BASIL2022GV3R8E: Difference between revisions

Line 14:

From here, we were able to form the conclusion that our POI interacts with glucose based on the alignment with a known hexokinase. To validate that glucose actually binds and interacts with our protein of interest, we conducted a PyRx in silico docking experiment with a total of five hexose substrates. Other substrates tested include fructose, galactose, lactose, and ribose, however, experimental in silico docking results for those substrates were significantly less than glucose. Along with the PyRx docking, we visualized ATP and <scene name='90/904995/Mesh_backbone_with_atp_glucose/3'>glucose</scene> within the proposed active site in the PyMol visualization software tool. We also were then able to find which active site amino acid were crucial to binding, which are highlighted <scene name='90/904995/~~3r8e_amino_acids~~/2~~'>here</scene>.<scene name='90/904995/3r8e_amino_acids_updated/1~~'>here</scene>. The binding affinity of glucose was -5.1 kcal/mol, which strengthens our idea that glucose is phosphorylated by our protein of interest. The confidence behind our in silico results allowed us to move into testing our hypothesis in vitro and because ATP aids in the phosphorylation of glucose, an <scene name='90/904995/3r8ec_w_glc_and_atp/1'>interactive structure</scene> has been provided to represent interactions of glucose and ATP in the active site.

From here, we were able to form the conclusion that our POI interacts with glucose based on the alignment with a known hexokinase. To validate that glucose actually binds and interacts with our protein of interest, we conducted a PyRx in silico docking experiment with a total of five hexose substrates. Other substrates tested include fructose, galactose, lactose, and ribose, however, experimental in silico docking results for those substrates were significantly less than glucose. Along with the PyRx docking, we visualized ATP and <scene name='90/904995/Mesh_backbone_with_atp_glucose/3'>glucose</scene> within the proposed active site in the PyMol visualization software tool. We also were then able to find which active site amino acid were crucial to binding, which are highlighted <scene name='90/904995/3r8e_amino_acids_updated/2'>here</scene>. The binding affinity of glucose was -5.1 kcal/mol, which strengthens our idea that glucose is phosphorylated by our protein of interest. The confidence behind our in silico results allowed us to move into testing our hypothesis in vitro and because ATP aids in the phosphorylation of glucose, an <scene name='90/904995/3r8ec_w_glc_and_atp/1'>interactive structure</scene> has been provided to represent interactions of glucose and ATP in the active site.

BASIL2022GV3R8E: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

Revision as of 19:06, 19 October 2022 view source Michel Evertsen (talk \| contribs) 92 edits No edit summary ← Older edit		Revision as of 19:15, 19 October 2022 view source Michel Evertsen (talk \| contribs) 92 edits No edit summary Newer edit →
Line 14:		Line 14:


	From here, we were able to form the conclusion that our POI interacts with glucose based on the alignment with a known hexokinase. To validate that glucose actually binds and interacts with our protein of interest, we conducted a PyRx in silico docking experiment with a total of five hexose substrates. Other substrates tested include fructose, galactose, lactose, and ribose, however, experimental in silico docking results for those substrates were significantly less than glucose. Along with the PyRx docking, we visualized ATP and <scene name='90/904995/Mesh_backbone_with_atp_glucose/3'>glucose</scene> within the proposed active site in the PyMol visualization software tool. We also were then able to find which active site amino acid were crucial to binding, which are highlighted <scene name='90/904995/~~3r8e_amino_acids~~/2~~'>here</scene>.<scene name='90/904995/3r8e_amino_acids_updated/1~~'>here</scene>. The binding affinity of glucose was -5.1 kcal/mol, which strengthens our idea that glucose is phosphorylated by our protein of interest. The confidence behind our in silico results allowed us to move into testing our hypothesis in vitro and because ATP aids in the phosphorylation of glucose, an <scene name='90/904995/3r8ec_w_glc_and_atp/1'>interactive structure</scene> has been provided to represent interactions of glucose and ATP in the active site.		From here, we were able to form the conclusion that our POI interacts with glucose based on the alignment with a known hexokinase. To validate that glucose actually binds and interacts with our protein of interest, we conducted a PyRx in silico docking experiment with a total of five hexose substrates. Other substrates tested include fructose, galactose, lactose, and ribose, however, experimental in silico docking results for those substrates were significantly less than glucose. Along with the PyRx docking, we visualized ATP and <scene name='90/904995/Mesh_backbone_with_atp_glucose/3'>glucose</scene> within the proposed active site in the PyMol visualization software tool. We also were then able to find which active site amino acid were crucial to binding, which are highlighted <scene name='90/904995/3r8e_amino_acids_updated/2'>here</scene>. The binding affinity of glucose was -5.1 kcal/mol, which strengthens our idea that glucose is phosphorylated by our protein of interest. The confidence behind our in silico results allowed us to move into testing our hypothesis in vitro and because ATP aids in the phosphorylation of glucose, an <scene name='90/904995/3r8ec_w_glc_and_atp/1'>interactive structure</scene> has been provided to represent interactions of glucose and ATP in the active site.