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===Smooth Transitions===
===Smooth Transitions===
====Tip #1: When developing a series of scenes illustrating related parts of a protein, use the “transition options” to create smooth transitions void of peculiar zoom-outs, etc.====
====Tip #1: When developing a series of scenes illustrating related parts of a protein, use the “transition options” to create smooth transitions void of peculiar zoom-outs, etc.====
=====Example from the page [[HMG-CoA Reductase]]: =====
=====Example from the page [[The Structure of PI3K]]: =====
<center><scene name='HMG-CoA_Reductase/1dq8_starting_scene/1'>Initial Scene (Reset)</scene> </center>
<center><scene name='User:David_Canner/Sandbox_P/Nsh2_full/1'>Initial Scene (Reset)</scene> </center>
The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/2'> The “cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/2'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>. It is this K691 that likely stabilizes the negatively charged oxygen of the first mevaldyl-CoA intermediate. The mevaldyl CoA intermediate is subsequently converted to Mavaldehyde with added stabilization from <scene name='HMG-CoA_Reductase/1dqa_h866/2'>H866, which is within hydrogen bonding distance of the thiol group</scene>. It is then believed that the close proximity of <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.<br />
Although no <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>crystal structure of PI3K</scene> with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. In this model, the headgroup of PIP2 is <scene name='User:David_Canner/Sandbox_P/Catalytic_cavity/2'>positioned in a cavity</scene> between the <scene name='User:David_Canner/Sandbox_P/Catalytic_site/1'>C-terminal helix 12 of the kinase domain, the “activation” loop, and the “catalytic” loop</scene>. This puts the 5-phosphate of PIP2 near Lys 973 and the <scene name='User:David_Canner/Sandbox_P/Catalytic_site_atp_lys/1'>I-phosphate of ATP near Lys 807 and Lys 808</scene>. The <scene name='User:David_Canner/Sandbox_P/Catalytic_site_pip2/1'>basic residues Arg 947</scene> and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed <scene name='User:David_Canner/Sandbox_P/Catalytic_site_his/1'>His 948 rotates to interact with PIP2</scene>, deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3.
=====Compared with:=====
The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/3'> The“cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/3'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/3'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>...
 
====Tip #2: It is best to establish a color scheme for all domains of interest and to stick with this color scheme throughout the analysis====
====Tip #2: It is best to establish a color scheme for all domains of interest and to stick with this color scheme throughout the analysis====
=====Example from the page [[The Structure of PI3K]] =====
=====Example from the page [[The Structure of PI3K]] =====
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<center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center>
<center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center>
LY294002, a competitive inhibitor of ATP binding in the PI3K kinase domain, was first discovered by scientists at Eli Lilly. Quercetin, Myricetin & Staurosporine are natural compounds which broadly inhibit protein kinases. Understanding how ATP binds to the ATP binding site <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>within the kinase domain</scene> of PI3Kγ and how various inhibitors prevent this interaction helps elucidate ways to develop effective, selective inhibitors. See p110γ bound to <scene name='User:David_Canner/Sandbox_P/Inhibitor_atp/5'>ATP</scene> ([[1e8x]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_wortmannin/7'>Wortmannin</scene> ([[1e7u]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_ly294002/2'>LY294002</scene> ([[1e7v]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_quer/2'>Quercetin</scene> ([[1e8w]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_staur/1'>Staurosporine</scene> ([[1e8z]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_myrice/1'>Myricetin</scene> ([[1e90]]).
LY294002, a competitive inhibitor of ATP binding in the PI3K kinase domain, was first discovered by scientists at Eli Lilly. Quercetin, Myricetin & Staurosporine are natural compounds which broadly inhibit protein kinases. Understanding how ATP binds to the ATP binding site <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>within the kinase domain</scene> of PI3Kγ and how various inhibitors prevent this interaction helps elucidate ways to develop effective, selective inhibitors. See p110γ bound to <scene name='User:David_Canner/Sandbox_P/Inhibitor_atp/5'>ATP</scene> ([[1e8x]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_wortmannin/7'>Wortmannin</scene> ([[1e7u]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_ly294002/2'>LY294002</scene> ([[1e7v]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_quer/2'>Quercetin</scene> ([[1e8w]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_staur/1'>Staurosporine</scene> ([[1e8z]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_myrice/1'>Myricetin</scene> ([[1e90]]).
====Tip #6: Whenever possible, try to illustrate points using same .pdb file to avoid "choppy" scene transitions. If unavoidable, include "reorienting" scenes which provide a view of the entire protein.====
=====Example from the page [[PI3K Activation, Inhibition, & Medical Implications]]:=====
<center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center>
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