Macromolecular Visualization or… Where to go when ChemDraw just isn’t enough Martin Case Chem

Macromolecular viewing software Over 150 visualization programs exist 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 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 screenshots

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 The ALH receptor complexed with its autoinducer is 2uv0.pdb We’ll use this structure for this tutorial

Download the biological unit You might need to unzip/unstuff the file And you might need to change the.pdb1 to.pdb

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 JRNL REFN ASTM JBCHA3 US ISSN JRNL PMID JRNL DOI /JBC.M 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) ATOM 1 N GLY E N ATOM 2 CA GLY E C ATOM 3 C GLY E C ATOM 4 O GLY E O ATOM 5 N PHE E N ATOM 6 CA PHE E C ATOM 7 C PHE E C ATOM 8 O PHE E O ATOM 9 CB PHE E C ATOM 10 CG PHE E C ATOM 11 CD1 PHE E C ATOM 12 CD2 PHE E C ATOM 13 CE1 PHE E C ATOM 14 CE2 PHE E C ATOM 15 CZ PHE E C ATOM 16 N LEU E N ATOM 17 CA LEU E C ATOM 18 C LEU E C ATOM 19 O LEU E O ATOM 20 CB LEU E C ATOM 21 CG LEU E C ATOM 22 CD1 LEU E C ATOM 23 CD2 LEU E C

PDB coordinates (non-protein) HETATM 2627 C21 OHN E C HETATM 2628 C20 OHN E C HETATM 2629 C19 OHN E C HETATM 2630 C18 OHN E C HETATM 2631 C17 OHN E C HETATM 2632 C16 OHN E C HETATM 2633 C15 OHN E C HETATM 2634 C14 OHN E C HETATM 2635 C13 OHN E C HETATM 2636 C11 OHN E C HETATM 2637 O12 OHN E O HETATM 2638 C10 OHN E C HETATM 2639 C8 OHN E C HETATM 2640 O9 OHN E O HETATM 2641 N7 OHN E N HETATM 2642 C1 OHN E C HETATM 2643 C5 OHN E C HETATM 2644 C4 OHN E C HETATM 2645 C2 OHN E C HETATM 2646 O6 OHN E O HETATM 2647 OAP OHN E O

Loading a PDB file Choose the file 2uv0.pdb

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 C 2

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 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 Define chain G as a selection Type at the prompt (bottom left) PyMOL> select junk, chain G PyMOL> remove junk PyMOL> delete junk Recenter:

Showing the autoinducer as sticks

Turn on the helices and sheets Hide ribbon Show cartoon Play with the colors Run the ray-tracer (Ray)