Talk:Hen Egg-White (HEW) Lysozyme

From Proteopedia

proteopedia linkproteopedia link

Contents 1 How some of the figures were made 1.1 Opening scene 1.2 Hydrogen bonds 2 Substrate complex with sugar not in chair conformation 3 List of figures: Lysozyme 3.1 Initial view 3.2 ribbon view 3.3 colored by conservation 3.4 this hypothetical model 3.5 covalent intermediate 3.6 product complex with five sugar units 3.7 Jmol commands: buttons etc 3.7.1 Lysozyme 3.7.2 ☼ 3.7.3 ☼ 3.7.4 ☼ 3.7.5 ☼ 3.7.6 ☼ 3.7.7 ☼ 3.7.8 ☼ 3.7.9 Hydrophobic residues 3.7.10 hydrophilic residues and proline 3.7.11 water 3.7.12 Choice of 3.7.13 Choice of 3.7.14 [± backbone spacefill] 3.7.15 [± ligand] 3.7.16 [± water] 3.7.17 hydrogen bonds 3.7.18 helices 3.7.19 beta turns 3.7.20 between strands 3.7.21 Ordered waters 3.7.22 between protein and ligand 3.7.23 toggle fading and slabbing 3.7.24 turn centering on 3.7.25 turn centering off 3.7.26 modeled extra sugars 3.7.27 Choice of 3.7.28 just ring 3.7.29 front view 3.7.30 side view 3.7.31 side view too 3.7.32 active site 3.7.33 active site too 3.7.34 wobble 3.7.35 bobble 3.8 Summary 3.8.1 coordinates used 4 3D scenes

How some of the figures were made

Opening scene

This is a script to create the opening scene after loading coordinate 1HEW (you could also use the screen authoring tool)

restrict none                                       #clean slate
select ligand; wireframe 0.3; spacefill 0.5;        #make bonds on ligand a bit thicker
select protein; backbone 0.4; color backbone group  #rainbow c-alpha trace
color background black                              #as it says
select *.CA; spacefill 0.8;                         #spheres on alpha carbons
label "%m";set labelOffset 0 0; color label yellow  #...with yellow labels on top
hover "%n %r, Chain=%c, Element=%e";                #show 3-letter code number, chain and element
select cys.sg; wireframe 0.25; set ssbonds backbone #disulfide bonds

Here is an animation to see what the commands do

and a screen shot of the finished scene with captions for reference

Hydrogen bonds

To enable centering with the mouse for this scene ("set picking center"), the green link was made as a JmolLink rather than using the Screen Authoring tool. The following was used:

<jmol>
  <jmolLink>
    <script>set picking center; display all; script /scripts/37/376372/Hbonds/5.spt </script>
    <text>hydrogen bonds</text>
  </jmolLink>
</jmol>

Except for the two Jmol commands that are explicitly shown above, the rest of the figure was saved as the usual state file in the scene authoring tool, and then called to generate the figure ("script ...Hbonds/5.spt"). For the other green links in the section, I was able to use the the conventional method because the command "set picking center" had already been issued. Below are the commands to show the hydrogen bonds in the context of the protein, ligand and water.

restrict none                                      # clean slate
select protein; wireframe 0.1                      # thin bonds for protein
select backbone; wireframe 0.3                     # but thick bonds for main chain
set ssbondsbackbone false                          # disulfide bonds between sulfur atoms, not C-alpha
color background white                             # as it says
select water; spacefill 0.2;                       # water oxygens as spheres
select ligand; spacefill 0.6; wireframe 0.3        # ligand in ball and stick
select ligand and _C;color atoms opaque [x800080]  # carbon atoms of ligand in purple
set hbondsRasmol FALSE; calculate HBONDS           # calculate and display hydrogen bonds (not just main chain)
slab 60;depth 20;slab on                           # slab away atoms in foreground
set zShade true                                    # fade away atoms in background

Substrate complex with sugar not in chair conformation

1QBB, 1OVW, discussed in https://pubs.acs.org/doi/pdfplus/10.1021/jacs.5b01156

List of figures: Lysozyme

Initial view

script: https://proteopedia.org/wiki/scripts/37/376372/Overall/3.spt Available on this page: Hen_Egg-White_(HEW)_Lysozyme

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?2f267243b1cf263a27c03cd5ce051b66

Overview of the 1HEW structure. The trace of the protein chain is shown in rainbow colors with the alpha carbons as gray spheres labeled with the residue one letter code. The carbohydrate ligand is shown as ball and stick in CPK colors (carbon: gray, oxygen: red, nitrogen: blue).

