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| | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> | | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> |
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| - | =='''Hemoglobin 1qxd'''== | + | |
| | + | =='''YourMacromolecule'''== |
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| | ===Introduction=== | | ===Introduction=== |
| - | <Structure load='1qxd' size='400' frame='true' align='right' caption='Polymerization of hemoglobin occurs when a mutant HbS molecule, in which the Glu6 residues have been replaced by a Val6 residue, binds to the another hemoglobin molecule at the region defined by Phe85 - Leu88. In other words, a hydrophobic interaction is formed between the Glu6 residue of one hemoglobin molecule, and the Phe85 - Leu88 region of another hemoglobin molecule' scene='Sandbox_Reserved_426/Hb_intro/1'/> | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
| - | | + | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> |
| - | Individuals with Sickle Cell Anemia, or Sickle Cell Disease, contain a mutated form of hemoglobin, the oxygen binding protein found in red blood cells. Mutated hemoglobin causes normal disk-shaped red blood cells to become sickle-shaped. These sickle cells are fragile, deliver less oxygen to the body's tissues, and clog small blood vessels and capillaries, which results in a variety of adverse symptoms and detrimental complications. Some of these symptoms include abdominal and bone pain, breathlessness, fatigue, and rapid heart rate. Over time, irreversible tissue damage leads to the failure of many organ systems.<ref>Geller AK, O'Connor MK. The sickle cell crisis: a dilemma in pain relief. Mayo Clin Proc. 2008;83:320-323.</ref>
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| - | Sickle Cell Disease results from a single point mutation in the Hemoglobin amino acid sequence. Normal Hb contains hydrophilic <span style="color:lime">'''Glu6'''</span> residues in the 2 beta strands, shown <scene name='Sandbox_Reserved_426/Glu6_residue_of_hb/5'>here</scene>, whereas in HbS, these residues have been changed to hydrophobic Val6. The mutation region of one HbS molecule will then bind to a region defined by <span style="color:magenta">'''β Phe85, βAla86, βThr87, β Leu88'''</span> in the Heme pocket of another HbS molecule via noncovalent hydrophobic interactions.<scene name='Sandbox_Reserved_426/Phe85_-_leu88/5'>Hydrophobic Binding Region</scene>. The subsequent polymerization of HbS molecules leads to the sickling of red blood cells. <ref> Safo MK, Abdulmalik O, Danso-Danquah R, Burnett JC, Nokuri S, Joshi GS, Musayev FN, Asakura T, Abraham DJ. Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds. J Med Chem. 2004 Sep 9;47(19):4665-76. PMID:15341482 doi:10.1021/jm0498001</ref>
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| - | The cooperative binding of oxygen leads to a conformation change in hemoglobin from the tense, or T state, to the R, or relaxed state. Recently, studies have shown that multiple relaxed Hb conformers exist, such as the R2, RR2, and R3 states.<ref> Shibayama N, Sugiyama K, Park SY. Structures and oxygen affinities of crystalline human hemoglobin C (β6 Glu->Lys) in the R and R2 quaternary structures.J Biol Chem. 2011 Sep 23;286(38):33661-8.</ref> It has been proven that sickling only occurs with the deoxygenated T-state Hb, and it is therefore desirable to explore ways in which allosteric equilibrium can be shifted toward the oxygenated R-state conformations. Compounds that achieve such an equilibrium shift are being sought. Vanillin, a food flavoring compound, as well as the furanic aldehyde compounds 5-hydroxymethyl-2-furfural (5HMF), 5-methyl-2-furfural (5MF), 5-ethyl-furfural (5EF), and furfural (FUF) all exhibit such antisickling properties and are nontoxic to humans. These compounds are therefore promising candidates for potential SCD drug treatments. Of the compounds studied, 5HMF was the most potent, shifting the oxygen equilibrium curve to the left by over 25 mmHg. Additionally, an equilibrium shift of approximately 16 mmHG was observed in FUF. It will later be seen that these compounds bind and stabilize the R2 conformation.<ref> Safo MK, Abdulmalik O, Danso-Danquah R, Burnett JC, Nokuri S, Joshi GS, Musayev FN, Asakura T, Abraham DJ. Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds. J Med Chem. 2004 Sep 9;47(19):4665-76. PMID:15341482 doi:10.1021/jm0498001</ref>.
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| | ===Overall Structure=== | | ===Overall Structure=== |
| - | <Structure load='1qxd' size='400' frame='true' align='left' caption='Hemoglobin is a tetramer of two types of globular subunits: Alpha Chains, shown initially in Blue and Pink, and Beta Chains, shown in Yellow and Green' scene='' /> | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, insert caption here' scene='Sandbox_Reserved_430/Intra-strand_phosphate/1' /> |
| - | | + | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> |
| - | Ordinary human hemoglobin is a tetramer of globular protein subunits: two <span style="color:orange">'''α chains'''</span> and two <span style="color:lightgreen">'''β chains'''</span>.
