Sandbox Reserved 199: Difference between revisions

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Overall, the bovine Ribonuclease NMR tertiary structure matches closely the corresponding X-Ray Crystallography structure. The overall shape, main-chain fold, and side chain positions of most residues are similar between the structures of the two methods. Experimentally determined tertiary structural differences between the two methods were suggested to be due to pH differences, crystal packing, solvation, and temperature variability.

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 Asp 14 and His 48 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, there exist a few discrepancies. In the NMR structure, there was determined to be a hydrogen bond between the amide proton on Thr 17 (NH)-Asp 14 (CO) carbonyl, as well as between Glu 49 (NH)-Val 47 (CO). The researchers suggested these differences are most likely due to the same pH phenomenon mentioned above. Other hydrogen bonds present in the NMR structure but not present in the crystal structure are: Ser 32 (NH)-Gln 28 (CO), Val 54 (NH)-Leu 51 (CO), and Cys 72 (NH)-Val 63 (CO).

Sandbox Reserved 199: Difference between revisions

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 Overall, the bovine Ribonuclease NMR tertiary structure matches closely the corresponding X-Ray Crystallography structure.  The overall shape, main-chain fold, and side chain positions of most residues are similar between the structures of the two methods.  Experimentally determined tertiary structural differences between the two methods were suggested to be due to pH differences, crystal packing, solvation, and temperature variability.
-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 Asp 14 and His 48 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, there exist a few discrepancies.  In the NMR structure, there was determined to be a hydrogen bond between the amide proton on Thr 17 (NH)-Asp 14 (CO) carbonyl, as well as between Glu 49 (NH)-Val 47 (CO).  The researchers suggested these differences are most likely due to the same pH phenomenon mentioned above.  Other hydrogen bonds present in the NMR structure but not present in the crystal structure are: Ser 32 (NH)-Gln 28 (CO), Val 54 (NH)-Leu 51 (CO), and Cys 72 (NH)-Val 63 (CO).