1. Tutorials for protein data bank and swiss PDB viewer 2010/04/12 Prof. Jinn-Moon Yang Yen-Fu Chen and Kai-Cheng Hsu http://140.113.239.67/spv.ppt

2. Contents Introduction of protein structures Using thymidine kinase as an example Download and install Tutorial Download protein structures from PDB Basic Operation Advance Operation Resources for tutorial http://www.youtube.com/watch?v=yFE3CAHNkZg&feature=rel ated

3. Introduction of protein structures Proteins present in all biological organisms Polymers of amino acids (20 L-α-amino acids) Nanoparticles Perform particular biochemical functions NatureNature: Mattson, M. Nature. 422, 385-387 (2003)stemcells.nih.go: Early DevelopmentEarly Development Transcription and translation Cell regulation and catalysis reactions

4. Introduction of protein structures To enable to perform protein’s biological function, protein fold into one or more specific spatial conformations driven by noncovalent interactions Hydrogen bonding, ionic interactions, van der Waals forces and hydrophobic packing 3D protein structures are necessary for understanding the functions of protein at molecular level Adapted from Protein Structure in WikipediaProtein Structure in Wikipedia Hemoglobin: oxy-deoxy states Adapted from structural biology Wikipediastructural biology Wikipedia Protein structure: from amino acid to quaternary structure

5. Noncovalent interactions for protein structure and function Ionic bond A bond formed by the attraction between two oppositely charged ions Hydrogen bond An attractive interaction of a hydrogen atom with an electronegative atom, like N,O, and F Potential energy of Na and Cl

6. Noncovalent interactions for protein structure and function van der Waals force Attractive or repulsive force between molecules Hydrophobic interaction The physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water An example of van der Waals force: Gecko climbs on the glass An example of hydrophobic interaction: Water drops on hydrophobic surface

7. Protein structure database: Protein data bank (PDB) Techniques for determining atomic structures X-ray crystallography, NMR spectroscopy and electron microscopy PDB contains information about experimentally- determined structures of biological marcomoleculeas (proteins, and DNA/RNA) Proteins (1kim) DNAs/RNAs (2k7e) Biological complexes (1zrc) X-ray NMR EM http://www.pdb.org/

8. Search protein structures in PDB PDB provides search by protein name, ligand, or structrue related keywords Search example: thymidine kinase (TK) Function: DNA synthesis Therapeutic: Anticancer and antivirus drug target

9. Example: X-ray structures of virus’ thymidine kinase with substrates/inhibitors Protein name Source spices Experimental method has ligands

10. Search result of “X-ray structures of virus’ thymidine kinase with substrates/inhibitors” TK of virus TK with ligand (substrate) PDB ID of this structure X-ray structure 23 structures for these keywords

11. Structure and related data (1kim) The citation of this structure Related data of this structure The title of this structure Visualization of biological assembly

12. Structure and ligand data (1kim) Ligand in this structure

13. Structure and sequence data (1kim) Related data of this structure Sequence ID of 1kim in UniProtKB Structure classification ID of 1kim

14. Advance inspection for protein structure: download structure from PDB 1.Save the data on your PC 2.Open the file on a structure viewer program (swiss PDBviewer, pymol, and etc.)

15. Classification of Drug Development Protein (receptor) Structure Compound structure Known Unknown Known Unknown Structure-based Drug Design (SBDD) SBDD or de novo design High-Throughput Screening (HTS) Compound similarity search query Similar compounds DDT 2002

16. Discovering new leads Curr. opin. Chem. Biol. 2002, 439 Yellow: virtual screening (SBDD) Blue: high-throughput screening (HTS) HTS SBDD There are more than 5 H-bond donors. The molecular weight is over 500. The LogP is over 5. There are more than 10 H-bond acceptors.

17. Drugs derived from structure-based approaches Drug Discovery Today, 10, 895, 2005

19. Tutorial for Swiss PDB viewer

20. Download and install Download Swiss PdbViewer http://spdbv.vital-it.ch/download.html Download user guide http://spdbv.vital-it.ch/Swiss- PdbViewerManualv3.7.pdf Tutorial video (English) http://www.youtube.com/watch?v=nYT5qwtfNew&fe ature=related http://www.youtube.com/watch?v=yFE3CAHNkZg

21. Download page

22. Install and execute swiss pdb viewer

23. Workspace Control panel Layer info Main window Viewer

24. General Terms Gray: C atom Blue: N atom Red: O atom Residue Arginine Side chain Main chain Atom radius Chain Secondary Structure (Ribbon) A protein may have multiple chains

25. Load PDB 1

26. Load PDB 2

27. Move & Rotate Center Zoom Translate Rotate

28. Open control panel control panel

29. Display or hide residues -for some residues Press left button of mouse

30. Display or hide residues -for all residues Press right button of mouse

31. Display or hide side chains of residues

32. Display or hide residue labels GLU111

33. Display or hide atom radius

34. Render in solid 3D

35. Show secondary structures -Display or hide ribbons

36. Change color

37. Visualization of biological assembly -color by chain

38. Change color by chain -act on Ribbons

39. Show residue properties -Change color by Type TypeReisdue NegativeASP GLU PositiveHIS LYS ARG PolarSER TYR ASN THR GLN HydrophobicCYS MET PHE ALA TRP LEU ILE PRO VAL GLY

40. Show structure flexibility Change color by B-factor A low B-factor meaning that the position of the atom has been determined with accuracy High B-factor Low B-factor

41. Other color types Secondary Structure Selected residues Relative accessibility default atom colors Root mean square between 2 molecules

42. Analyze protein-ligand interactions -Select ligands (or residues) Press left button of mouse to select the ligand (THM, thymidine) of 1kim

43. Identify binding site -Show protein (ribbon) and ligand (stick)

44. Select residues in the binding site -Neighbors of selected residues

45. Center selected residues

46. H-bonds of the binding site -Compute H-bonds

47. H-bonds between protein and ligand -Show H-bonds of selection

48. H-bonds between TK and THM -Show residues from selection

49. Show residue label Press right button of mouse 1.Q125 recognize the thymine moiety 2. Activity was decreased by over 90% if Q125 mutated (Biochemistry, 2000. 39: p. 4105-4111)

50. van der Waal forces -Stacking interactions M128 and Y172 sandwich the thymine moiety Stabilize the binding of substrate (JBC, 1999. 274: p. 31967-31973)

51. Observe the protein surface -Compute Surface

52. Surface preference

53. Show ligand in the surface

54. Discard surface

55. Comparison of multiple structures -Import PDB PDB code: 3vtk Another structure of thymidine kinase

56. Open layer info 1kim 3vtk Show or hide

57. Superimpose two molecules

58. Results of superimposition RMS: 0.63 Ǻ Measure the structure similarity

59. Comparison of binding sites -Neighbors of selected residues

60. Comparison of ligands 1kim: substrate(CPK)3vtk: inhibitor (Green)

61. Save files

62. Homework Keyword 1. How many structures of N1 neuraminidase with ligand ? 2. Capture a picture of N1 neuraminidase (ribbon) and its ligand (stick) 3. Capture a picture of H-bonds between protein and ligand E-mail pikihsu@gmail.com Mail title: 學號姓名 _HW1_ 第一題答案的數字