Group:SMART:Tangible Models of Cdc42 Interacting With Intersectin: Difference between revisions

1) <scene name='SMART_Lincoln_2009/Cdc42_and_gdp/1'>Cdc42</scene> (<font color = '#FFFF00'><b> yellow </b></font>) is off when GDP is in its binding pocket. <font color = '#FF1493'><b> Mg++ </b></font>is shown in magenta, <font color = '#00FF00'><b> Alanine 59 </b></font> in green, <font color = '#FFA500'><b>Switch 1</b></font> in light gold, and <font color = '#FF6600'><b>Switch 2</b></font> in dark orange. Brown depicts the residues interacting with <font color = '#8B4513'><b>GDP</b></font> (<font color = '#8B4513'><b>Lys16 and Cys18</b></font>).

3) Thee interaction causes conformational changes in <font color = '#FFA500'><b>Switch 1</b></font> and <font color = '#FF6600'><b>Switch 2</b></font> of Cdc42. <font color = '#FF0000'><b>Thr35</b></font> hydrogen bonds to a residue (<font color = '#802AAB'><b>Glu1244</b></font>) of the <font color = '#6A5ACD'><b>DH domain</b></font> of Intersectin. Most important is the noticeable change in the orientation of residue 59 (<font color = '#00FF00'><b>Ala59</b></font>). Its sidechain flips into the magnesium-binding pocket, causing the release of the <font color = '#FF1493'><b> Mg++ </b></font> ion and in turn the release of <font color = '#8B4513'><b>GDP</b></font> from <font color = '#FFFF00'><b>Cdc42</b></font>.

4) <font color = '#FF1493'><b> Mg++ </b></font> and <font color = '#8B4513'><b>GDP</b></font> fall off from <font color = '#FFFF00'><b> Cdc42</b></font>. The nucleotide-binding pocket of <font color = '#FFFF00'><b>Cdc42</b></font> is now empty.

5) Because the intracellular ratio of <font color = '#2F6E46'><b>GTP</b></font> to <font color = '#8B4513'><b>GDP</b></font> is high, a <font color = '#2F6E46'><b>GTP</b></font> molecule (dark green) will float into the binding pocket of <font color = '#FFFF00'><b>Cdc42</b></font> and activate it.