User:Cody Couperus/Sandbox 1: Difference between revisions

Line 73:

Binding of thrombin by sodium or at exosite I stabilizes a form of thrombin that improves substrate recognition.<ref name='seven'/> This occurs due to energetic linkage between these sites to the S1 binding pocket and oxyanion hole. Rapid kinetic analysis suggests that thrombin is in a dynamic equilibrium that consists of a fast, slow, and inactive state<ref name='seven'/>. There is question as to the physiologic relevance of the inactive state. Regardless, there will be a proportion of fast:slow thrombin and sodium binding to the fast form stabilizes that conformation. Indeed, mutation of the residues involved in sodium binding diminishes the activity of thrombin.<ref name='seven'/> It should be restated, that current data suggest that sodium binding does not induce a conformation change, rather, it stabilizes a conformation of thrombin that has greater activity.

==~~Interesting~~ Secondary Structure==

==Secondary Structure Features==

Thrombin has a <scene name='58/583418/Cis_proline/1'>cis peptide bond</scene> in a loop containing proline 37. The dihedral (Cα-C'-N-Cα) angle omega is 142.7 degrees.

@@ Line 73: / Line 73: @@
 Binding of thrombin by sodium or at exosite I stabilizes a form of thrombin that improves substrate recognition.<ref name='seven'/> This occurs due to energetic linkage between these sites to the S1 binding pocket and oxyanion hole. Rapid kinetic analysis suggests that thrombin is in a dynamic equilibrium that consists of a fast, slow, and inactive state<ref name='seven'/>. There is question as to the physiologic relevance of the inactive state. Regardless, there will be a proportion of fast:slow thrombin and sodium binding to the fast form stabilizes that conformation. Indeed, mutation of the residues involved in sodium binding diminishes the activity of thrombin.<ref name='seven'/> It should be restated, that current data suggest that sodium binding does not induce a conformation change, rather, it stabilizes a conformation of thrombin that has greater activity.
-==Interesting Secondary Structure==
+==Secondary Structure Features==
 Thrombin has a <scene name='58/583418/Cis_proline/1'>cis peptide bond</scene> in a loop containing proline 37. The dihedral (Cα-C'-N-Cα) angle omega is 142.7 degrees.