Alcaligenes faecalis]] | + | [[Category: Shapliegh, J.]] |
| - | [[Category: Alexandre, M.]] | + | [[Category: Sjolin, L.]] |
| - | [[Category: Canters, G W.]] | + | [[Category: Crystal structure]] |
| - | [[Category: Diederix, R E.M.]] | + | [[Category: Electron transfer]] |
| - | [[Category: MacPherson, I S.]] | + | [[Category: Mutant h287a]] |
| - | [[Category: Murphy, M E.P.]] | + | [[Category: Nitrite oxide]] |
| - | [[Category: Verbeet, M P.]] | + | [[Category: Nitrite reductase]] |
| - | [[Category: Wijma, H J.]] | + | |
| - | [[Category: Metal-binding]] | + | |
| - | [[Category: Nitrate assimiliation]] | + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:39:37 2009''
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| - | cene> identical gray, red, blue and orange colored, made-of-balls elements. Let's take a closer look to <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_bio/6'>one</scene> of them. This is the ''''heme'''' group, the functional unit of hemoglobin.
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| - | ''WAIT'': are those the true colors of the heme group? Not really. We are looking at a representation of the real structure, artificially colored following the [[CPK|Corey-Pauling-Koltun]] scheme ( {{Template:ColorKey_Element_C}}
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| - | {{Template:ColorKey_Element_H}}
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| - | {{Template:ColorKey_Element_O}}
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| - | {{Template:ColorKey_Element_N}}
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| - | {{Template:ColorKey_Element_S}}
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| - | {{Template:ColorKey_Element_Fe}} ). ''Remember'': these are artificial representations, using colors, textures, styles and forms chosen with the purpose of helping us to better understand the reality in its rich spacial configuration.
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| - | This model of the heme group is represented here in a
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| - | <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_hem_styles/1'>spacefill</scene> mode, but we can also draw it as
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| - | <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_hem_styles/2'>ball and sticks</scene>, maintaining always the same spacial structure and color coded information.
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| - | | + | |
| - | =====Capturing Oxygen and other molecules ...=====
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| - | The "heart" of the hemoglobin is the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme_deoxy/2'>heme</scene> group which is a flat ring molecule containing {{Template:ColorKey_Element_C}}arbon, {{Template:ColorKey_Element_N}}itrogen and {{Template:ColorKey_Element_H}}ydrogen atoms, with a single <font color="#E06633">Fe2+</font> ion at the center. In a heme molecule, the iron is held within the flat plane by four nitrogen ligands from that ring (rotate the structure with your mouse to see the flat plane from its side). <!-- The iron ion makes a fifth bond to a histidine side chain from one of polypeptide chain that forms the heme pocket. --> In the proper conditions, an oxygen molecule gets
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| - | <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>attached to the Fe</scene> in the heme group. ''OBSERVE'' Are there other changes besides the oxygen being attached to the Fe?
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| - | We can watch the capturing of an oxygen molecule in the context of a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/2'>protein single chain</scene> or on a close-up view of the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>isolated Heme</scene> group. {{Template:Button Toggle Animation2}}
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| - | And now is when things get interesting. The hem group has the chemical and structural capabilities to capture an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/O2/1'>oxygen</scene> molecule, which happens to be too close to the general shape of a molecule of <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Co/1'>carbon monoxide</scene>, which binds hemoglobin about 240 times faster and better than oxygen, meaning that if both gases are available, hemoglobin will prefer CO over O2. ''THINK'': Can you imagine what will happen if by accident we breathe in a carbon monoxide rich atmosphere?
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| - | =====The whole molecule=====
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| - | Let's go back and take a look to the whole picture. Do you remember the four '''heme''' groups in a ribbon-like structure we noticed at the beginning?. This is because the biological active molecule of hemoglobin is a ''tetramer'', this is, a polymer comprising four monomer units: two alpha chains, each with 141 amino acids and two beta chains, each with 146 amino acids. The protein of each of these chains is called ''globin''.
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| - | ===Sickle-cell disease===
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| - | Sickle hemoglobin differs from normal hemoglobin by a single amino acid: valine (hydrophobic) replaces glutamate (hydrophilic) at position 6 on the surface of the beta chain. This creates an hydrophobic spot. ''THINK'': Why a simple additional hydrophobic spot (actually two spots in the structure ''WHY?''), generated by the change of a single amino acid on a protein with over 500 amino acids becomes so problematic?
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| - | <applet load='1hbs' size='300' frame='true' align='right' caption='' scene='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_one_protein/4'/>
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| - | On the right, we can see the structure of a deoxygenated hemoglobin, this is, an hemoglobin shortly after releasing the load of oxygen. We can distinguish it's four chains (by it's artificial colors) and the four heme groups with no oxygen attached. This time, the representation is of style ''spacefill'', which is Ok because you know by now that representations are only a different way of drawing a real structure that we can't see.
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| - | Both normal and sickle hemoglobin, when in deoxygenated state, have an
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| - | <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Dexygenated_hemoglobin/3'>hydrophobic spot</scene> (colored white here)
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| - | on the beta chains. Two beta chains = two hydrophobic spots on the dehydrogenated hemoglobin. ''WATCH'': Can you find the spots on the two chains?.
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| - | The <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin/1'>hydrophobic spot</scene> present on Sickle hemoglobin sticks to the hydrophobic spot present on dehydrogenized hemoglobin, causing hemoglobin molecules to
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| - | <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain/1'>aggregate</scene> into chains forming long fibers.
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| - | A <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Sickle_hemoglobin_chain_close/1'>closer look</scene>
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| - | shows us that Alanine and Leucine from one molecule attract the Valine from another, chaining the two hemoglobin molecules together.
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| - | {{Clear}}
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| - | ==Content advisors==
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| - | This lesson plan was developed together with Dr. Dvora Cohen, Biology Teacher and Dr Mira Kipnis, Chemistry Teacher, both from the Davidson Institute of Science Education, Weizmann Institute of Science. This page include scenes, structures and ideas from [[User:Eric_Martz|Eric Martz]], [[User:Frieda S. Reichsman|Frieda S. Reichsman]] and [[User:Angel_Herraez|Angel Herraez]].
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