ribbon view

script: https://proteopedia.org/wiki/scripts/37/376372/Secondary_structure/7.spt Available on this page: Hen_Egg-White_(HEW)_Lysozyme

coords: same as Initial view

Overview of the 1HEW secondary structure: Alpha Helices, 3-10 helix, Beta Strands, with loops in white and disulfide bonds in yellow. Arrow tips point towards the C-terminal end.

colored by conservation

script: https://proteopedia.org/wiki/ConSurf/he/1hew_consurf.spt coords: none

this hypothetical model

script: https://proteopedia.org/wiki/scripts/37/376372/Hex_model/1.spt Available on this page: Hen_Egg-White_(HEW)_Lysozyme

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?caa67c01c8140e2b3f7b60e4e749f1dd

1HEW with additional three sugars modeled into the active site.

covalent intermediate

script: https://proteopedia.org/wiki/scripts/37/376372/Covalent_intermediate/2.spt Available on this page: Hen_Egg-White_(HEW)_Lysozyme

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?932c10afc4e1e94cdeab12d300cbb47b (always reloads)

Structure of the covalent enzyme intermediate. The active site residue Asp 52 and the carbohydrate are shown in CPK colors, with the 2FO-FC electron density within 1.5 A of these atoms as blue mesh. The backbone trace is shown in gold.

product complex with five sugar units

script: https://proteopedia.org/wiki/scripts/37/376372/Product_complex/6.spt Available on this page: Hen_Egg-White_(HEW)_Lysozyme

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?09a5df19589b9b4571d13eef460f52bf

Comparison of covalent intermediate (1H6M) and product complex (2WAR), both for the almost inactive Glu35Gln mutant. Backbone in gold, with ligand in thick wireframe and side chains of active site residues 35 and 52 in thin wireframe. Fluorine is shown in green.

Jmol commands: buttons etc

Lysozyme

script /scripts/37/376372/Overall/3.spt; hide water; set zshade off; spin off;

☼

select ligand; selectionHalos ON; delay 0.5;selectionHalos OFF;

☼

select 1.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;

☼

select *.ca and 1; selectionhalos on;\ndelay 0.5;\nselect *.ca and 1-10; delay 0.3;\nselect *.ca and 5-15; delay 0.2;\nselect *.ca and 11-20; delay 0.1;\nselect *.ca and 15-25; delay 0.1;\nselect *.ca and 21-30; delay 0.1;\nselect *.ca and 25-35; delay 0.1;\nselect *.ca and 31-40; delay 0.1;\nselect *.ca and 35-45; delay 0.1;\nselect *.ca and 41-50; delay 0.1;\nselect *.ca and 45-55; delay 0.1;\nselect *.ca and 51-60; delay 0.1;\nselect *.ca and 55-65; delay 0.1;\nselect *.ca and 61-70; delay 0.1;\nselect *.ca and 65-75; delay 0.1;\nselect *.ca and 71-80; delay 0.1;\nselect *.ca and 75-85; delay 0.1;\nselect *.ca and 81-90; delay 0.1;\nselect *.ca and 85-95; delay 0.1;\nselect *.ca and 91-100; delay 0.1;\nselect *.ca and 101-110; delay 0.1;\nselect *.ca and 111-122; delay 0.1;\nselect *.ca and 122-127; delay 0.2;\nselect *.ca and 124-129; delay 0.3;\nselect *.ca and 129; delay 0.5;\nselectionhalos off;

☼

select 129.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;

☼

select BONDS ({0:3}); wireframe 0.6; delay 0.5; wireframe 0.1

☼

select helix and *.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;

☼

select sheet and *.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;

Hydrophobic residues

select backbone or water; spacefill off; hide ligand or (sidechain and not (met, cys, ile, leu, val, phe, tyr, trp))

hydrophilic residues and proline

select backbone or water; spacefill off; hide ligand or (sidechain and (met, cys, ile, leu, val, phe, tyr, trp))

water

select backbone; spacefill on; select water; spacefill 1.0; display all

Choice of

• hydrophobic side chains: hide (hidden and not sidechain) or (sidechain and not (met, cys, ile, leu, val, phe, tyr, trp))
• hydrophilic side chains: hide (hidden and not sidechain) or (sidechain and (met, cys, ile, leu, val, phe, tyr, trp))
• all side chains: display (displayed and not sidechain) or sidechain

