https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Brooklyn+Mills 2026-09-21T11:59:06Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3757060 2023-04-26T15:42:43Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's &lt;scene name='95/957646/Secondary_structure/1'&gt;secondary structure&lt;/scene&gt; is made up of mostly alpha helices, but also has beta sheets and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using Nickle affinity chromatography. The band at 75kD and 25kD we believe are there from the imaging and is not from our actual protein sample.<br /> [[Image:SDS.png]]<br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate (table 5). We didn't have to modify the kinase assay protocol for Abl Kinase other than changing the substrate and ensuring we were using a high enough substrate concentration that was greater than the protein concentration. <br /> [[Image:Kinase_assay.png]] <br /> <br /> == Conclusions ==<br /> Although we determined that neither glucose or guanosine were the substrate for P76586, we are unsure if this may have been from experimental error. But looking back at the docking results I think we should have tried a wider range of substrates. Maybe a substrate that had closer hydrogen bond interactions. If we were to continue our research we would spend much more time on the docking portion in order to really dissect the active site and its interactions with the substrates. Overall this research experience was really educational and we gained a lot of skills from working in the lab and working as a team. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3756003 2023-04-26T04:32:09Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's &lt;scene name='95/957646/Secondary_structure/1'&gt;secondary structure&lt;/scene&gt; is made up of mostly alpha helices, but also has beta sheets and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate (table 5). <br /> [[Image:Kinase_assay.png]] <br /> <br /> == Conclusions ==<br /> Although we determined that neither glucose or guanosine were the substrate for P76586, we are unsure if this may have been from experimental error. But looking back at the docking results I think we should have tried a wider range of substrates. Maybe a substrate that had closer hydrogen bond interactions. If we were to continue our research we would spend much more time on the docking portion in order to really dissect the active site and its interactions with the substrates. Overall this research experience was really educational and we gained a lot of skills from working in the lab and working as a team. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3756002 2023-04-26T04:22:19Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate (table 5). <br /> [[Image:Kinase_assay.png]] <br /> <br /> == Conclusions ==<br /> Although we determined that neither glucose or guanosine were the substrate for P76586, we are unsure if this may have been from experimental error. But looking back at the docking results I think we should have tried a wider range of substrates. Maybe a substrate that had closer hydrogen bond interactions. If we were to continue our research we would spend much more time on the docking portion in order to really dissect the active site and its interactions with the substrates. Overall this research experience was really educational and we gained a lot of skills from working in the lab and working as a team. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755998 2023-04-26T03:06:08Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate (figure 6). <br /> [[Image:Kinase_assay.png]] <br /> <br /> == Conclusions ==<br /> Although we determined that neither glucose or guanosine were the substrate for P76586, we are unsure if this may have been from experimental error. But looking back at the docking results I think we should have tried a wider range of substrates. Maybe a substrate that had closer hydrogen bond interactions. If we were to continue our research we would spend much more time on the docking portion in order to really dissect the active site and its interactions with the substrates. Overall this research experience was really educational and we gained a lot of skills from working in the lab and working as a team. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755996 2023-04-26T02:54:45Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate (figure 6)<br /> [[Image:Kinase_assay.png]] <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:Kinase_assay.png&diff=3755995 2023-04-26T02:54:24Z

<p>Brooklyn Mills: </p> <hr /> <div></div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755994 2023-04-26T02:53:11Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate (figure 6)<br /> [[Image:Figure_6.png]] <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755936 2023-04-24T18:25:33Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755935 2023-04-24T18:23:22Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> [[Image:Sugar_substrates.png]] <br /> <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> <br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755934 2023-04-24T18:21:50Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> [[Image:Sugar_substrates.png]] <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> [[Image:SDS.png]]<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:SDS.png&diff=3755933 2023-04-24T18:01:22Z