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| - | <scene name='Sandbox_Reserved_426/A_and_b_chains/1'>α and β Subunits</scene> Both the α and β subunits are identical, and form two identical αβ dimers, which in turn form a dimer to create the complete structure of hemoglobin. | + | |
| - | <scene name='Sandbox_Reserved_426/Ab_dimers/3'>αβ Dimers</scene> Each of the subunits consists largely of alpha helices, with 8 in both the α and β chains and short, non-helical residue sequences binding them. In total, each α chain contains 141 residues, and each β chain contains 146. | + | |
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| - | Hemoglobin can exist in two possible conformations of its quaternary structure, depending on whether it is bound to oxygen. The state shown in our green scenes is the T-state (tense state), so named because it's structure is constrained by interactions between subunits. The fully oxygenated state is known as the R-state (relaxed state), as the binding of oxygen results in a 15 degree rotation between the two αβ dimers, thus disrupting many subunit interactions.
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| - | The structure of sickle hemoglobin is identical to that of healthy hemoglobin, save for the substitution of a single residue within the β chains. The sixth residue in each chain, a glutamic acid, has been changed to a valine, resulting from a single point mutation. This mutation doesn't actually lead to any interference with the bonding interactions that lend hemoglobin its quaternary structure, and doesn't lead to structural changes within the hemoglobin or the β chain. It does, however, allow for hydrophobic interactions between separate hemoglobin proteins, leading to the polymerization of Hb molecules that causes sickling.
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| - | Each of the four globular domains within hemoglobin contains a heme group, the non-protein components that allow hemoglobin to bind to oxygen. Each heme group consists of an iron ion bound within four cyclically bonded pyrrole molecules, referred to as a whole as a porphyrin ring. Each pyrrole molecule consists of a heterocyclic ring of four carbons and one nitrogen, with the nitrogen from each ring bound to the Fe ion at the heme group's center. <scene name='Sandbox_Reserved_426/Heme_a1/2'>α1 Heme Group</scene> Each heme group is anchored in place in its respective subunit primarily by a histidine sidechain; a nitrogen atom in the imidazole ring on the sidechain anchors to the iron ion in the heme group, and the propanoate groups attached to the porphyrin ring are held in place by hydrophobic interaction with the hydrophobic residues within the subunit.
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| | ===Binding Interactions=== | | ===Binding Interactions=== |
| - | <Structure load='1qxd' size='400' frame='true' align='right' caption='Binding of 5HMF involves 6 water-mediated hydrogen bonds that link the 2 alpha chains together, stabilizing the R2 Hb conformation' scene='' /> | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
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| - | The binding interactions of two of the four aforementioned heterocyclic aldehydes, <scene name='Sandbox_Reserved_426/Fuf_basic/2'>furfural</scene> (<span style="color:magenta">'''FUF'''</span>) and <scene name='Sandbox_Reserved_426/5hmf_alone/4'>5-hydroxymethyl-2-furfural</scene> (<span style="color:royalblue">'''5HMF'''</span>), were investigated. Both bind to the <span style="color:yellowgreen">'''N-terminal αVal1 residues'''</span> in the α cleft (two binding sites, since hemoglobin is a tetramer with two α chains)<scene name='Sandbox_Reserved_426/Furfural_binding/1'></scene>.
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| - | A covalent bond is formed between the ligand aldehyde and the Val1 nitrogen. <scene name='Sandbox_Reserved_426/Fuf_bound/1'>FUF binding to alpha Val1 </scene>. Furfural can assume two different conformations when compelxed with Hemoglobin. In one conformer, the ring oxygen faces the α2Ser138 residue and forms a weak intersubunit hydrogen bond with this moiety. In the second conformer, the ring oxygen faces the water cavity, and forms a weak hydrogen bond with <span style="color:cadetblue">'''α1Ser131'''</span>. <scene name='Sandbox_Reserved_426/Fuf_hb_edited/3'>The second conformer</scene>, in which the the ring oxygen is facing the water cavity. Notice that the furfural molecule bound to the α2 chain is interacting with the <span style="color:deepskyblue">'''α1Ser131'''</span> residue via water-mediated hydrogen bonds, thus linking the α1 and α2 chains together. Weak hydrophobic interactions are also formed between the furan ring and <span style="color:indianred">'''Lys127'''</span> and <span style="color:burlywood">'''Ala130'''</span> residues on the same chain. For simplicity, interactions involving only one of the furfural molecules is depicted, as those involving the other furfural are identical.
