Sandbox GGC12

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==Crystal Structure of Fab12==
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== Human Serum Albumin==
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<StructureSection load='3ULS' size='340' side='right' caption='Crystal Structure of Fab12' scene=''>
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<StructureSection load='1AO6' size='340' side='right' caption='Serum Albumin Protein' scene='78/781196/00_green_cartoon/1'>
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Toll-like Receptors are a part of a family of proteins that consist of ten type 1 transmembrane receptor proteins in human beings. Toll-like Receptor 11 is active in mice with a response to unropathogenic bacteria has been described as not functional in humans. Toll-like receptors that have evolved and are expressed in insects and higher animals. Toll-like receptor proteins mainly have two functional regions. The extracellular domain consists of leucine-rich repeats and one or two cysteine-rich regions that are recognized as an array of microbial components that include sugars, proteins, lipids, DNA motifs, and double-stranded RNA. The intracellular region does consist of a Toll/IL-1 receptor domain, which are like the intracellular domain of the IL-1 receptor. The Toll/IL-1 receptor domain it provides an intracellular scaffold their interacts with several adapter proteins that will initiate and integration as a well-defined signaling cascades resulting in a cellular activation, and the production of a number of cytokines and chemokines <ref>DOI 10.1016/B978-O7216-3695-5.50016-X</ref> or to the article describing Jmol <ref>PMID:22579623</ref> to the rescue.
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Human serum albumin or HSA is one of the major types of proteins that are present in the plasma composition. It is such abundant that its concentration on a common blood sample is 5 grams per 100 milliliters. Due to its high concentration in plasma as well as its physiological and pharmaceutical features, it has been subjected to several studies to determine its 3D structure, function, domains, important binding sites, and diseases. The primary structure of HSA describes a single polypeptide with 585 amino acids with the characteristics of having 17 pairs of disulfide bridges, one free cysteine <ref>PMID: 6275391</ref>. It has been discovered that there are highly conserved sequences between bovine, human and rat albumins such as Trp-212, 143-155 and 244-263 sequence <ref>PMID: 6192439</ref>. It is composed of three domains at positions 19-210, 211-403, and 404-601 with two subdomains each (Ia&b, IIa&b, and IIIa&b). The subcellular location of these protein is the extracellular region on the outside of the cell membrane or secreted. There are 11 metal binding sites, including 1 copper site, 7 calcium sites, 3 zinc sites, additionally, 1 binding site for bilirubin and 1 site for aspirin-acetylated lysine <ref>PMID: 10388840</ref>.
== Function ==
== Function ==
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Controls the host immune response system against any pathogens through the recognition of molecular patterns tahat are specific to each microorganism. TLR3 is a nuclear-sensing TLR which is going to be essentially activated by a double-stranded RNA, which is a sign of a viral infection. Acts via the adapter TRIF/TICAM1, that leads to a NF-kappa-B activation, IRF3 nuclear translocation, cytokine secretion and the inflammatory response <ref>PMID:12471095</ref>.
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HSA functions as the essential protein for the circulatory system, however, it has been discovered that possesses a high affinity an extensive range of amino acids, ligands, fatty acids, metals like copper and zinc, and metabolites such as bilirubin and drugs ingredients <ref>PMID: 10388840</ref>.Its fundamental role is to transport these varied types of solutes through the bloodstream to specific organs, control the level of pH and osmotic pressure of the plasma, and interaction with the cell membrane exchange of molecules at binding sites <ref>PMID: 3548415</ref>. It is considered to be the vital carrier of zinc in the plasma as well as the calcium and magnesium. In terms of affinity, the order from higher to lower affinity follows this pattern: zinc, calcium and magnesium <ref>PMID:19021548</ref>. Pharmaceutically, it has been used to target certain organs with some drugs by HSA being the carrier. By performing experiments on E.coli, it was discovered that it inhibits enterobactin-mediated iron absorption from ferric transferrin due to its binding to the bacterial siderophore limiting the uptake of iron, and consequently, blocking the growth of E.coli <ref>PMID: 6234017</ref>.
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== Disease ==
== Disease ==
