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Macromolecular Visualization or… Where to go when ChemDraw just isn’t enough. Martin Case. Chem258 2009. Macromolecular viewing software. Over 150 visualization programs exist http://molvis.sdsc.edu/visres/index.html 100 of these are free to academic users

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Macromolecular visualization or where to go when chemdraw just isn t enough

Macromolecular Visualizationor…Where to go when ChemDraw just isn’t enough

Martin Case

Chem258 2009


Macromolecular viewing software
Macromolecular viewing software

  • Over 150 visualization programs exist http://molvis.sdsc.edu/visres/index.html

  • 100 of these are free to academic users

  • Many are supported across all common platforms:

    • Mac OS X

    • Windows

    • Linux/Unix

  • This introduction to visualization uses PyMol


Pymol
PyMol

  • Reads files from in Protein Data Bank format (PDB)

    • You can convert to PDB from any other file format using a program called Babel

  • Renders objects as lines, sticks, CPK, ribbons, surface etc

  • Objects are easily manipulated (spin, translate) with the mouse

  • Includes a toolkit for local protein building, energy minimization etc.



Pymol basics loading a pdb file
PyMol basics: loading a PDB file

  • The “raw data” for protein structure viewing and manipulation is the PDB file

  • ASCII text files

    • You can read and edit them with eg WordPad or TextEdit

  • A header with experimental details, references etc

  • xyz coordinates from x-ray crystallography of NMR experiments

  • The Protein Data Bank is at http://www.rcsb.org

  • The ALH receptor complexed with its autoinducer is 2uv0.pdb

    • We’ll use this structure for this tutorial



Pdb headers
PDB headers

HEADER TRANSCRIPTION 08-MAR-07 XXXX

TITLE STRUCTURE OF THE P. AERUGINOSA LASR LIGAND-BINDING DOMAIN

TITLE 2 BOUND TO ITS AUTOINDUCER

COMPND TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR

KEYWDS TRANSCRIPTION, ACYL-HOMOSERINE LACTONE RECEPTOR, QUORUM

KEYWDS 2 SENSING, TRANSCRIPTION REGULATION, ALPHA-BETA-ALPHA

KEYWDS 3 SANDWICH, TRANSCRIPTIONAL REGULATOR, ACTIVATOR, DNA-BINDING

EXPDTA X-RAY DIFFRACTION

AUTHOR M.J.BOTTOMLEY, E.MURAGLIA, R.BAZZO, A.CARFI

JRNL AUTH M.J.BOTTOMLEY, E.MURAGLIA, R.BAZZO, A.CARFI

JRNL TITL MOLECULAR INSIGHTS INTO QUORUM SENSING IN THE

JRNL TITL 2 HUMAN PATHOGEN PSEUDOMONAS AERUGINOSA FROM THE

JRNL TITL 3 STRUCTURE OF THE VIRULENCE REGULATOR LASR BOUND TO

JRNL TITL 4 ITS AUTOINDUCER.

JRNL REF J.BIOL.CHEM. V. 282 13592 2007

JRNL REFN ASTM JBCHA3 US ISSN 0021-9258

JRNL PMID 17363368

JRNL DOI 10.1074/JBC.M700556200

SEQRES 1 E 175 GLY ALA MSE ALA LEU VAL ASP GLY PHE LEU GLU LEU GLU

SEQRES 2 E 175 ARG SER SER GLY LYS LEU GLU TRP SER ALA ILE LEU GLN

SEQRES 3 E 175 LYS MSE ALA SER ASP LEU GLY PHE SER LYS ILE LEU PHE

SEQRES 4 E 175 GLY LEU LEU PRO LYS ASP SER GLN ASP TYR GLU ASN ALA

SEQRES 5 E 175 PHE ILE VAL GLY ASN TYR PRO ALA ALA TRP ARG GLU HIS


Pdb coordinates protein
PDB coordinates (protein)

