1. Structure and Function of Proteins Lecturer: Dr. Ora Furman 19-20 Oct 2009 Winter 2009/10 Teaching Assistants: Miraim Oxsman Sivan Pearl

2. Exercises outline:  Molecules visualization: getting to know Deep-View.  Illustrative examples of concepts learnt in each lesson.  Some basic bioinformatic skills.Introduction Grades policy:  2/3 : exam  1/3 : exercise grades: 10 exercises, 8 compulsory.  Exercises are done in pairs and handed as hard copies.

3. What is PDB ? PDB (Protein Data Bank): A repository for the processing and distribution of 3-D biological macromolecular structure data.

4. PDB Files (i) Title: name of protein and protein source. HEADER HISTOCOMPATIBILITY ANTIGEN 30-JUN-93 1HHK 1HHK 2 COMPND HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) 1HHK 3 COMPND 2 COMPLEX WITH A NONAMERIC PEPTIDE FROM HTLV-1 TAX PROTEIN 1HHK 4 COMPND 3 (RESIDUES 11-19) 1HHK 5 SOURCE HUMAN (HOMO SAPIENS) RECOMBINANT FORM. EXTRACELLULAR 1HHK 6 SOURCE 2 FRAGMENT EXPRESSED IN (ESCHERICHIA COLI) AND 1HHK 7 SOURCE 3 RECONSTITUTED WITH SYNTHETIC PEPTIDE 1HHK 8 References: AUTHOR D.R.MADDEN,D.N.GARBOCZI,D.C.WILEY 1HHK 9 REVDAT 1 31-OCT-93 1HHK 0 1HHK 10 JRNL AUTH D.R.MADDEN,D.N.GARBOCZI,D.C.WILEY 1HHK 11 JRNL TITL THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC 1HHK 12 JRNL TITL 2 COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE 1HHK 13 JRNL TITL 3 PEPTIDES PRESENTED BY /HLA$-*A2 1HHK 14 JRNL REF TO BE PUBLISHED 1HHK 15 JRNL REFN 353 1HHK 16 REMARK 1 REFERENCE 1 1HHK 17 REMARK 1 AUTH D.N.GARBOCZI,D.T.HUNG,D.C.WILEY 1HHK 18 REMARK 1 TITL /HLA$-*A2-PEPTIDE COMPLEXES: REFOLDING AND 1HHK 19

5. PDB Files (ii) Information about the structural model of the protein: crystallization and refinement data REMARK 2 RESOLUTION. 2.5 ANGSTROMS. 1HHK 69 REMARK 3 REFINEMENT. 1HHK 71 REMARK 3 PROGRAM X-PLOR 1HHK 72 REMARK 3 AUTHORS BRUNGER 1HHK 73 REMARK 3 R VALUE 0.262 1HHK 74 REMARK 3 RMSD BOND DISTANCES 0.014 ANGSTROMS 1HHK 75 REMARK 3 RMSD BOND ANGLES 2.9 DEGREES 1HHK 76 Documents about protein chains, domains, etc : REMARK 4 THERE ARE TWO COMPLEXES PER ASYMMETRIC UNIT, EACH COMPOSED 1HHK 78 REMARK 4 OF THREE POLYPEPTIDE CHAINS: 1HHK 79 REMARK 4 ONE COMPLEX INCLUDES: 1HHK 81 REMARK 4 1. HLA HEAVY CHAIN IDENTIFIED AS CHAIN *A* IN THIS ENTRY. 1HHK 82 REMARK 4 THIS CHAIN IS DIVIDED INTO THREE DOMAINS 1HHK 83 REMARK 4 ALPHA 1 - RESIDUES GLY A 1 THROUGH ALA A 90 1HHK 84 REMARK 4 ALPHA 2 - RESIDUES GLY A 91 THROUGH THR A 182 1HHK 85 REMARK 4 ALPHA 3 - RESIDUES ASP A 183 THROUGH GLU A 275 1HHK 86 REMARK 4 2. BETA-2-MICROGLOBULIN IDENTIFIED AS CHAIN *B*. THIS 1HHK 88 REMARK 4 CHAIN CONSISTS OF RESIDUES MET B 0 THROUGH MET B 99. 1HHK 89 REMARK 4 3. A HTLV-1 TAX PEPTIDE IDENTIFIED AS CHAIN *C*. THIS 1HHK 91 REMARK 4 CHAIN CONSISTS OF RESIDUES LEU C 1 THROUGH VAL C 9. 1HHK 92

6. PDB Files (iii) Protein sequence: listed for every chain SEQRES 1 A 275 THR GLN THR TRP ALA GLY SER HIS SER MET ARG TYR PHE 1HHK 111 SEQRES 2 A 275 PHE THR SER VAL SER ARG PRO GLY ARG GLY GLU PRO ARG 1HHK 112 SEQRES 3 A 275 PHE ILE ALA VAL GLY TYR VAL ASP ASP THR GLN PHE VAL 1HHK 113 Further information about specific residues : FTNOTE 1 SIDE CHAIN ATOMS OF A 17, A 194, A 196, B 48, B 58, D 17, 1HHK 174 FTNOTE 1 D 194, D 196, E 48, AND E 58 ARE DISORDERED, AND HAVE 1HHK 175 FTNOTE 1 OCCUPANCIES EQUAL TO ZERO IN THIS ENTRY. 1HHK 176 Definition of secondary structure and disulfide bonds : HELIX 1 H1 ALA A 49 GLU A 53 1 1HHK 184 HELIX 2 H2 PRO A 57 TYR A 84 1 1HHK 185... SHEET 1 SA 8 GLU A 46 PRO A 47 0 1HHK 196 SHEET 2 SA 8 THR A 31 ASP A 37 -1 O ARG A 35 N GLU A 46 1HHK 197...

7. PDB Files (iv) Protein structure: Coordinates (the coordinates are used by Deep-View to display the structure on your screen) : the structure on your screen) : 1.number of atom 2.atom type 3.residue type 4.name of chain 5.number of residue 6.x-coordinates 7.y-coordinates 8.z-coordinates 9.B-factor 1 2 3 4 5 6 7 8 9 ATOM 1 N GLY A 1 14.851 -6.104 13.115 1.00 30.79 1HHK 273 ATOM 2 CA GLY A 1 15.736 -5.423 12.197 1.00 28.36 1HHK 274 ATOM 3 C GLY A 1 15.249 -3.991 12.170 1.00 26.32 1HHK 275 ATOM 4 O GLY A 1 14.679 -3.545 13.170 1.00 26.79 1HHK 276 ATOM 5 N SER A 2 15.443 -3.339 11.045 1.00 24.58 1HHK 277 ATOM 6 CA SER A 2 15.070 -1.952 10.856 1.00 22.79 1HHK 278

8. Technical Remarks Files extensions .pdb files are represented as.txt files.  When uploading files, select the “all file types” tab. Recommendation  Use the table of content !  Follow the “hands”

9. Website Information Exercises website address: http://courses.md.huji.ac.il/81817 Lectures website address (EDU portal): https://eduportal.ekmd.huji.ac.il/default.aspx (course #81817) sPDBv path: (from EKMD terminal desktop) Applications for students > Bioinformatics > sPDBv open 2 windows Software exercises website

10. How to open an EKMD account ? http://agcc.ekmd.huji.ac.il/ekmd.asp Open this website: You’ll need  The 1 st 8 digits of your ID number  4 digit code Follow the instructions…