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| - | Unlike FUF, <scene name='Sandbox_Reserved_426/5hmf_bound_val1/4'>5HMF bound to alpha Val1</scene> cannot rotate within the α cleft and thus assumes only a single conformation, in which the ring oxygen faces the water cavity. Also, 5HMF cannot form a hydrogen bond with α2Ser138, as does FUF in one of its conformations. 5HMF does form an intrasubunit hydrogen bond with <span style="color:deepskyblue">'''α1Ser131'''</span> that is stronger than that formed by FUF. In addition, the 5-hydroxymethyl group of 5HMF forms a strong intrasubunit hydrogen bond with the <span style="color:lime">'''α1Thr134'''</span> residue. As mentioned before, FUF linked together the two α chains via hydrogen bonds with Ser131. When 5HMF is bound, this feat is accomplished by a strong network of 6 water-mediated hydrogen bonds via the ring oxygens and hydroxyl groups between the two 5HMF molecules. <scene name='Sandbox_Reserved_426/5hmf_-_hb_binding_interactions/4'>5HMF molecule bound</scene> to the α1 chain forming these interactions.
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| | ===Additional Features=== | | ===Additional Features=== |
| - | <Structure load='1qxd' size='400' frame='true' align='left' caption='Hemoglobin polymerization' scene='' /> | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
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| - | A hemoglobin polymer looks like this: http://www.rcsb.org/pdb/101/motm.do?momID=41
| + | ===Quiz Question 1=== |
| - | The polymer shows how sickle cell hemoglobin looks when polymerized and the picture also shows where the mutation of replacing a Glu6 residue with Val6 occurs in the structure. <ref>Dutta, Shuchismita; Goodsell, David, May 2003, Hemoglobin. RCSB Protein Data Bank http://www.rcsb.org/pdb/101/motm.do?momID=41, 2012.</ref>
| + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
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| | + | ===Quiz Question 2=== |
| | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
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| - | <scene name='Sandbox_Reserved_426/Polymerized_hemoglobin/1'>2Hbs Val6 interaction with hydrophobic patch</scene>
| + | ===Credits=== |
| - | As discussed earlier in the introduction section, normal Hb contains a hydrophilic Glu6 residues in the 2 beta strands, whereas in HbS, these residues have been changed to hydrophobic <span style="color:darkgreen">'''Val6'''</span>. In normal Hb, the hydrophillic negatively charged Glu6 residues do not interact with the hydrophobic <span style="color:crimson">'''Ala86'''</span>, <span style="color:navy">'''Phe85'''</span>, <span style="color:darkviolet">'''Thr87'''</span>, and <span style="color:peru">'''Leu88'''</span> residues. This ensures that hemoglobin does not polymerize.
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| - | The contrast happens in sickle-cell hemoglobin. Since in sickle-cell hemoglobin Glu6 is mutated and is replaced with Val6, hydrophobic interactions occurs with <span style="color:darkgreen">'''val6'''</span> and <span style="color:crimson">'''Ala86'''</span>, <span style="color:navy">'''Phe85'''</span>, <span style="color:darkviolet">'''Thr87'''</span>, and <span style="color:peru">'''Leu88'''</span> residues. The reason for this is because valine, leucine, phenylalanine, threonine, and alanine are all hydrophobic due to their non-polar attributes. <span style="color:darkgreen">'''Val6'''</span> from one hemoglobin interacts with the hydrophobic patch formed by <span style="color:crimson">'''Ala86'''</span>, <span style="color:navy">'''Phe85'''</span>, <span style="color:darkviolet">'''Thr87'''</span>, and <span style="color:peru">'''Leu88'''</span> residues of another deoxygenated form of hemoglobin leads to polymerization of hemoglobin under low oxygen conditions.<ref>Harrington DJ, Adachi K, Royer WE Jr. The high resolution crystal structure of deoxyhemoglobin S. J Mol Biol. 1997 Sep 26;272(3):398-407. PMID:9325099 doi:10.1006/jmbi.1997.1253</ref>
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| | + | Introduction - name of team member |
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| - | ===Credits===
| + | Overall Structure - name of team member |
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| - | Introduction - Ryan Colombo
| + | Drug Binding Site - name of team member |
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| - | Overall Structure - Will Yarr
| + | Additional Features - name of team member |
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| - | Drug Binding Site - Jacqueline Pasek-Allen
| + | Quiz Question 1 - name of team member |
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| - | Additional Features - Joey Nguyen
| + | Quiz Question 2 - name of team member |
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| | ===References=== | | ===References=== |
| - | <references> | + | <references/> |
