Protein Structure and Visualisation. Introduction to PDB and PyMOL

Transcription

1 Protein Structure and Visualisation Introduction to PDB and PyMOL 1

2 Feedback Persons 2

3 Program Quiz results Introduction to PDB & PyMOL Break PyMOL tutorial Break Summary Quiz 3

4 Program Quiz results Introduction to PDB & PyMOL Break PyMOL tutorial Break Summary Quiz 4

5 PDB Growth February

6 Protein Data Bank Contents File structure Types of structures Structure reports & summaries Quality check Searching Molecule of the Month 6

7 PDB File Header HEADER IMMUNE SYSTEM 16-AUG-04 1X7Q TITLE CRYSTAL STRUCTURE OF HLA-A*1101 WITH SARS NUCLEOCAPSID TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-11 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : SEQRES 1 C 9 LYS THR PHE PRO PRO THR GLU PRO LYS HET SO4 B HETNAM SO4 SULFATE ION HELIX 1 1 ALA A 49 GLU A CRYST P

8 PDB File Atom Coordinates ATOM 1 N THR A N ATOM 2 CA THR A C ATOM 3 C THR A C ATOM 4 O THR A O ATOM 5 CB THR A C ATOM 6 OG1 THR A O ATOM 7 CG2 THR A C HETATM 3284 O3 GOL B O HETATM 3285 O HOH A O ATOM 1 N GLY A N ANISOU 1 N GLY A N ATOM 2 CA GLY A C ANISOU 2 CA GLY A C ATOM 3 C GLY A C ANISOU 3 C GLY A C

9 PDB File Fields COLUMNS DATA TYPE FIELD DEFINITION Record name "ATOM" 7-11 Integer serial Atom serial number Atom name Atom name. 17 Character altloc Alternate location indicator Residue name resname Residue name. 22 Character chainid Chain identifier Integer resseq Residue sequence number. 27 AChar icode Code for insertion of residues Real(8.3) x Orthogonal coordinates for X in Angstroms Real(8.3) y Orthogonal coordinates for Y in Angstroms Real(8.3) z Orthogonal coordinates for Z in Angstroms Real(6.2) occupancy Occupancy Real(6.2) tempfactor Temperature factor LString(2) element Element symbol, right-justified LString(2) charge Charge on the atom.

10 Worldwide Structural Genomics Fold space coverage " Complete genomes Disease-causing organisms Model organisms" Membrane proteins" Protein-ligand interactions Hou et al., PNAS 2003, 100: "

11 Protein Folds in PDB New folds Total folds

12 Protein Structure Visualisation PyMOL 12

13 What is PyMOL? Open-source molecular viewing program

14 Benefits It s free! For academia not for industry. Version 0.99rc6 Users can always compile the latest version. But you should contribute! Pay to get support, manual, latest version etc.

15 Potential Weaknesses Few! Not a fully integrated modelling environment. Not fully developed for experimental structure determination/fitting. Mostly for qualitative analyses. No undo function

16 PyMOL Representations Lines, sticks, ribbon, spheres, cartoon(s) Surfaces Transparency, quality Ray-tracing (rendering) Modes 16

17 Selections & Objects Every molecule (pdb file) is an object. Selections refer to objects Make smaller or composite objects Changes in representation can affect objects or selections.

18 Links PDB (protein structure database) PyMOL home: PyMOL manual: PyMOL Wiki: PyMOL settings (documented): modules/pymol/setting.py

19 Installation Windows Mac OS X Special behaviour Rename to get plugin menu! MacPyMOL MacPyMOLX11Hybrid Linux

20 PyMOL scripting

21 Scripts PyMOL is based on the programming language Python. PyMOL will read python commands. PyMOL also has a set of native commands. See PyMOLWiki and elsewhere for examples. pymol/

22 Automating Tasks Scripts are useful for automating tasks Repeated analyses Reading in large numbers of structures Making illustrations! get_view set_view viewport Saves space! Relative to PyMOL session files (.pse)