Choice of

• colored by hydrophobiticity: select sidechain; color magenta; select sidechain and (cys, met, ile, leu, val, phe, tyr, trp); color gray; set echo ID bla 80% 0%; echo \"hydrophobic\"; color echo gray; frank off; set echo ID bla2 0% 0%; echo \"hydrophilic\"; color echo magenta
• colored by charge: select sidechain; color white; select sidechain and (asp, glu); color red; select sidechain and (lys, arg, his); color blue; set echo ID bla 80% 0%; echo \"positive\"; color echo blue; frank off; set echo ID bla2 0% 0%; echo \"negative\"; color echo red
• colored by conservation: select sidechain; define ~consurf_to_do selected; define ~consurf_to_color selected; useFullScript = true; consurf_initial_scene = false; script /wiki/ConSurf/he/1hew_consurf.spt; set echo ID bla 80% 0%; echo \"conserved\"; color echo palevioletred; frank off; set echo ID bla2 0% 0%; echo \"variable\"; color echo darkturquoise

[± backbone spacefill]

if ({*.O and backbone and visible}.size\x3e0) {select backbone; spacefill off} else {select backbone; spacefill on}

[± ligand]

if ({ligand and hidden}.size\x3e0) {display displayed or ligand} else {hide ligand or hidden}

[± water]

if ({water and visible}.size\x3e0) {select water; spacefill off} else {select water; spacefill 1.0}

hydrogen bonds

set picking center; display all; script /scripts/37/376372/Hbonds/5.spt

helices

script /scripts/37/376372/Hbonds/1.spt; select helix and backbone; hbonds 0.2; delay 1.2; hbonds 0.04;

beta turns

script /scripts/37/376372/Hbonds/5.spt; select 74,77; hbonds 0.2; delay 1.2; hbonds 0.04;

between strands

script /scripts/37/376372/Hbonds/2.spt; select sheets and backbone; hbonds 0.2; delay 1.2; hbonds 0.04;

Ordered waters

hide none; script /scripts/37/376372/Hbonds/4.spt

between protein and ligand

script /scripts/37/376372/Hbonds/3.spt; select ligand and not 201:A.O1; set bondMode OR; hbonds 0.2; delay 1.2; hbonds 0.04;

toggle fading and slabbing

if (zshade) {set zshade off; slab off} else {set zshade on; slab on}

turn centering on

set picking center

turn centering off

set picking identify

modeled extra sugars

• [On]: display all
• [Off]: hide 204-206

Choice of

• product: anim off; delay 1.0; model 1
• intermediate: anim off; delay 1.0; model 2
• animate: anim fps 1; anim mode loop; anim on;

just ring

• [On]: hide ligand and not ((1134 or G2F) and (*.O1, *.C1, *.C2, *.C3, *.C4, *.C5, *.O5, *.N5, *.O4))
• [Off]: hide water

front view

moveto 2.0 { 579 257 774 163.39} 120.0 0.0 0.0 {-0.33203837 20.866533 19.55904} 31.371292 {0 0 0} 0 0 0 3.0 0.0 0.0;

side view

moveto /* time, axisAngle */ 2.0 { -919 -290 -267 175.7} /* zoom, translation */ 120.0 0.0 0.0 /* center, rotationRadius */ {-0.33203837 20.866533 19.55904} 31.371292 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;\n

side view too

moveto /* time, axisAngle */ 2.0 { -430 -10 903 146.05} /* zoom, translation */ 120.0 0.0 0.0 /* center, rotationRadius */ {-0.33203837 20.866533 19.55904} 31.371292 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;

active site

moveto /* time, axisAngle */ 2.0 { 14 -997 -82 164.64} /* zoom, translation */ 615.28 0.0 0.0 /* center, rotationRadius */ {6.174519999999999 24.04584 25.138840000000002} 40.46755187629986 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;

active site too

moveto /* time, axisAngle */ 2.0 { 311 -943 -118 125.09} /* zoom, translation */ 500.88 16.86 6.57 /* center, rotationRadius */ {5.804955513628509 21.50459857126935 17.894926846396874} 35.7306153511559 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;

wobble

script http://proteopedia.org/wiki/images/7/76/Wobble.spt

• • What is http://proteopedia.org/wiki/images/7/76/Wobble.spt','wobble');

bobble

script http://proteopedia.org/wiki/images/b/b9/Bobble2.spt

• • What is http://proteopedia.org/wiki/images/b/b9/Bobble2.spt','bobble');

Summary

Total of green links: 6

Total of Jmol buttons etc: 35

coordinates used

• 1HEW: https://proteopedia.org/cgi-bin/getfrozenstructure?2f267243b1cf263a27c03cd5ce051b66
• do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?caa67c01c8140e2b3f7b60e4e749f1dd
• 1H6M: https://proteopedia.org/cgi-bin/getfrozenstructure?932c10afc4e1e94cdeab12d300cbb47b
• do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?09a5df19589b9b4571d13eef460f52bf

3D scenes

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

--Karsten Theis 15:19, 3 September 2020 (UTC)