|
|
| (236 intermediate revisions not shown.) |
| Line 3: |
Line 3: |
| | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> | | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> |
| | | | |
| - | =='''Hemoglobin 1qxd'''== | + | =='''Structure of Oligonucleotide/Drug Complex (1xcs)<ref>PMID: 15926069 </ref>'''== |
| | + | by Michael Beauregard, Annie Burton, Jianlong Li, Daniel Marco, and Nathaneal Park |
| | | | |
| - | ===Introduction===
| + | [[Student Projects for UMass Chemistry 423 Spring 2016]] |
| - | <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align='right' caption='Polymerization of hemoglobin occurs when a mutant HbS molecule, in which the Glu6 residues have been replaced by a Val6 residue, binds to the another hemoglobin molecule at the region defined by Phe85 - Leu88.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'/> | + | <StructureSection load='1xcs' size='350' side='right' caption='This cancer-treating complex is formed by an anthraquinone drug that intercalates into DNA (PDB entry [[1xcs]])' scene='48/483883/Homecomplex/2'> |
| | | | |
| - | 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>
| + | ==Introduction== |
| | + | The intercalation of DNA and drug compounds has been studied thoroughly as a inhibitor of tumorigenesis or pathogenesis which is key in the progression of most cancers. Most intercalated ligands are aromatic compounds that bond <scene name='48/483883/1xcs_binding_site/3'>between base pairs</scene> through non-covalent interactions. In this case the nucleotide d(CGTACG) was complexed with an anthraquinone derivative. This derivative, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione, provided researchers with the information needed to solve <scene name='48/483883/Rainbow_sheet/1'>the structure of the complex</scene> using X-Ray crystallography. Along with the structure, the important forces involved in binding were analyzed and described as heavily reliant on cations. Furthermore, the binding site seems to be specific to anthracene and similar molecules. Therefore, the potential for drug compounds to be carried by this nucleotide complex requires further research with respect to binding affinity, solubility, toxicology, and specificity with other analogues. |
| | | | |
| | + | The 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione complex was studied using synchrotron radiation, which is the energy emitted from particles traveling near the speed of light, which identified ionic sites and areas of high electron density. The binding site of the drug compound is one of these high electron density areas, and was a key component in it's identification. The electron density mappings also provides insight on issues typical with the intercalation of aromatic ligands such as their degrees of freedom and the effect of counterions. The aromatic anthraquinone derivative ligand is disordered disordered in the binding site with two solvable positions which are 180 degree rotations of each other. With respect to the issue of ionic strength, DNA is a polyanion therefore positively charged counterions shielding the interactions between the DNA and the drug is worth noting. In the case of Na+, it has been resolved near the binding site of the drug. In short, this DNA/Anthraquinone derivative complex provides a potential anti-cancer drug and information about the role of positively charged ions in the intercalation of the drug compound. |
| | | | |
| - | 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>
| + | ==Overall Structure== |
| | | | |
| | + | The 1xcs (model at right) complex is a small, simple globular DNA-drug complex, and as such lacks any traditional protein-associated structures such as secondary beta sheets or alpha helices. The complex consists of two complimentary strands of DNA. A simplified model of 1xcs is shown <scene name='48/483883/Title/4'>here,</scene> with the nitrogenous bases removed for clarity. The deoxyribose backbones can be followed from 5' to 3' following along each strand from blue to red. Note that the strands are antiparallel where they are (hydrogen) bonded. <scene name='48/483883/1xcs_with_side_chains/2'>1xcs with its hydrogen bonding regions displayed (black)</scene> visualizes this bonding in the middle region of the complex, again following each strand from blue to red from 5' to 3' ends. |
| | | | |
| - | 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>. | + | The 1xcs complex also binds to metal ions in more than one location, which have been shown to be important to the drug's binding ability. Different metal ions may be present, including Na(+) and Co(2+). The main metal ions sites are colored pink in <scene name='48/483883/1xcs_with_pink_metal_ions/2'>this</scene> scene. One other metal binding site was noted, which had the ability to bind <scene name='48/483883/Barium_binding_site/1'>Ba(2+)</scene> (teal). This ability to strongly bind metal ions was also important for x-ray crystallographic purposes, as it enabled researchers to form crystals of the complex by relying on interactions between neighboring molecules' binding sites. It is also believed that the tight packing of the 1xcs complex in its solid form contributes to its ability to retain drug molecules (see "Binding Interactions"). |
| | | | |
| - | ===Overall Structure=== | + | ==Binding Interactions== |
