1. Part II : Introduction To Protein Structure Kong Lesheng Victor Tong Joo Chuan National University of Singapore

2. Structure Visualization 1.1 Where can we find structure information? 1.2 Program for Visualization 1.3 Different representation of structure 1.4 Different coloring scheme

3. 1.1 Where can we find structure information? Protein Data Bank(PDB):maintained by the Research Collaboratory of Structural Bioinformatics(RCSB) http://www.rcsb.org/pdb/ > 19,000 structures of proteins (19-Aug-2003) Also contains of structures of Protein/Nucleic Acid Complexes, Nucleic Acids, Carbohydrates Each entry in PDB is identified by a unique 4- letter code, such as 1SHA.

4. 1SHA Click Here

6. Click here to download the structure file (1SHA.pdb)

7. The PDB file Structure file 1SHA.pdb is text file. It has two parts: HEADER Data – 3D coordinates

8. PDB Header details identifies the molecule, any modifications, date of release of PDB entry organism, keywords, method Authors, reference, resolution if X-ray structure Smaller the number, better the structure. Sequence, heterogen group. HEADER PHOSPHOTRANSFERASE 18-AUG-92 1SHA 1SHA 2 COMPND V-SRC TYROSINE KINASE TRANSFORMING PROTEIN (PHOSPHOTYROSINE 1SHA 3 COMPND 2 RECOGNITION DOMAIN SH2) (E.C.2.7.1.112) COMPLEX WITH 1SHA 4 COMPND 3 PHOSPHOPEPTIDE A (TYR-VAL-PRO-MET-LEU, PHOSPHORYLATED TYR) 1SHA 5 SOURCE ROUS SARCOMA VIRUS (SCHMIDT-RUPPIN STRAIN A) 1SHA 6 AUTHOR G.WAKSMAN,J.KURIYAN 1SHA 7

9. The data itself ATOM 1 N ALA A 2 40.757 22.808 12.014 1.00 61.89 1SHA 65 ATOM 2 CA ALA A 2 39.528 23.448 12.431 1.00 59.98 1SHA 66 ATOM 3 C ALA A 2 38.513 23.693 11.308 1.00 56.31 1SHA 67 ATOM 4 O ALA A 2 37.607 24.536 11.413 1.00 64.00 1SHA 68 ATOM 5 CB ALA A 2 39.882 24.777 13.140 1.00 56.35 1SHA 69 ATOM 6 N GLU A 3 38.694 22.905 10.238 1.00 40.05 1SHA 70 ------ ATOM 878 OXT LEU B 205 61.380 28.054 2.998 1.00 62.30 1SHA 942 TER 879 LEU B 205 1SHA 943 Coordinates for each heavy (non-hydrogen) atom from the first residue to the last Any ligands (starting with HETATM) follow the biomacromolecule O atoms of water molecules at the end Usually, resolution is not high enough to locate H atoms: hence only heavy atoms shown in data.

10. 1.2 Program for Visualization RASMOL ( authored by Roger A. Sayle ) is one of the most frequently used software. Downloadable at http://www.OpenRasMol.org/http://www.OpenRasMol.org/ Available for most of computer systems PC/Windows, Macintosh, Unix Easy to operate and generate nice pictures. Swiss PDB Viewer ( authored by Nicolus Guex, etc) Downloadable at http://tw.expasy.org/spdbv/http://tw.expasy.org/spdbv/ Complex but provides more computational functions.

11. 1.3 Different representation of structure There is a variety of representation methods for structure, which are suitable for different purposes. Spacefill Ball and stick Cartoons Others

12. 1SHA: Spacefill Protein: Phosphotyrosine Recognition Domain Sh2 Ligand: tyrosine- phosphorylated peptides

13. Ball and stick

14. Cartoons

15. 1.4 Different coloring schemes By CPK Color by atom type. By structure Basing on secondary structure By group

16. CPK: The assignment of colors to the most commonly used element types :

17. 1SHA: By CPK

18. By Group

19. By Structure

20. 2. Protein structure prediction 2.1 Why protein structure prediction important? 2.2 Secondary structure prediction 2.3 Tertiary structure prediction

21. 2.1 Why protein structure prediction? Structure determination methods Most structures were determined by X-Ray diffraction, and a large proportion by NMR (Nuclear Magnetic Resonance) and EM (Electron Microscopy) The experimental methods are both difficult and time-consuming. The rapid growth of protein sequences is far beyond the capacity of experimental structure determination methods. SWISS-PROT (16-Aug-2003) contains 132,675 protein sequence entries while PDB (19-Aug-2003) has 19,953 protein structures. Structures are relatively conserved and only adopt a limited number of folds, so it is possible to model 3-D structures based on known structures.

22. 2.2 Secondary structure predication For each residues in a protein structure, three possible states: α (α-helix), β (β-strand), t (others). amino acid sequence Secondary structure sequence

23. Currently the accuracy of secondary structure methods is nearly 80% (CASP4, 2000). Secondary structure prediction can provide useful information to improve other sequence and structure analysis methods, such as sequence alignment and 3-D modeling.

24. Secondary structure prediction methods SAM-T02:Kevin Karplus (http://www.cse.ucsc.edu/research/compbio/HMM- apps/T02-query.html)http://www.cse.ucsc.edu/research/compbio/HMM- apps/T02-query.html PSIPRED: David T. Jones (http://bioinf.cs.ucl.ac.uk/psipred/)http://bioinf.cs.ucl.ac.uk/psipred/ PHD or PredictProtein: Rost and Sander (http://dodo.cpmc.columbia.edu/predictprotein)http://dodo.cpmc.columbia.edu/predictprotein

25. 2.3 Tertiary structure prediction Tertiary structure prediction can be divided into three groups: comparative modeling, threading (fold recognition), ab-initio modeling. Currently the most accurate and reliable 3-D structure prediction methods is comparative modeling, which is based on known homologous structure.

26. Comparative modeling Structure is conserved. For homologous sequence, the structures are also likely to be similar. If the sequence identity > 40% and a structure is available, using comparative modeling is reasonable. If the sequence identity >70%, very high quality models can be obtained.

27. Procedure for comparative modeling Template selection Target-template alignment Model building Evaluation

28. Useful server and Program Program MODELLER: Andrej Sali (http://www.salilab.org/modeller/modeller.html )http://www.salilab.org/modeller/modeller.html Server SWISS-MODEL server: Peitsch and Geux (http://www.expasy.ch/swissmod/SWISS-MODEL.html)http://www.expasy.ch/swissmod/SWISS-MODEL.html

29. Reading materials If you want to know more about protein structure, you can refer to the following website and book. http://www.paccd.cc.ca.us/instadmn/physcidv/chem_d p/chemweb/protein/intro.htm Introduction to Protein Structure. Second Edition Carl Branden and John Tooze © 1999.Garland Publishing, Inc. For protein structure prediction http://www.bmm.icnet.uk/people/rob/CCP11BBS/ http://www.salilab.org/modeller/modeller.html

30. Summary Introduction to protein structure Basics, levels of protein structure, structural classification. Structure visualization Different representation and coloring scheme. Protein structure prediction Secondary structure prediction Tertiary structure prediction

31. End of Lecture