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Reminder of Day 1 using Insight II

Reminder of Day 1 using Insight II. Use pulldown menus or commands get molecule eg from pdb file display only parts/atoms of interest color different parts/atoms differently render as lines, balls & spokes or CPK. Syntax molecule:residue(s):atom(s) wild card *.

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Reminder of Day 1 using Insight II

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  1. Reminder of Day 1using Insight II • Use pulldown menus or commands • get molecule eg from pdb file • display only parts/atoms of interest • color different parts/atoms differently • render as lines, balls & spokes or CPK Syntax molecule:residue(s):atom(s) wild card *

  2. Building Molecules & Assembliesusing source files • Instead of typing commands into Insight create file with one or more commands, then use source filename Advantages: • quicker • avoids repetitive typing & mistakes • can incorporate into automatic procedures • can revise for a new task

  3. source file to get, display & color myosin head # getS1 get molecule pdb pdb2mys.ent S1 disp off * disp S1::ca color molecule atoms S1:a* cyan color molecule atoms S1:b* red color molecule atoms S1:c* yellow color molecule atoms S1:a131 green color molecule atoms S1:a324 magenta render molecule ball_and_stick S1:a131,a324 3,0

  4. subsets • A subset is a region of a molecule. • Can be used to define a zone around a target group or an interface between subunits • Example • To display the active site of myosin • use zone subset to define a zone (atpzone) of all residues within 2.5 Å of bound ATP. • Disp atpzone

  5. building small organic molecules • get fragment(s) from fragment library or get existing molecule • Modify/Create bond • Modify/Bond order • set potentials (type of atom) Example 1: make methylamine Example 2: make tetraphenylethylene Example 3: make GTP from ATP

  6. WIN95: alpha helix show backbone and then add h bonds beta strand show backbone copy and then move until hbonds for parallel Building polypeptide chains • Use biopolymer module • Use Residue Append menu Example 1 make alpha-helix with sequence RATTLESNAKE Example 2 make beta strand with sequence SALSASALSA

  7. Building an a-helical coiled coil • Use Crick equations to define the coordinates of the backbone atoms • Decide on number of strands • Decide on pitch, radius & relative rotation • Choose sequence • Use program to make pdb file

  8. Creating a protein molecule from fragments • get fragments eg from pdb files • superpose common regions • break old bonds • make new bonds • delete redundant protein Example 1: making two-headed myosin molecule from coiled-coil + head fragments Example 2: adding RLC domain to chicken smooth MDE

  9. Source files for making head-tail junction of myosin get mol arc 1 newbestscallopcc3.cor cor color molecule atoms cor_1 cyan color molecule atoms cor_2 blue merge cor_1 cor_2 rotate cor_1 relative -90,0,0 screen move cor_1 relative 50,0,0 screen get mol pdb card.pdb card heteroatom copy card cardb move card relative -50,50,0 screen move cardb relative -50,-50,0 screen color molecule atoms :a* cyan ............................... super card:a835:n,ca,c,o,cb,cg,cd cor_1:835:n,ca,c,o,cb,cg,cd super end_def super cardb:b835:n,ca,c,o,cb,cg,cd cor_1:835b:n,ca,c,o,cb,cg,cd super end_def bond break card:a835:c card:a836:n ............................

  10. Source file for adding RLC domain to chicken smooth MDE # makemderlc get mol pdb c2.pdb c2 heteroatom disp off * disp ::ca disp c2:mg,adp,alf color molecule atoms c2:a* cyan color molecule atoms c2:b* yellow color molecule atoms c2:mg magenta color molecule atoms c2:adp red color molecule atoms c2:alf green get mol pdb pdb2mys.ent S1 disp off S1 disp S1::ca color molecule atoms S1:a* blue color molecule atoms S1:b* red color molecule atoms S1:c* orange super S1:a790-a809:ca c2:a799-a818:ca super end_def

  11. Flexing a protein molecule • Proteins often flex between domains • get molecule eg from pdb file • choose hinge point • unmerge region of protein beyond hinge point • choose axes • rotate distal region Example: flexing myosin molecule between RLC & ELC domains

  12. Source file for flexing myosin molecule get mol pdb rotscmyosin.pdb myosin1a color molecule atoms myosin1a:a*,g* cyan color molecule atoms myosin1a:b*,h* blue color molecule atoms myosin1a:c*,d* yellow color molecule atoms myosin1a:e*,f* red unmerge myosin1a:g4-g204,g216-g571,g575-g626, g647-g731,g738-g784,a780-a799,c4-c152 gac unmerge myosin1a:h4-h204,h216-h571,h575-h626, h647-h731,h738-h784,b780-b799,d4-d152 hbd axes gac coordinates recenter 0, 0, 0 50, 0, 0 0, 50, 0 center -world gac atom gac:a799:ca rotate gac relative 0,0,1 alternate rotate gac relative 0,0,1 alternate ................................ axes hbd Coordinates Recenter 0, 0, 0 50, 0, 0 0, 50, 0 center -world hbd atom hbd:b799:ca rotate hbd relative 0,0,2 alternate rotate hbd relative 0,0,2 alternate

  13. Making Assemblies • get subunit eg from pdb files • make copies of subunit • use Transform Move & Rotate to position each subunit using symmetry of assembly Example: making tarantula myosin filaments from myosin molecules

  14. get mol pdb rotscmyosin.pdb myosin1a color molecule atoms myosin1a:a*,g* cyan rotate myosin1a 0,-105,0 screen rotate myosin1a 0,0,28 screen rotate myosin1a 0,0,50 alternate copy myosin1a myosin1b copy myosin1a myosin1c copy myosin1a myosin1d rotate myosin1b 0,0,-90 screen rotate myosin1c 0,0,-180 screen rotate myosin1d 0,0,-270 screen move myosin1a relative -124,0,0 screen move myosin1b relative 0,-124,0 screen move myosin1c relative 124,0,0 screen move myosin1d relative 0,124,0 screen associate assembly myosin1* unused crown1 copy myosin1a myosin2a copy myosin1b myosin2b copy myosin1c myosin2c copy myosin1d myosin2d associate assembly myosin2* unused crown2 rotate crown2 0,0,-30 screen move crown2 relative 0,0,145 screen copy myosin1a myosin3a .............

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