23 A Useful Example Using PyMOL commands: list=[]! iterate (name ca),list.append((resi,resn))! print list!! [('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), ('LEU',! '6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', '11'),! ('CYS', '12'), ('THR', '13')]!! or using a Python script (in PyMOL):!! from pymol import cmd,stored! stored.list=[]! cmd.iterate("(name ca)","stored.list.append((resi,resn))")! print stored.list!! [('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), ('6', '! LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', 'TRP'),! ('12', 'CYS'), ('13', 'THR')]

24 color_b.py To colour proteins according to the values of the B-factor column (can be replaced with any desired value). Syntax: (see script header) color_b (c;a or c;b), mode=ramp, gradient=bwr, nbins=30, sat=0.5, value=1 to color chains A and B with the Blue-White-Red gradient in 30 colors of equal numbers of atoms in each color.

25 PyMOL Log Function Records all actions as commands in a PyMOL session GUI clicks Written commands Needs to be opened at start of session Is only written when closed (File Close log)

26 Example 1 rrna Large subunit: Catalytic mechanism Protein mrna Small subunit: Specificity 26

27 Example 2 27 René Magritte

28 Aesthetics of Molecular Images Personal taste General guidelines: Focus on relevant parts Strip away unnecessary information Find good viewing angle! Choice of representation No need for excessive graphics Good figures are (almost) self-explanatory. 28

29 Molecular Images Molecular graphics is an example of selective reduction of complexity. 29

30 Molecular Images Molecular graphics is an example of selective reduction of complexity. 30

31 Molecular Images Molecular graphics is an example of selective reduction of complexity. 31

32 Molecular Images Molecular graphics is an example of selective reduction of complexity. 32

33 Molecular Images Molecular graphics is an example of selective reduction of complexity. 33

34 Molecular Images Molecular graphics is an example of selective reduction of complexity. 34

35 Molecular Images Molecular graphics is an example of selective reduction of complexity. 35

36 Molecular Images Molecular graphics is an example of selective reduction of complexity. 36

37 Molecular Images Molecular graphics is an example of selective reduction of complexity. 37

38 Figures in PyMOL 38

39 Representations ray_trace_mode 0 39

40 Representations ray_trace_mode 1 40

41 Representations ray_trace_mode 2 41

42 Representations ray_trace_mode 3 42

43 Representations 43

44 Representations 44

45 Representations 45

46 Representations Standard stickrepresentation Sphere_scale = 0.3 With hydrogen atoms With shadows 46

47 Representations Standard stickrepresentation Sphere_scale = 0.3 With hydrogen atoms No shadows 47

48 Representations Standard stickrepresentation Sphere_scale = 0.3 With hydrogen atoms No shadows With depth cue 48

49 Representations Standard stickrepresentation Sphere_scale = 0.3 With hydrogen atoms No shadows With depth cue Larger image 49

50 Representations Standard stickrepresentation Sphere_scale = 0.3 With hydrogen atoms No shadows With depth cue Even larger image 50

51 Focus on the Relevant Parts Homologous peptides in different proteins Intuitive colouring 51

52 Residue Conservation 52

53 T-Cell Receptor Interactions I II III 53

54 Cross-Sections Proteasome 54

55 Electrostatic Surface Potentials 55

56 Composite Images MHC-I binding groove Images combined in Adobe Illustrator. C F B A E D 56

57 Simplified Composite Images C N P 2 57

58 Cross-Sections 58

59 Comparing Active Sites 59

60 Compiled Graphics Objects 60

61 PyMOL Links PyMOL home: PyMOL manual: toc.html PyMOL Wiki: PyMOL settings (documented): 61

62 Program Quiz results Introduction to PDB & PyMOL Break PyMOL tutorial Break Summary Quiz 62

63 Program Quiz results Introduction to PDB & PyMOL Break PyMOL tutorial Break Summary Quiz 63

64 Program Quiz results Introduction to PDB & PyMOL Break PyMOL tutorial Break Summary Quiz 64