User:Daniel Seeman/DELETE: Difference between revisions

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<~~applet load~~=~~'Caspmorph~~.~~pdb' size~~=~~'300' frame='true' align='right' caption='Toggle between active site inhibitor bound and allosterically inhibited caspase-7'~~ />

Caspases are a family of [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

~~Conformational dynamics~~ in ~~Caspase-7 are mediated by an~~ '~~Allosteric Toggle~~' ~~mechanism in which binding of allosteric inhibitor DICA is bound to CYS 290 and pushes TYR 223 into~~ 'up' ~~conformation forcing ARG 187~~ '~~out~~' ~~into a form that is physically incompatible with substrate binding~~.

=== Conformation Dynamics studied in [http://www.chem.umass.edu/~jhardy/ the Hardy Lab] ===

The cleaved termini of the large and small subunits which form the active site loop bundle become highly ordered in active ~~site~~ conformation, and highly disordered in allosterically inhibited form (so much so that they cannot be resolved crystallographically).

Conformational dynamics in Caspase-7 are mediated by an 'Allosteric Toggle' mechanism in which binding of allosteric inhibitor DICA to CYS 290 pushes TYR 223 into 'up' conformation forcing ARG 187 'out' into a form that is physically incompatible with substrate binding.

The cleaved termini of the large and small subunits which form the active site loop bundle become highly ordered in active conformation, and highly disordered in allosterically inhibited form (so much so that they cannot be resolved crystallographically).

=== Forms of Caspase-7 ===

*<scene name='~~User:Daniel_Seeman~~/~~Caspase-7_Dynamics~~/1f1j/1'>Caspase-7 bound to ~~dead-end~~ substrate mimic DEVD-CHO</scene>, trapping protein in active/substrate bound conformation.

*<scene name='Molecular_Playground/Caspase_Dynamics/1f1j/2'>Caspase-7 bound to suicide inhibitor/substrate mimic DEVD-CHO</scene>, trapping protein in active/substrate bound conformation.

*<scene name='~~User:Daniel_Seeman~~/~~Caspase-7_Dynamics~~/1shj-234234/1'>Caspase-7 bound to allosteric inhibitor DICA through CYS290</scene> trapping protein in a form incompatible with substrate binding.

*<scene name='Molecular_Playground/Caspase_Dynamics/1shj-234234/1'>Caspase-7 bound to allosteric inhibitor DICA through CYS290</scene> trapping protein in a form incompatible with substrate binding.

*<scene name='~~User:Daniel_Seeman~~/~~Caspase-7_Dynamics~~/~~Morph1~~/1'>Conformational change between substrate bound and substrate incompatible forms</scene> of Caspase-7.

*<scene name='Molecular_Playground/Caspase_Dynamics/Morph2/1'>Conformational change between substrate bound and substrate incompatible forms</scene> of Caspase-7.

=== Molecular Playground banner ===

'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.

@@ Line 1: / Line 1: @@
-<applet load='Caspmorph.pdb' size='300' frame='true' align='right' caption='Toggle between active site inhibitor bound and allosterically inhibited caspase-7' />
+Caspases are a family of [[CBI Molecules]] being studied in the  <span class="plainlinks">[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]</span> at UMass Amherst and on display at the <span class="plainlinks">[http://www.molecularplayground.org/ Molecular Playground]</span>.
-Conformational dynamics in Caspase-7 are mediated by an 'Allosteric Toggle' mechanism in which binding of allosteric inhibitor DICA is bound to CYS 290 and pushes TYR 223 into 'up' conformation forcing ARG 187 'out' into a form that is physically incompatible with substrate binding.
+=== Conformation Dynamics studied in <span class="plainlinks">[http://www.chem.umass.edu/~jhardy/ the Hardy Lab] </span>===
+<applet load='Caspmorph.pdb' size='300' frame='true' scene='Molecular_Playground/Caspase_Dynamics/Morph2/1' align='right' caption='Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.' />
-The cleaved termini of the large and small subunits which form the active site loop bundle become highly ordered in active site conformation, and highly disordered in allosterically inhibited form (so much so that they cannot be resolved crystallographically).
+Conformational dynamics in Caspase-7 are mediated by an 'Allosteric Toggle' mechanism in which binding of allosteric inhibitor DICA to CYS 290 pushes TYR 223 into 'up' conformation forcing ARG 187 'out' into a form that is physically incompatible with substrate binding.
+The cleaved termini of the large and small subunits which form the active site loop bundle become highly ordered in active conformation, and highly disordered in allosterically inhibited form (so much so that they cannot be resolved crystallographically).
 === Forms of Caspase-7 ===
-*<scene name='User:Daniel_Seeman/Caspase-7_Dynamics/1f1j/1'>Caspase-7 bound to dead-end substrate mimic DEVD-CHO</scene>, trapping protein in active/substrate bound conformation.
+*<scene name='Molecular_Playground/Caspase_Dynamics/1f1j/2'>Caspase-7 bound to suicide inhibitor/substrate mimic DEVD-CHO</scene>, trapping protein in active/substrate bound conformation.
-*<scene name='User:Daniel_Seeman/Caspase-7_Dynamics/1shj-234234/1'>Caspase-7 bound to allosteric inhibitor DICA through CYS290</scene> trapping protein in a form incompatible with substrate binding.
+*<scene name='Molecular_Playground/Caspase_Dynamics/1shj-234234/1'>Caspase-7 bound to allosteric inhibitor DICA through CYS290</scene> trapping protein in a form incompatible with substrate binding.
-*<scene name='User:Daniel_Seeman/Caspase-7_Dynamics/Morph1/1'>Conformational change between substrate bound and substrate incompatible forms</scene> of Caspase-7.
+*<scene name='Molecular_Playground/Caspase_Dynamics/Morph2/1'>Conformational change between substrate bound and substrate incompatible forms</scene> of Caspase-7.
 === Molecular Playground banner ===
 '''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.