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Contents 1 Physical model 2 List of figures: Insulin 2.1 Initial view 2.2 reload initial figure 2.3 surface of insulin 2.4 Proinsulin 2.5 T or R 2.6 animation 2.7 T6 hexamer (e.g. structure 4INS) 2.8 insulin binding sites 2.9 contact residues 2.10 Binding sites 1 and 1\ 2.11 Jmol commands: buttons etc 2.11.1 (☼) 2.11.2 (☼) 2.11.3 (☼) 2.11.4 Choice of 2.11.5 Choice of 2.11.6 disordered 2.11.7 (☼) 2.11.8 (☼) 2.12 Summary 2.12.1 coordinates used 3 3D scenes

Physical model

List of figures: Insulin

Initial view

script: https://proteopedia.org/wiki/scripts/82/821037/Ribbon/1.spt Available on this page: User:Karsten_Theis/Insulin

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?6ad5dfaced99e610859115fe197f5ef6 (always reloads)

Ribbon view of a monomer of mature insulin (chain A in green, chain B in orange, disulfide bridges in yellow). PDB ID 4ins.

reload initial figure

script: https://proteopedia.org/wiki/scripts/82/821037/Ribbon/1.spt Available on this page: User:Karsten_Theis/Insulin

coords: same as Initial view (always reloads)

Ribbon view of a monomer of mature insulin (chain A in green, chain B in orange, disulfide bridges in yellow). PDB ID 4ins.

surface of insulin

script: https://proteopedia.org/wiki/scripts/82/821037/Spacefilling/2.spt Available on this page: User:Karsten_Theis/Insulin

coords: same as Initial view (always reloads)

Spacefilling view of single insulin molecule (main chain carbon atoms in white, side chains colored by element, charge or hydrophobic/hydrophilic). PDB ID 4ins.

Proinsulin

script: https://proteopedia.org/wiki/scripts/82/821037/Proinsulin/1.spt Available on this page: User:Karsten_Theis/Insulin

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?c6d5c9b879b8d9ac872a6b8043ac4284

NMR structure of proinsulin, 20 models. Chains B, C, and A are show as green, gray and orange alpha-carbon trace. Disulfide links are sketched in yellow.

T or R

script: https://proteopedia.org/wiki/scripts/82/821037/Rvst/1.spt Available on this page: User:Karsten_Theis/Insulin

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?38e438064650097d9c9f87c964200009

Comparison of two conformations of insulin, R and T (PDB ID 4trz). The alpha-carbon trace of one conformation is shown in blue (chains A and B), the other in gold (chains C and D). The largest differences are at the N-terminus of the B (or D) chain.

animation

script: https://proteopedia.org/wiki/scripts/82/821037/Rvst/2.spt Available on this page: User:Karsten_Theis/Insulin

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?c9eb17b4c76bc6071648e20be1513872

Animation (takes a while to load) showing a hypothetical transitions between insulin in the relaxed R-state and the tight T-state. Two insulin molecules (both with chain A and B linked by disulfides) combine to form a dimer via the beta sheet interaction in the center with residues 24-26 (shown as wireframe) forming a hydrophobic core.

T6 hexamer (e.g. structure 4INS)

script: https://proteopedia.org/wiki/scripts/82/821037/T6/1.spt Available on this page: User:Karsten_Theis/Insulin

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?id=4INS

Hexamer of insulin with all 6 insulins in the T-conformation (PDB ID 4INS). The two zinc atoms are shown as gray spheres, coordinated by three histidine side chains each (yellow and green wireframe).

insulin binding sites

script: https://proteopedia.org/wiki/scripts/82/821037/Spacefilling/5.spt Available on this page: User:Karsten_Theis/Insulin

coords: same as Initial view

Spacefilling view of insulin highlighting selected contacts made when insulin binds to site 1 (red and orange) and site 2 (blue and sky blue) of the insulin receptor. Contacts mapped on insulin in a closed conformation. The darker colors refer to higher contact occupancy^[1].

contact residues

script: https://proteopedia.org/wiki/scripts/82/821037/Ribbon/2.spt Available on this page: User:Karsten_Theis/Insulin

coords: same as Initial view

Ribbon view of a monomer of mature insulin (chain A in green, chain B in orange, disulfide bridges in yellow), with contacts to receptor site 1 highlighted in red and orange and to site 2 in blue and skyblue. PDB ID 4ins.

Binding sites 1 and 1\

script: https://proteopedia.org/wiki/scripts/82/821037/Receptor_bound/1.spt Available on this page: User:Karsten_Theis/Insulin

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?065018542545372618282fe2d6d5b804

Detail of insulin bound in site 1 of the insulin receptor. Insulin is shown as cartoon in green and orange. Selected parts of the receptor contacting insulin are shown (sky blue: parts of N-terminal domain L1, dark red: C-terminal alpha helix). PDB ID 6ce9.

Jmol commands: buttons etc

(☼)

select backbone and *:A; selectionHalos ON; delay 0.5;selectionHalos OFF; 

(☼)

select backbone and *:B; selectionHalos ON; delay 0.5;selectionHalos OFF; 

(☼)

select (*:A or *:B) and cys and (*.CA or *.SG); selectionHalos ON; delay 0.5;selectionHalos OFF; 

Choice of

• hydrophobiticity: background white; select sidechain; color magenta; select sidechain and (cys, met, ile, leu, val, phe, tyr, trp); color gray; set echo OFF; set echo ID bla 80% 0%; echo \"hydrophobic\"; color echo gray; frank off; set echo ID bla2 0% 0%; echo \"hydrophilic\"; color echo magenta
• charge: select sidechain; color white; select sidechain and (asp, glu); color red; select sidechain and (lys, arg, his); color blue; set echo OFF; set echo ID bla 80% 0%; echo \"positive\"; color echo blue; frank off; set echo ID bla2 0% 0%; echo \"negative\"; color echo red
• element: select sidechain; color cpk;set echo OFF; set echo ID bla 80% 0%; echo \"oxygen\"; color echo red; frank off; set echo ID bla2 0% 0%; echo \"nitrogen\"; color echo blue; set echo ID bla4 25% 0%; echo \"sulfur\"; color echo gold; set echo ID bla3 55% 0%; echo \"carbon\"; color echo gray;

Choice of

• mature insulin: select (29-64); backbone off;
• proinsulin: select (29-64); backbone on;

disordered

anim mode loop; anim on

(☼)

select *:A; selectionHalos ON; delay 0.5;selectionHalos OFF; 

(☼)

select *:P; selectionHalos ON; delay 0.5;selectionHalos OFF; 

Summary

Total of green links: 10

Total of Jmol buttons etc: 8

coordinates used

• 4INS: https://proteopedia.org/cgi-bin/getfrozenstructure?6ad5dfaced99e610859115fe197f5ef6
• 2KQP: https://proteopedia.org/cgi-bin/getfrozenstructure?c6d5c9b879b8d9ac872a6b8043ac4284
• 1TRZ: https://proteopedia.org/cgi-bin/getfrozenstructure?38e438064650097d9c9f87c964200009
• multi-model file, check uploads: https://proteopedia.org/cgi-bin/getfrozenstructure?c9eb17b4c76bc6071648e20be1513872
• 4INS: https://proteopedia.org/cgi-bin/getfrozenstructure?id=4INS
• 6CE9: https://proteopedia.org/cgi-bin/getfrozenstructure?065018542545372618282fe2d6d5b804

3D scenes

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

--Karsten Theis 15:16, 3 September 2020 (UTC)