User:Yunlong Zhao/Sandbox 1: Difference between revisions

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==Introduction==

~~Antithrombin~~ and ~~thrombin interactions play~~ an ~~important role~~ in ~~multiple functions~~. ~~Interestingly~~, an heparin ~~or polysaccharides~~ can ~~regulate~~ the ~~function of~~ antithrombin to ~~different signaling.~~ <ref>~~DOI 10.1021/bi034524y~~</ref>

Heparin is often identified as a proteoglycan, in which heparin or heparin sulfate associates with other proteins in a strong intrinsic affinity. It has also been found that HS chains are usually localized on the surface of cells and the complex with matrix proteins. This interesting discovery suggests that HS usually exists as an “immobile phase” attaching antithrombin and activates its function as an anticoagulant factor in the circulation system. In an anticoagulant process, antithrombin needs to bind to some coagulant proteases such as Factor Xa or thrombin and “neutralizes” their activity. There are several hypotheses to explain how the heparin chains activate this process. A simple model is that a long heparin chain could be a scaffold to improve the possibility of antithrombin contacting with other proteins <ref>PMCID: PMC1153400</ref>. Another direct model is that specific sulfate-containing heparin fragments (oligosaccharides) can allosterically enhance the binding affinity between antithrombin and thrombin or Factor Xa. We are going to describe the structural basis of the second model in the rest of contexts <ref>PMID:1618758</ref>.

== Heparin Binding site on antithrombin ==

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 ==Introduction==
 <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
-Antithrombin and thrombin interactions play an important role in multiple functions. Interestingly, an heparin or polysaccharides can regulate the function of antithrombin to different signaling. <ref>DOI 10.1021/bi034524y</ref>
+Heparin is often identified as a proteoglycan, in which heparin or heparin sulfate associates with other proteins in a strong intrinsic affinity. It has also been found that HS chains are usually localized on the surface of cells and the complex with matrix proteins. This interesting discovery suggests that HS usually exists as an “immobile phase” attaching antithrombin and activates its function as an anticoagulant factor in the circulation system. In an anticoagulant process, antithrombin needs to bind to some coagulant proteases such as Factor Xa or thrombin and “neutralizes” their activity. There are several hypotheses to explain how the heparin chains activate this process. A simple model is that a long heparin chain could be a scaffold to improve the possibility of antithrombin contacting with other proteins <ref>PMCID: PMC1153400</ref>. Another direct model is that specific sulfate-containing heparin fragments (oligosaccharides) can allosterically enhance the binding affinity between antithrombin and thrombin or Factor Xa. We are going to describe the structural basis of the second model in the rest of contexts <ref>PMID:1618758</ref>.
 == Heparin Binding site on antithrombin ==