<p>Brooklyn Mills: </p> <hr /> <div></div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755932 2023-04-24T18:00:46Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> [[Image:Sugar_substrates.png]] <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> [[Image:Docked_guanosine.png]]<br /> [[Image:Docked_glucose.png]]<br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not including our induction samples and our fractions from protein purification using nickle affinity chromatography. <br /> <br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:Docked_guanosine.png&diff=3755931 2023-04-24T17:52:28Z

<p>Brooklyn Mills: </p> <hr /> <div></div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:Docked_glucose.png&diff=3755930 2023-04-24T17:52:08Z

<p>Brooklyn Mills: </p> <hr /> <div></div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755929 2023-04-24T17:45:10Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. <br /> [[Image:Sugar_substrates.png]] <br /> Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. <br /> [[Image:Nitrogenous_Bases_Structures.png]]<br /> From the results of the docked sugars, shown in table 4, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> [[Image:Sugar_affinities.png]]<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> Guanosine experienced possible hydrogen bonding with residues Arg183, Gln393, and Tyr23. Glucose experienced possible hydrogen bonds with Tyr23, Asp81, Arg183, and a possible pi stacking interaction with Tyr389. <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755928 2023-04-24T17:29:11Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. [[Image:Sugar_substrates.png]] Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2. [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755927 2023-04-24T17:28:15Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. [[Image:Sugar_substrates.png]] Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2 [[Image:Nitrogenous_Bases_Structures.png]]<br /> <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755926 2023-04-24T17:27:30Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. [[Image:Sugar_substrates.png]] Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2 [[Image:Nitrogenous_bases_structures.png]]<br /> <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755925 2023-04-24T17:26:48Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. [[Image:Sugar_substrates.png]] Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides, the structures of the nitrogenous bases are shown in figure 2 [[Image:Nitrogenous_bases.png]]<br /> <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755924 2023-04-24T17:23:16Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [[Image:Sugar_substrates.png]]<br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:Sugar_affinities.png&diff=3755923 2023-04-24T17:21:23Z

<p>Brooklyn Mills: </p> <hr /> <div></div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:SDS_PAGE.png&diff=3755922 2023-04-24T17:21:08Z

<p>Brooklyn Mills: </p> <hr /> <div></div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:Nitrogenous_Bases_Structures.png&diff=3755921 2023-04-24T17:20:48Z

<p>Brooklyn Mills: This is a picture of the bases we docked</p> <hr /> <div>This is a picture of the bases we docked</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755920 2023-04-24T17:18:21Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. Taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [figure 1 sugars docked. <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> In conclusion we learned that neither glucose or guanosine were substrates. This project also made us realize just how frustrating research can be. We also hope that the research we did can help groups in the future that work with this protein. Some other things that we learned was amazing pipetting skills that we can take with us in future classes and our careers in the future. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755866 2023-04-22T17:42:37Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was InterPro which can be seen in Table 3 (InterPro figure).<br /> The InterPro figure really help us narrow down that it could be either of those to substrates because again it shown a sugar kinase and a ATPase which would mean that there is potentially a nucloeside or something to with ATP.<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [figure 1 sugars docked. <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assays, one with glucose and one with guanosine. After calculating the specific activity of our protein with glucose and guanosine we determined there was not enough activity for glucose or guanosine to be the substrate. <br /> <br /> == Conclusions ==<br /> IN conclusion we l<br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755864 2023-04-22T17:36:54Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1. (blast figure).<br /> From the Blast results we saw that it was from the ROK family and that it was a putative kinase.<br /> The next tool we used was Dali shown in table 2.(Dali figure).<br /> From the Dali results the best results we saw were from a putative kinase, glucokinase and a DNA-binding kinase. These results are what showed us that there could be a potential nucleosides though we weren't for sure which one it could be until we go to docking.<br /> The next tool we used was <br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [figure 1 sugars docked. <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. Potential amino acids in the active site are Tyr23, Asp81, Arg183, Gln393, and Tyr389. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better.