ATOM 1 N GLY E 6 29.335 -0.940 63.260 1.00 17.84 N

ATOM 2 CA GLY E 6 29.407 0.297 62.504 1.00 17.95 C

ATOM 3 C GLY E 6 28.906 1.490 63.294 1.00 17.84 C

ATOM 4 O GLY E 6 27.701 1.663 63.477 1.00 18.09 O

ATOM 5 N PHE E 7 29.835 2.315 63.764 1.00 17.68 N

ATOM 6 CA PHE E 7 30.323 3.445 62.983 1.00 17.46 C

ATOM 7 C PHE E 7 29.628 3.519 61.627 1.00 17.40 C

ATOM 8 O PHE E 7 28.718 4.324 61.428 1.00 17.42 O

ATOM 9 CB PHE E 7 31.838 3.350 62.792 1.00 17.57 C

ATOM 10 CG PHE E 7 32.478 4.642 62.369 1.00 17.61 C

ATOM 11 CD1 PHE E 7 33.386 4.670 61.324 1.00 17.36 C

ATOM 12 CD2 PHE E 7 32.170 5.827 63.015 1.00 17.59 C

ATOM 13 CE1 PHE E 7 33.976 5.857 60.932 1.00 17.50 C

ATOM 14 CE2 PHE E 7 32.757 7.017 62.627 1.00 17.62 C

ATOM 15 CZ PHE E 7 33.661 7.032 61.584 1.00 17.40 C

ATOM 16 N LEU E 8 30.039 2.631 60.727 1.00 17.17 N

ATOM 17 CA LEU E 8 29.697 2.728 59.315 1.00 17.22 C

ATOM 18 C LEU E 8 28.192 2.768 59.079 1.00 17.06 C

ATOM 19 O LEU E 8 27.722 3.478 58.191 1.00 17.28 O

ATOM 20 CB LEU E 8 30.322 1.572 58.532 1.00 17.34 C

ATOM 21 CG LEU E 8 30.213 0.185 59.167 1.00 17.70 C

ATOM 22 CD1 LEU E 8 29.138 -0.640 58.477 1.00 17.98 C

ATOM 23 CD2 LEU E 8 31.553 -0.533 59.126 1.00 17.59 C


Pdb coordinates non protein
PDB coordinates (non-protein)

HETATM 2627 C21 OHN E1169 28.316 19.063 77.652 1.00 7.59 C

HETATM 2628 C20 OHN E1169 27.312 19.933 76.888 1.00 6.96 C

HETATM 2629 C19 OHN E1169 26.399 19.052 76.036 1.00 6.87 C

HETATM 2630 C18 OHN E1169 25.305 19.850 75.325 1.00 7.62 C

HETATM 2631 C17 OHN E1169 24.113 20.065 76.244 1.00 6.73 C

HETATM 2632 C16 OHN E1169 23.381 18.755 76.511 1.00 6.04 C

HETATM 2633 C15 OHN E1169 22.384 18.934 77.643 1.00 4.71 C

HETATM 2634 C14 OHN E1169 21.910 17.570 78.135 1.00 2.14 C

HETATM 2635 C13 OHN E1169 23.043 16.837 78.847 1.00 2.00 C

HETATM 2636 C11 OHN E1169 22.528 15.724 79.762 1.00 2.00 C

HETATM 2637 O12 OHN E1169 21.330 15.448 79.830 1.00 2.00 O

HETATM 2638 C10 OHN E1169 23.563 14.956 80.595 1.00 2.00 C

HETATM 2639 C8 OHN E1169 22.908 13.701 81.181 1.00 2.00 C

HETATM 2640 O9 OHN E1169 22.782 12.678 80.517 1.00 2.00 O

HETATM 2641 N7 OHN E1169 22.500 13.817 82.437 1.00 2.00 N

HETATM 2642 C1 OHN E1169 21.856 12.720 83.157 1.00 2.00 C

HETATM 2643 C5 OHN E1169 22.417 12.612 84.569 1.00 2.00 C

HETATM 2644 C4 OHN E1169 21.209 12.035 85.304 1.00 2.00 C

HETATM 2645 C2 OHN E1169 20.403 13.049 83.438 1.00 2.00 C

HETATM 2646 O6 OHN E1169 19.679 13.688 82.679 1.00 2.00 O

HETATM 2647 OAP OHN E1169 20.010 12.548 84.638 1.00 2.00 O


Loading a pdb file
Loading a PDB file

  • Choose the file 2uv0.pdb


It should look something like this
It should look something like this…

  • Water molecules are shown as red crosses

  • C green, N blue, O red, S yellow

  • Default rendering is “line”

  • Notice there are 2 molecules in the asymmetric unit

    • Not identical: pseudo C2


Impressive but not very helpful
Impressive, but not very helpful

  • We’d like to know some simple things, eg

  • How many polypeptide chains per protein?

  • Where is the autoinducer?

  • What contacts does the protein make with the autoinducer?


View the chains using the ribbon function
View the chains using the ribbon function

1. hide everything

2. show ribbons

  • If you don’t want to see something, hide it

  • The default is to overlay images


Removing one copy of the protein
Removing one copy of the protein

  • Define chain G as a selection

  • Type at the prompt (bottom left)

    • PyMOL> select junk, chain G

    • PyMOL> remove junk

    • PyMOL> delete junk

  • Recenter:



Turn on the helices and sheets
Turn on the helices and sheets

  • Hide ribbon

  • Show cartoon

  • Play with the colors

  • Run the ray-tracer (Ray)


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