Sandbox Reserved 199: Difference between revisions
From Proteopedia
Jump to navigationJump to search
| Line 75: | Line 75: | ||
Previously, researchers found the side chain position of <scene name='Sandbox_Reserved_199/2aas_-_his_119/1'>His 119</scene> in the enzyme’s <scene name='Sandbox_Reserved_199/2aas_-_all_models/5'>active site</scene> (<scene name='Sandbox_Reserved_199/2aas_-_active_site_space_fill/1'>spacefill</scene>) of NMR structures to be different than that of X-Ray Crystallography studies. Crystals show a static position of this His 119 residue, yet NMR structures suggest a dynamic equilibrium between the two conformational puckers of the <scene name='Sandbox_Reserved_199/2aas_-_his_119_imidazole/1'>His 119 imidazole ring</scene>. This single residue difference between crystal and solution studies amplifies to cause a major difference in surrounding amino acid residues: <scene name='Sandbox_Reserved_199/2aas_-_residue_4/1'>4</scene>, <scene name='Sandbox_Reserved_199/2aas_-_residue_4_106_107_108/1'>106-108</scene>, and <scene name='Sandbox_Reserved_199/2aas_-_residue_4_106_107_108_1/1'>116-118</scene>. The researchers proposed that this difference is most likely due to pH induced charge repulsion of His 119 with <scene name='Sandbox_Reserved_199/2aas_-_asp_14/1'>Asp 14</scene> and <scene name='Sandbox_Reserved_199/2aas_-_his_48/2'>His 48</scene> in solution. | Previously, researchers found the side chain position of <scene name='Sandbox_Reserved_199/2aas_-_his_119/1'>His 119</scene> in the enzyme’s <scene name='Sandbox_Reserved_199/2aas_-_all_models/5'>active site</scene> (<scene name='Sandbox_Reserved_199/2aas_-_active_site_space_fill/1'>spacefill</scene>) of NMR structures to be different than that of X-Ray Crystallography studies. Crystals show a static position of this His 119 residue, yet NMR structures suggest a dynamic equilibrium between the two conformational puckers of the <scene name='Sandbox_Reserved_199/2aas_-_his_119_imidazole/1'>His 119 imidazole ring</scene>. This single residue difference between crystal and solution studies amplifies to cause a major difference in surrounding amino acid residues: <scene name='Sandbox_Reserved_199/2aas_-_residue_4/1'>4</scene>, <scene name='Sandbox_Reserved_199/2aas_-_residue_4_106_107_108/1'>106-108</scene>, and <scene name='Sandbox_Reserved_199/2aas_-_residue_4_106_107_108_1/1'>116-118</scene>. The researchers proposed that this difference is most likely due to pH induced charge repulsion of His 119 with <scene name='Sandbox_Reserved_199/2aas_-_asp_14/1'>Asp 14</scene> and <scene name='Sandbox_Reserved_199/2aas_-_his_48/2'>His 48</scene> in solution. | ||
More than 60 main-chain hydrogen bonds were observed, which closely corresponds to the number of hydrogen bonds determined in crystals; however, a few discrepancies existed such as hydrogen bonds between the amide proton on <scene name='Sandbox_Reserved_199/2aas_-_17_14_dbl/1'>Thr 17 (NH)-Asp 14 (CO) carbonyl</scene>, <scene name='Sandbox_Reserved_199/2aas_-_49_47/ | More than 60 main-chain hydrogen bonds were observed, which closely corresponds to the number of hydrogen bonds determined in crystals; however, a few discrepancies existed such as hydrogen bonds between the amide proton on <scene name='Sandbox_Reserved_199/2aas_-_17_14_dbl/1'>Thr 17 (NH)-Asp 14 (CO) carbonyl</scene>, <scene name='Sandbox_Reserved_199/2aas_-_49_47/2'>Glu 49 (NH)-Val 47 (CO)</scene>, <scene name='Sandbox_Reserved_199/2aas_-_32_28/1'>Ser 32 (NH)-Gln 28 (CO)</scene>, <scene name='Sandbox_Reserved_199/2aas_-_51-54/1'>Val 54 (NH)-Leu 51 (CO)</scene>, and <scene name='Sandbox_Reserved_199/2aas_-_73_63/1'>Cys 72 (NH)-Val 63 (CO)</scene>. The researchers suggested these differences are most likely due to the same pH phenomenon mentioned above. | ||
The NMR structure also highlighted flexibility of RNase A. Overall, the largest conformational flexibility was found in the side-chains. Specifically, side-chain mobility is greatest in residues <scene name='Sandbox_Reserved_199/2aas_-_side_chain_flexibility/1'>1, 7, 15, 18, 24, 37, 59, 66, 94, 123, and 124</scene> (shown in white). As expected, the backbone torsion angles were seen to be more rigid (less conformational flexibility) within the <scene name='Sandbox_Reserved_199/2aas_-_active_site_rigidity/1'>active site (shown in white)</scene> of RNase A. | The NMR structure also highlighted flexibility of RNase A. Overall, the largest conformational flexibility was found in the side-chains. Specifically, side-chain mobility is greatest in residues <scene name='Sandbox_Reserved_199/2aas_-_side_chain_flexibility/1'>1, 7, 15, 18, 24, 37, 59, 66, 94, 123, and 124</scene> (shown in white). As expected, the backbone torsion angles were seen to be more rigid (less conformational flexibility) within the <scene name='Sandbox_Reserved_199/2aas_-_active_site_rigidity/1'>active site (shown in white)</scene> of RNase A. | ||