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A rare complication of human herpesvirus 1 (HHV-1) infection, it occurs in only a small minority of HHV-1 infected individuals. There are characterized by a hemorrhagic necrosis of parts from both the temporal and frontal lobes. One of the onsets are that it invloves several days of fear, headache, seizures, stupor, and often coma, frequently with a fatal outcome <ref>PMID:17872438</ref>.
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HSA is involved in two important diseases, Hyperthyroxinemia, familial dysalbuminemic (FDAH) and Analbuminemia (ANALBA).
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== Relevance ==
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TRIF pathway
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Various of the pathogens do target the signaling molecules and transcriptional regulators which are acting in the TRIF pathway, it goes on to demonstrate the main importance of this particular pathway which contributes to control of both viral and bacterial pathogens through a promotion of the inflammatory mediators and activators of antimicrobial responses. TRIF signaling also has both protective and pathologic roles in several chronic inflammatory disease conditions, as well as an essential function in wound‐repair processes <ref>DOI 10.1189/jlb.2RI1115-531R</ref>.
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First, FDAH is a condition based on the genetic composition of the individual. It is caused by a mutation in the ALB gene, which corresponds to an increased affinity of the protein HSA for thyroxine. In detail, this autosomal dominant genetic disorder is characterized by the mutation of HSA causing the assembly of thyroxine in a higher proportion. There are two positions with three natural variants identified on the HSA that mutate to cause this disorder. The first position (red) is at 90 amino acid, where leucine is replaced by a proline. The second position (green) at 242 amino acid, where arginine is substituted by histidine or proline <scene name='78/781196/Hyperthyroxinemia/1'>3D View</scene>. This disorder could lead to confusion and several misdiagnoses of hyperthyroidism because it is difficult to detect it due to the normal TSH and free thyroxine levels but with an elevated total of thyroxine <ref>PMID: 32665066</ref>.
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TICAM1
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Second, ANALBA is an uncommon autosomal recessive genetic mutation characterized by the identification of very low levels of HSA circulating in the bloodstream <ref>PMID: 8134387</ref>. The affected individuals have symptoms corresponding to mild edema, hypotension, fatigue, and lower body lipodystrophy in females. The mutagenesis is located in the position 91 where histidine is replaced by alanine impairing metal binding <ref>PMID: 28567254</ref>. The complications of this disorder could lead to early atherosclerosis and heart problems.
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It is involved in an innate immunity against invading pathogens. The main adapter used by TLR3, TLR4 (through TICAM2) and TLR5 to mediate the NF-kappa-B and interferon-regulatory factor (IRF) activation, and they go on to induce apoptosis. Ligand binding for these receptors would result in TRIF recruitment through its TIR domain. It is a quite distinct protein-interaction motif which allows a recruitment of the effector proteins TBK1, TRAF6 and RIPK1, which in turn, leads to the activation of transcription factors IRF3 and IRF7, NF-kappa-B and FADD respectively. Phosphorylation by TBK1 on the pLxIS motif will lead to recruitments and subsequent activation of the transcription factor IRF3 to induce expression of type I interferon and exert a potent immunity against invading pathogens. With the component of a multi-helicase-TICAM1 complex which will act as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and it plays a significant role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines. Ubiquitously expressed but with higher levels in liver <ref>DOI 10.1016/j.jmb.2013.11.024</ref>.
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== Relevance ==
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The relevance of this protein, HSA, relies on the its capacity to transports molecules through out the bloodstream. It helps move substances such as metals, amino acids, drugs, fatty acids to every part of the body because it is a protein present in the blood that flows around the body. It is a significant protein because it allows us to use it pharmaceutically to target certain organs with specific drugs. Additionally, it is essential for the control of the levels of pH and the osmotic pressure in the plasma. And finally, it is a protein that allows the cell membrane interact with the outer space of the cell by the help of HSA in the targeting of binding sites.
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IRF3
 