| - | <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='' /> | + | There are three main locations where ion ligands bind to the oligonucleotide/drug complex. The key ligand is shown <scene name='48/483883/Annie_scene/1'>here</scene> in pink. Its function is to close the drug cavity, holding the anthraquinone derivative in place. It can be an Na(+), Mg(2+), or Ba(2+) ion. The two other ligands, shown in cyan bind four to five nucleotides away from the drug itself. Co(2+) ions were always present at these locations in this complex and in similar complexes. Complexes that did not contain Co(2+) did not diffract. Literature states that the variable ion gives strength to the binding of the Co(2+) ions. It may be reasoned that this interaction may also behave oppositely. The binding of the Co(2+) ions may strengthen the closure of the pocket containing the drug. Co(2+) and Ba(2+) ions were found in more locations that are not shown here because they only appeared sporadically and in differing locations. Therefore, they are probably not precisely important to the function of this drug complex. |
| | | | |
| - | 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>. | |
| - | <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. | |
| | | | |
| | + | ==Additional Features== |
| | + | In <scene name='48/483883/Mikescene/1'>this depiction</scene>, one can see that the anthraquinone derivative is located between the backbones and base pairs of DNA. The drug is squeezed or intercalated between the nucleotides <scene name='48/483883/Mikescene/3'>shown in red</scene>. In the human body, the <scene name='48/483883/Mikescene/2'>nucleotide in gold</scene> would also be interacting with the drug shown in black, but in order for this complex to be studied, a short segment of DNA had to be used. Consequently the gold nucleotide is involved in abnormal molecular interactions and is out of place. This intercalation interrupts the function of taq polymerase and telomerase.<ref>Human Telomerase Inhibition by Regioisomeric Disubstituted Amidoanthracene-9,10-diones |
| | + | Philip J. Perry,†, Anthony P. Reszka,†, Alexis A. Wood,†, Martin A. Read,†, Sharon M. Gowan,‡, Harvinder S. Dosanjh,†, John O. Trent,†,§, Terence C. Jenkins,†,‖, Lloyd R. Kelland,‡ and, and Stephen Neidle*,† |
| | + | Journal of Medicinal Chemistry 1998 41 (24), 4873-4884 |
| | + | DOI: 10.1021/jm981067o</ref> Taq polymerase is in part responsible for the replication of DNA and consequently, cell replication. Telomeres are repeating sections of non-coding DNA that protect the ends of coding sections of DNA from degradation. Each time a cell divides, telomeres shorten. Over time, telomeres shorten to the point of disappearance, causing DNA degradation and cell death. Telomerase builds up these protective sections of DNA. Cancer is characterized as an uncontrolled rate of cell growth. By inhibiting the replication of DNA and the construction of protective telomeres, this drug serves to slow and stop cancerous cell growth. |
| | | | |
| - | 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. | |
| | | | |
| | + | ==Quiz Question 1== |
| | + | This complex serves to interrupt two enzymes involved in cell replication: Taq polymerase and <scene name='48/483883/This_complex/1'>this enzyme</scene>. |
| | + | A. nuclease |
| | + | B. telomerase |
| | + | C. ligase |
| | + | D. topoisomerase |
| | | | |
| - | 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.
| + | ==See Also== |
| | + | *[[1bp8]] |
| | + | *[[1d3x]] |
| | + | *[[1p3x]] |
| | | | |
| | + | ==Credits== |
| | | | |
| - | 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.
| + | Introduction - Daniel Marco |
| | | | |
| - | ===Binding Interactions===
| + | Overall Structure - Nathaneal Park |
| - | <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='' />
| + | |
| | | | |
| - | 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>.
| + | Drug Binding Site - Annie Burton |
| | | | |
| - | 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.
| + | Additional Features - Michael Beauregard |
| | | | |
| - | 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.
| + | Quiz Question 1 - Jianlong Li |
| | | | |
| - | ===Additional Features===
| + | ==References== |
| - | <Structure load='1qxd' size='400' frame='true' align='left' caption='Hemoglobin polymerization' scene='' />
| + | <references/> |
| - | | + | |
| - | A hemoglobin polymer looks like this: http://www.rcsb.org/pdb/101/motm.do?momID=41
| + | |
| - | 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>
| + | |
| - | | + | |
| - | | + | |
| - | <scene name='Sandbox_Reserved_426/Polymerized_hemoglobin/1'>2Hbs Val6 interaction with hydrophobic patch</scene>
| + | |
| - | 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.
| + | |
| - | 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>
| + | |
| - | | + | |
| - | | + | |
| - | ===Credits===
| + | |
| - | | + | |
| - | Introduction - Ryan Colombo
| + | |
| - | | + | |
| - | Overall Structure - Will Yarr
| + | |
| - | | + | |
| - | Drug Binding Site - Jacqueline Pasek-Allen
| + | |
| - | | + | |
| - | Additional Features - Joey Nguyen
| + | |
| - | | + | |
| - | ===References===
| + | |
| - | <references> | + | |
by Michael Beauregard, Annie Burton, Jianlong Li, Daniel Marco, and Nathaneal Park