<br /> We ran two coupled kinase assay<br /> <br /> == Conclusions ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755862 2023-04-22T17:29:18Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.<br /> The first computational tool we used was Blast the results of which are shown below on Table 1.<br /> &lt;img src=&quot;blob:chrome-untrusted://media-app/376d84bf-5fc2-4328-a234-9d0eb5134dde&quot; alt=&quot;Screenshot 2023-04-22 11.49.44 AM.png&quot;/&gt;<br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [figure 1 sugars docked. <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the &lt;scene name='95/957646/Active_site/1'&gt;active site&lt;/scene&gt; of P76586. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not running our pre and post inductions samples.<br /> <br /> == Conclusions ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755859 2023-04-22T16:58:18Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> <br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [figure 1 sugars docked. <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> &lt;scene name='95/957646/Globular_structure/1'&gt;P76586 is a globular protein&lt;/scene&gt; with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the active site of P76586. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not running our pre and post inductions samples.<br /> <br /> == Conclusions ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:P76586_with_ATP.pdb&diff=3755648 2023-04-19T22:15:18Z

<p>Brooklyn Mills: P76586 structure</p> <hr /> <div>P76586 structure</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755647 2023-04-19T22:13:46Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> <br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [figure 1 sugars docked. <br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> P76586 is a globular protein with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the active site of P76586. <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not running our pre and post inductions samples.<br /> <br /> == Conclusions ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=File:Sugar_substrates.png&diff=3755646 2023-04-19T22:02:37Z

<p>Brooklyn Mills: </p> <hr /> <div></div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3755640 2023-04-19T19:28:37Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> <br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5. <br /> [docked sugars figure 1]<br /> [table 4 results docked sugars]<br /> [docked nucleoside structures figure 2]<br /> [table 5 results docked nucleosides-bases]<br /> From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.<br /> We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4). <br /> <br /> ==Structural Highlights==<br /> <br /> == Results == <br /> Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not running our pre and post inductions samples.<br /> <br /> == Conclusions ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3753430 2023-04-18T18:06:58Z

<p>Brooklyn Mills: </p> <hr /> <div>== Investigating the Function of Protein P76586 ==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> <br /> == Molecular Docking ==<br /> From the initial search throughout all of the computational tools, we decided that our putative kinase was either a glucokinase, or possibly a nucleoside kinase. <br /> <br /> == Results == <br /> <br /> == Conclusions ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=BASIL2023GVP76586&diff=3744740 2023-04-05T17:56:38Z

<p>Brooklyn Mills: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''BASIL2023GVP76586'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == The Initial Search ==<br /> <br /> == Molecular Docking ==<br /> <br /> == Methods ==<br /> <br /> == Results == <br /> <br /> == Conclusions ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679934 2022-12-13T02:49:30Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The protein Ornithine Aminotransferase (OAT), in humans (hOAT), is an enzyme that catalyzes the the transfer of an amino group from L-ornithine(L-Orn) to α-ketoglutarate (α-KG). Its ligand, pyridoxal-5'-phosphate (&lt;scene name='93/934004/Plp/1'&gt;PLP&lt;/scene&gt;), is a cofactor of this reaction. An amino group from L-Orn is transferred to PLP which converts it to pyridoxamine phosphate (PMP) and L-Orn is converted to L-glutamate-γ-semialdehyde. When the amino group of PMP is transferred to the α-KG, it forms glutamate and regenerates PLP. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the ligand PLP and provided a tighter binding to hOAT than L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. Other amino acids that have served importance to PLP and binding the substrate L-Orn appear to be &lt;scene name='93/934004/Ph_sites/1'&gt;Arg 413 and Glu 235&lt;/scene&gt;. At a pH of 6.0 a salt bridge is formed between Arg 413 and Glu 235, these amino acids also regulate the width of the active site and establish the size of the channel that the substrate passes through. At a pH of 7.8 conformational changes of Arg 413 and Glu 235 causes the distance between the side chains to increase therefore that restriction of the active-site isn't as prevalent. Another conformational change occurs from a pH of 6.0 to 7.8 with Arg 180. At a pH of 6.0 Arg 180 is able to interact with PLP as previously described but that interaction is disrupted at a pH of 7.8. These conformational changes alter the binding affinity and contribute to a slower catalytic rate due to the decrease in interactions with less acidic conditions. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/2'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. Two of the subunits are bound and fit more closely together leaving a pocket/space between the two subunits shown in purple and orange and the subunit shown in green. Since there is an active within each subunit, the observed conformational changes seen in Arg 180, Arg 413, and Glu 235 that cause a decrease in reaction rate at a pH of 6.0 could also be contributed by the protonation state of other active sites within hOAT that don't induce conformational changes. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets exposed slightly can help other competitive substrates bind to this active site and inhibit the enzyme if necessary. <br /> The ligand PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the molecule, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;ligand and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the molecule were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind the ligand in the active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> Butrin A, Butrin A, Wawrzak Z, Moran GR, Liu D. Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase. J Biol Chem. 2022 Jun;298(6):101969. doi: 10.1016/j.jbc.2022.101969. Epub 2022 Apr 20. PMID: 35460691; PMCID: PMC9136103.</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679930 2022-12-13T02:36:21Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The protein Ornithine Aminotransferase (OAT), in humans (hOAT), is an enzyme that catalyzes the the transfer of an amino group from L-ornithine(L-Orn) to α-ketoglutarate (α-KG). Its ligand, pyridoxal-5'-phosphate (PLP), is a cofactor of this reaction. An amino group from L-Orn is transferred to PLP which converts it to pyridoxamine phosphate (PMP) and L-Orn is converted to L-glutamate-γ-semialdehyde. When the amino group of PMP is transferred to the α-KG, it forms glutamate and regenerates PLP. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the ligand PLP and provided a tighter binding to hOAT than L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. Other amino acids that have served importance to PLP and binding the substrate L-Orn appear to be &lt;scene name='93/934004/Ph_sites/1'&gt;Arg 413 and Glu 235&lt;/scene&gt;. At a pH of 6.0 a salt bridge is formed between Arg 413 and Glu 235, these amino acids also regulate the width of the active site and establish the size of the channel that the substrate passes through. At a pH of 7.8 conformational changes of Arg 413 and Glu 235 causes the distance between the side chains to increase therefore that restriction of the active-site isn't as prevalent. Another conformational change occurs from a pH of 6.0 to 7.8 with Arg 180. At a pH of 6.0 Arg 180 is able to interact with PLP as previously described but that interaction is disrupted at a pH of 7.8. These conformational changes alter the binding affinity and contribute to a slower catalytic rate due to the decrease in interactions with less acidic conditions. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/2'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. Two of the subunits are bound and fit more closely together leaving a pocket/space between the two subunits shown in purple and orange and the subunit shown in green. Since there is an active within each subunit, the observed conformational changes seen in Arg 180, Arg 413, and Glu 235 that cause a decrease in reaction rate at a pH of 6.0 could also be contributed by the protonation state of other active sites within hOAT that don't induce conformational changes. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets exposed slightly can help other competitive substrates bind to this active site and inhibit the enzyme if necessary. <br /> The ligand PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the molecule, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;ligand and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the molecule were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind the ligand in the active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> Butrin A, Butrin A, Wawrzak Z, Moran GR, Liu D. Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase. J Biol Chem. 2022 Jun;298(6):101969. doi: 10.1016/j.jbc.2022.101969. Epub 2022 Apr 20. PMID: 35460691; PMCID: PMC9136103.</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679927 2022-12-13T02:32:50Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The protein Ornithine Aminotransferase (OAT), in humans (hOAT), is an enzyme that catalyzes the the transfer of an amino group from L-ornithine(L-Orn) to α-ketoglutarate (α-KG). Its ligand, pyridoxal-5'-phosphate (PLP), is a cofactor of this reaction. An amino group from L-Orn is transferred to PLP which converts it to pyridoxamine phosphate (PMP) and L-Orn is converted to L-glutamate-γ-semialdehyde. When the amino group of PMP is transferred to the α-KG, it forms glutamate and regenerates PLP. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the ligand PLP and provided a tighter binding to hOAT than L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. Other amino acids that have served importance to PLP and binding the substrate L-Orn appear to be &lt;scene name='93/934004/Ph_sites/1'&gt;Arg 413 and Glu 235&lt;/scene&gt;. At a pH of 6.0 a salt bridge is formed between Arg 413 and Glu 235, these amino acids also regulate the width of the active site and establish the size of the channel that the substrate passes through. At a pH of 7.8 conformational changes of Arg 413 and Glu 235 causes the distance between the side chains to increase therefore that restriction of the active-site isn't as prevalent. Another conformational change occurs from a pH of 6.0 to 7.8 with Arg 180. At a pH of 6.0 Arg 180 is able to interact with PLP as previously described but that interaction is disrupted at a pH of 7.8. These conformational changes alter the binding affinity and contribute to a slower catalytic rate due to the decrease in interactions with less acidic conditions. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/2'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. Two of the subunits are bound and fit more closely together leaving a pocket/space between the two subunits shown in purple and orange and the subunit shown in green. Since there is an active within each subunit, the observed conformational changes seen in Arg 180, Arg 413, and Glu 235 that cause a decrease in reaction rate at a pH of 6.0 could also be contributed by the protonation state of other active sites within hOAT that don't induce conformational changes. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets exposed slightly can help other competitive substrates bind to this active site and inhibit the enzyme if necessary. <br /> The ligand PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the molecule, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;ligand and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the molecule were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind the ligand in the active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;ref&gt;PMID:35460691&lt;/ref&gt;.</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679925 2022-12-13T02:27:52Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The protein Ornithine Aminotransferase (OAT), in humans (hOAT), is an enzyme that catalyzes the the transfer of an amino group from L-ornithine(L-Orn) to α-ketoglutarate (α-KG). Its ligand, pyridoxal-5'-phosphate (PLP), is a cofactor of this reaction. An amino group from L-Orn is transferred to PLP which converts it to pyridoxamine phosphate (PMP) and L-Orn is converted to L-glutamate-γ-semialdehyde. When the amino group of PMP is transferred to the α-KG, it forms glutamate and regenerates PLP. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the ligand PLP and provided a tighter binding to hOAT than L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. Other amino acids that have served importance to PLP and binding the substrate L-Orn appear to be &lt;scene name='93/934004/Ph_sites/1'&gt;Arg 413 and Glu 235&lt;/scene&gt;. At a pH of 6.0 a salt bridge is formed between Arg 413 and Glu 235, these amino acids also regulate the width of the active site and establish the size of the channel that the substrate passes through. At a pH of 7.8 conformational changes of Arg 413 and Glu 235 causes the distance between the side chains to increase therefore that restriction of the active-site isn't as prevalent. Another conformational change occurs from a pH of 6.0 to 7.8 with Arg 180. At a pH of 6.0 Arg 180 is able to interact with PLP as previously described but that interaction is disrupted at a pH of 7.8. These conformational changes alter the binding affinity and contribute to a slower catalytic rate due to the decrease in interactions with less acidic conditions. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/2'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. Two of the subunits are bound and fit more closely together leaving a pocket/space between the two subunits shown in purple and orange and the subunit shown in green. Since there is an active within each subunit, the observed conformational changes seen in Arg 180, Arg 413, and Glu 235 that cause a decrease in reaction rate at a pH of 6.0 could also be contributed by the protonation state of other active sites within hOAT that don't induce conformational changes. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets exposed slightly can help other competitive substrates bind to this active site and inhibit the enzyme if necessary. <br /> The ligand PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the molecule, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;ligand and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the molecule were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind the ligand in the active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;ref&gt; PMID:35460691&lt;/ref&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679923 2022-12-13T02:16:48Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The protein Ornithine Aminotransferase (OAT), in humans (hOAT), is an enzyme that catalyzes the the transfer of an amino group from L-ornithine(L-Orn) to α-ketoglutarate (α-KG). Its ligand, pyridoxal-5'-phosphate (PLP), is a cofactor of this reaction. An amino group from L-Orn is transferred to PLP which converts it to pyridoxamine phosphate (PMP) and L-Orn is converted to L-glutamate-γ-semialdehyde. When the amino group of PMP is transferred to the α-KG, it forms glutamate and regenerates PLP. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the ligand PLP and provided a tighter binding to hOAT than L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. Other amino acids that have served importance to PLP and binding the substrate L-Orn appear to be &lt;scene name='93/934004/Ph_sites/1'&gt;Arg 413 and Glu 235&lt;/scene&gt;. At a pH of 6.0 a salt bridge is formed between Arg 413 and Glu 235, these amino acids also regulate the width of the active site and establish the size of the channel that the substrate passes through. At a pH of 7.8 conformational changes of Arg 413 and Glu 235 causes the distance between the side chains to increase therefore that restriction of the active-site isn't as prevalent. Another conformational change occurs from a pH of 6.0 to 7.8 with Arg 180. At a pH of 6.0 Arg 180 is able to interact with PLP as previously described but that interaction is disrupted at a pH of 7.8. These conformational changes alter the binding affinity and contribute to a slower catalytic rate due to the decrease in interactions with less acidic conditions. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/2'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets exposed slightly can help other competitive substrates bind to this active site and inhibit the enzyme if necessary. <br /> The ligand PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the molecule, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;ligand and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the molecule were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind the ligand in the active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679919 2022-12-13T02:06:52Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The protein Ornithine Aminotransferase (OAT), in humans (hOAT), is an enzyme that catalyzes the the transfer of an amino group from L-ornithine(L-Orn) to α-ketoglutarate (α-KG). Its ligand, pyridoxal-5'-phosphate (PLP), is a cofactor of this reaction. An amino group from L-Orn is transferred to PLP which converts it to pyridoxamine phosphate (PMP) and L-Orn is converted to L-glutamate-γ-semialdehyde. When the amino group of PMP is transferred to the α-KG, it forms glutamate and regenerates PLP. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the ligand PLP and provided a tighter binding to hOAT than L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. Other amino acids that have served importance to PLP and binding the substrate L-Orn appear to be &lt;scene name='93/934004/Ph_sites/1'&gt;Arg 413 and Glu 235&lt;/scene&gt;. At a pH of 6.0 a salt bridge is formed between Arg 413 and Glu 235, these amino acids also regulate the width of the active site and establish the size of the channel that the substrate passes through. At a pH of 7.8 conformational changes of Arg 413 and Glu 235 causes the distance between the side chains to increase therefore that restriction of the active-site isn't as prevalent. Another conformational change occurs from a pH of 6.0 to 7.8 with Arg 180. At a pH of 6.0 Arg 180 is able to interact with PLP as previously described but that interaction is disrupted at a pH of 7.8. These conformational changes alter the binding affinity and contribute to a slower catalytic rate due to the decrease in interactions with less acidic conditions. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets exposed slightly can help other competitive substrates bind to this active site and inhibit the enzyme if necessary. <br /> The ligand PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the molecule, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;ligand and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the molecule were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind the ligand in the active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679906 2022-12-12T18:59:08Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The protein Ornithine Aminotransferase (OAT), in humans (hOAT), is an enzyme that catalyzes the the transfer of an amino group from L-ornithine(L-Orn) to α-ketoglutarate (α-KG). Its ligand, pyridoxal-5'-phosphate (PLP), is a cofactor of this reaction. An amino group from L-Orn is transferred to PLP which converts it to pyridoxamine phosphate (PMP) and L-Orn is converted to L-glutamate-γ-semialdehyde. When the amino group of PMP is transferred to the α-KG, it forms glutamate and regenerates PLP. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the ligand PLP and provided a tighter binding to hOAT than L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets exposed slightly can help other competitive substrates bind to this active site and inhibit the enzyme if necessary. <br /> The ligand PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the molecule, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;ligand and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the molecule were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind the ligand in the active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679905 2022-12-12T18:26:50Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate. <br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679887 2022-12-12T06:07:20Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three subunits held together by non-covalent interactions like hydrogen bonds and salt bridges between the side chains of amino acids. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679886 2022-12-12T05:44:31Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a &lt;scene name='93/934004/Quaternary/1'&gt;globular structure&lt;/scene&gt; that has three sites for PLP binding. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679885 2022-12-12T05:29:41Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a more globular structure that has three sites for PLP binding. <br /> The &lt;scene name='93/934004/Binding_pocket/3'&gt;binding pocket&lt;/scene&gt; of PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679884 2022-12-12T05:17:32Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as fragmented-sized alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. GABA and AVA both displayed a stronger binding affinity and slower turnovers, making them strong demonstrators for potential drug targets of hOAT. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a more globular structure that has three sites for PLP binding. <br /> The &lt;scene name='93/934004/Binding_pocket/2'&gt;binding pocket&lt;/scene&gt; for PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679883 2022-12-12T05:07:54Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (&lt;scene name='93/934004/Ava/1'&gt;AVA&lt;/scene&gt;). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a more globular structure that has three sites for PLP binding. <br /> The &lt;scene name='93/934004/Binding_pocket/2'&gt;binding pocket&lt;/scene&gt; for PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679882 2022-12-12T04:01:05Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/2'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (AVA). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a more globular structure that has three sites for PLP binding. <br /> The &lt;scene name='93/934004/Binding_pocket/2'&gt;binding pocket&lt;/scene&gt; for PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679881 2022-12-12T03:56:21Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as alternative substrates such as γ-aminobutyric acid (&lt;scene name='93/934004/Gaba/1'&gt;GABA&lt;/scene&gt;) and 5-aminovaleric acid (AVA). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a more globular structure that has three sites for PLP binding. <br /> The &lt;scene name='93/934004/Binding_pocket/2'&gt;binding pocket&lt;/scene&gt; for PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills https://proteopedia.org/index.php?title=Sandbox_Reserved_1760&diff=3679880 2022-12-12T03:34:51Z

<p>Brooklyn Mills: </p> <hr /> <div>&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;&lt;scene name='93/934004/Plp_binding_site/2'&gt;Text To Be Displayed&lt;/scene&gt;{{Sandbox_Reserved_BHall_F22}}&lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&gt;<br /> ==Human Ornithine Aminotransferase==<br /> &lt;StructureSection load='7T9Z' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function of your protein ==<br /> The function of hOAT is to catalyze the transfer of the amino group from L-ornithine to an α-ketoglutarate.<br /> == Biological relevance and broader implications ==<br /> hOAT is found in most tissues in the body but predominates in the liver and kidney. There is a need to study the enzyme hOAT because the overexpression of this protein aids the proliferation of cancer cells, specifically Hepatocellular carcinoma (HCC), a common form of liver cancer. hOAT has been a target for mechanism-based inactivators (MBIs) in ongoing drug design efforts. HCC is normally diagnosed at advanced stages where the tumors tend to be resistant to radiotherapy and chemotherapy, making this type of cancer difficult to treat. <br /> In ongoing research, new hOAT inhibitors were created as alternative substrates such as γ-aminobutyric acid (GABA) and 5-aminovaleric acid (AVA). hOAT was soaked with GABA and AVA and the new substrates prevented original interactions with catalytic amino acids and the substrate PLP and provided a tighter binding to hOAT then L-ornithine. GABA covalently attached to PLP. While AVA covalently attached to PLP and Lysine 292, one of the catalytic enzymes in this binding pocket. <br /> == Important amino acids==<br /> Amino Acids in the &lt;scene name='93/934004/Plp_binding_site/6'&gt;PLP binding site&lt;/scene&gt; are Lys 292, Asp 263, Arg 180. They are essential to the active site by providing certain &lt;scene name='93/934004/Plp_ligand/2'&gt;interactions with PLP&lt;/scene&gt;. PLP is covalently bonded to the amino acid lysine. The nitrogen in the ring of PLP interacts with the negatively charged oxygen in the aspartate side chain. The phosphate group interacts with the positively charged nitrogen of the arginine side chain. Another interaction provided in this active site but not apart of the catalytic triad is the amino acid phenylalanine 177, there is a pi stacking interaction between its ring and the ring of the PLP. <br /> == Structural highlights ==<br /> hOAT is a protein with &lt;scene name='93/934004/Secondary_structure/1'&gt;secondary&lt;/scene&gt; structures consisting of alpha helices, parallel and antiparallel beta sheets, and random coil. It's a polymer with a more globular structure that has three sites for PLP binding. <br /> The &lt;scene name='93/934004/Binding_pocket/2'&gt;binding pocket&lt;/scene&gt; for PLP are semi-exposed to the &quot;outside world&quot; but also slightly hidden into the protein. Having binding pockets only slightly exposed can help prevent other competitive substrates from binding and and inhibiting the enzyme. <br /> The substrate PLP has a phosphate group that is surrounded by other polar amino acids but the rest of the substrate, the carbons are surrounded by other non-polar amino acids to satisfy the needs of the &lt;scene name='93/934004/Polar_non-polar_with_plp/1'&gt;substrate and active site&lt;/scene&gt;. PLP would not be very stable if the polar/hydrophilic portions of the substrate were trying to interact with all surrounding non-polar/hydrophobic amino acids. This allows interactions such as hydrogen bonding and pi-stacking to stabilize and bind a substrate in an active site. <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Brooklyn Mills