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Transcriptional regulator of type I interferon (IFN)-dependent immune responses which plays a critical role with the innate immune response against DNA and RNA viruses. It will occssionally regulate the transcription of type I IFN genes (IFN-alpha and IFN-beta) and IFN-stimulated genes (ISG) by binding to an interferon-stimulated response element (ISRE) with their promoters. It would act as a more potent activator of the IFN-beta (IFNB) gene than the IFN-alpha (IFNA) gene and plays a critical and significant role in both the early and late phases of the IFNA/B gene induction. There are going to be found in an inactive form within the cytoplasm of uninfected cells and following the viral infection, double-stranded RNA (dsRNA), or toll-like receptor (TLR) signaling, is going to be phosphorylated by IKBKE and TBK1 kinases. There are going to induce a conformational change, leading to its dimerization and nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of the type I IFN and ISG genes. Can activate distinct gene expression programs in macrophages and can induce significant apoptosis in primary macrophages <ref>DOI 10.1038/nri3581</ref> <ref>DOI 10.1016/j.coviro.2011.11.001</ref>.
 
== Structural highlights ==
== Structural highlights ==
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The structural highlights of this protein are four: the three domains that compose the protein, the binding site in domain II for salicylates, sulfonamides and several drug ingredients, the bilirubin binding site at position 264, and the free cysteine in the structure of the protein <ref> PMID: 32162429</ref>.
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. <scene name='78/781196/Sec_structure/2'>This shows the secondary structure</scene> of Crystal Structure of Fab12. Here is a <scene name='78/781196/Ser212/10'>Zoomed in view</scene>name='78/781196/Ser212/2'>Zoomed out view</scene><scene name='78/781196/Ser212/1'>This is Ser212</scene> which is important
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This is the structural view of <scene name='78/781196/3domains/1'>the three domains</scene> by different colors. Digitoxin, cardiac glycoside, could bind domain I for cardiac insufficiency, warfarin, anticouagulant, bind primarily in domain II, and the diazapines like benzodiazapine, muscular relaxor, in domain III. The shared binding site in domain II between zinc and calcium at residue <scene name='78/781196/273_asp/2'>Asp 273</scene> suggests a crosstalk between zinc and calcium transport in the blood. The <scene name='78/781196/264_bili/1'>bilirubin</scene> binding site at position 264, which is significant because it possess important functions as an antioxidant, but it also serves simply as a means to excrete unwanted heme, derived from various heme-containing proteins such as hemoglobin, myoglobin, and various P450 enzymes. <scene name='78/781196/Cys34/1'>Cys 34</scene> located in a loop between helice is the only cysteine residue that does not participate in any disulfide bridges. Its sulfhydryl group is prevented from coupling with the external counterparts giving a structure known as triclinic crystals. Sequence 143 through 155 and sequence 244 through 263 are involved in ligand binding. For example, residues <scene name='78/781196/Sequence/1'>143-155</scene>, an aromatic sequence, corresponds with the region of the second major long-chain fatty acid binding site <ref>PMID: 2155760</ref>.
</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Current revision

Human Serum Albumin

Serum Albumin Protein

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References

  1. Dugaiczyk A, Law SW, Dennison OE. Nucleotide sequence and the encoded amino acids of human serum albumin mRNA. Proc Natl Acad Sci U S A. 1982 Jan;79(1):71-5. PMID:6275391
  2. Morinaga T, Sakai M, Wegmann TG, Tamaoki T. Primary structures of human alpha-fetoprotein and its mRNA. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4604-8. PMID:6192439
  3. Sugio S, Kashima A, Mochizuki S, Noda M, Kobayashi K. Crystal structure of human serum albumin at 2.5 A resolution. Protein Eng. 1999 Jun;12(6):439-46. PMID:10388840
  4. Sugio S, Kashima A, Mochizuki S, Noda M, Kobayashi K. Crystal structure of human serum albumin at 2.5 A resolution. Protein Eng. 1999 Jun;12(6):439-46. PMID:10388840
  5. Pardridge WM. Plasma protein-mediated transport of steroid and thyroid hormones. Am J Physiol. 1987 Feb;252(2 Pt 1):E157-64. doi: 10.1152/ajpendo.1987.252.2.E157. PMID:3548415 doi:http://dx.doi.org/10.1152/ajpendo.1987.252.2.E157
  6. Lu J, Stewart AJ, Sadler PJ, Pinheiro TJ, Blindauer CA. Albumin as a zinc carrier: properties of its high-affinity zinc-binding site. Biochem Soc Trans. 2008 Dec;36(Pt 6):1317-21. doi: 10.1042/BST0361317. PMID:19021548 doi:10.1042/BST0361317
  7. Konopka K, Neilands JB. Effect of serum albumin on siderophore-mediated utilization of transferrin iron. Biochemistry. 1984 May 8;23(10):2122-7. doi: 10.1021/bi00305a003. PMID:6234017 doi:http://dx.doi.org/10.1021/bi00305a003
  8. Lai S, Gopalakrishnan G, Li J, Liu X, Chen Y, Wen Y, Zhang S, Huang B, Phornphutkul C, Liu S, Kuang J. Familial Dysalbuminemic Hyperthyroxinemia (FDH), Albumin Gene Variant (R218S), and Risk of Miscarriages in Offspring. Am J Med Sci. 2020 Nov;360(5):566-574. doi: 10.1016/j.amjms.2020.05.035. Epub, 2020 May 28. PMID:32665066 doi:http://dx.doi.org/10.1016/j.amjms.2020.05.035
  9. Watkins S, Madison J, Galliano M, Minchiotti L, Putnam FW. A nucleotide insertion and frameshift cause analbuminemia in an Italian family. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2275-9. doi: 10.1073/pnas.91.6.2275. PMID:8134387 doi:http://dx.doi.org/10.1073/pnas.91.6.2275
  10. Handing KB, Shabalin IG, Kassaar O, Khazaipoul S, Blindauer CA, Stewart AJ, Chruszcz M, Minor W. Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins. Chem Sci. 2016 Nov 1;7(11):6635-6648. doi: 10.1039/c6sc02267g. Epub 2016 Aug 15. PMID:28567254 doi:http://dx.doi.org/10.1039/c6sc02267g
  11. Wenskowsky L, Wagner M, Reusch J, Schreuder H, Matter H, Opatz T, Petry SM. Resolving Binding Events on the Multifunctional Human Serum Albumin. ChemMedChem. 2020 Mar 11. doi: 10.1002/cmdc.202000069. PMID:32162429 doi:http://dx.doi.org/10.1002/cmdc.202000069
  12. Kragh-Hansen U. Structure and ligand binding properties of human serum albumin. Dan Med Bull. 1990 Feb;37(1):57-84. PMID:2155760
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