Structure and Function

of Proteins

Lecturer: Dr. Ora Furman

19-20 Oct 2009

Winter 2009/10

Teaching Assistants:Miraim OxsmanSivan Pearl

Exercises outline:

Molecules visualization: getting to know Deep-View.

Illustrative examples of concepts learnt in each lesson.

Some basic bioinformatic skills.

IntroductionIntroduction

Grades policy:

2/3 : exam

1/3 : exercise grades: 10 exercises, 8 compulsory.

Exercises are done in pairs and handed as hard copies.

What is PDB ?What is PDB ?

PDB (Protein Data Bank):

A repository for the processing and distribution of 3-D biological macromolecular structure data.

PDB Files (i)PDB Files (i)

Title: name of protein and protein source.Title: name of protein and protein source.

HEADER HISTOCOMPATIBILITY ANTIGEN 30-JUN-93 1HHK 1HHK 2COMPND HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) 1HHK 3COMPND 2 COMPLEX WITH A NONAMERIC PEPTIDE FROM HTLV-1 TAX PROTEIN 1HHK 4COMPND 3 (RESIDUES 11-19) 1HHK 5SOURCE HUMAN (HOMO SAPIENS) RECOMBINANT FORM. EXTRACELLULAR 1HHK 6SOURCE 2 FRAGMENT EXPRESSED IN (ESCHERICHIA COLI) AND 1HHK 7SOURCE 3 RECONSTITUTED WITH SYNTHETIC PEPTIDE 1HHK 8

References:References:

AUTHOR D.R.MADDEN,D.N.GARBOCZI,D.C.WILEY 1HHK 9REVDAT 1 31-OCT-93 1HHK 0 1HHK 10JRNL AUTH D.R.MADDEN,D.N.GARBOCZI,D.C.WILEY 1HHK 11JRNL TITL THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC 1HHK 12JRNL TITL 2 COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE 1HHK 13JRNL TITL 3 PEPTIDES PRESENTED BY /HLA$-*A2 1HHK 14JRNL REF TO BE PUBLISHED 1HHK 15JRNL REFN 353 1HHK 16REMARK 1 REFERENCE 1 1HHK 17REMARK 1 AUTH D.N.GARBOCZI,D.T.HUNG,D.C.WILEY 1HHK 18REMARK 1 TITL /HLA$-*A2-PEPTIDE COMPLEXES: REFOLDING AND 1HHK 19

PDB Files (ii)PDB Files (ii)

Information about the structural model of the protein: Information about the structural model of the protein: crystallization and refinement datacrystallization and refinement data

REMARK 2 RESOLUTION. 2.5 ANGSTROMS. 1HHK 69REMARK 3 REFINEMENT. 1HHK 71REMARK 3 PROGRAM X-PLOR 1HHK 72REMARK 3 AUTHORS BRUNGER 1HHK 73REMARK 3 R VALUE 0.262 1HHK 74REMARK 3 RMSD BOND DISTANCES 0.014 ANGSTROMS 1HHK 75REMARK 3 RMSD BOND ANGLES 2.9 DEGREES 1HHK 76

Documents about protein chains, domains, etc :Documents about protein chains, domains, etc :REMARK 4 THERE ARE TWO COMPLEXES PER ASYMMETRIC UNIT, EACH COMPOSED 1HHK 78REMARK 4 OF THREE POLYPEPTIDE CHAINS: 1HHK 79REMARK 4 ONE COMPLEX INCLUDES: 1HHK 81REMARK 4 1. HLA HEAVY CHAIN IDENTIFIED AS CHAIN *A* IN THIS ENTRY. 1HHK 82REMARK 4 THIS CHAIN IS DIVIDED INTO THREE DOMAINS 1HHK 83REMARK 4 ALPHA 1 - RESIDUES GLY A 1 THROUGH ALA A 90 1HHK 84REMARK 4 ALPHA 2 - RESIDUES GLY A 91 THROUGH THR A 182 1HHK 85REMARK 4 ALPHA 3 - RESIDUES ASP A 183 THROUGH GLU A 275 1HHK 86REMARK 4 2. BETA-2-MICROGLOBULIN IDENTIFIED AS CHAIN *B*. THIS 1HHK 88REMARK 4 CHAIN CONSISTS OF RESIDUES MET B 0 THROUGH MET B 99. 1HHK 89REMARK 4 3. A HTLV-1 TAX PEPTIDE IDENTIFIED AS CHAIN *C*. THIS 1HHK 91REMARK 4 CHAIN CONSISTS OF RESIDUES LEU C 1 THROUGH VAL C 9. 1HHK 92

PDB Files (iii)PDB Files (iii)

Protein sequence: listed for every chainProtein sequence: listed for every chainSEQRES 1 A 275 THR GLN THR TRP ALA GLY SER HIS SER MET ARG TYR PHE 1HHK 111SEQRES 2 A 275 PHE THR SER VAL SER ARG PRO GLY ARG GLY GLU PRO ARG 1HHK 112SEQRES 3 A 275 PHE ILE ALA VAL GLY TYR VAL ASP ASP THR GLN PHE VAL 1HHK 113

Further information about specific residues : Further information about specific residues : FTNOTE 1 SIDE CHAIN ATOMS OF A 17, A 194, A 196, B 48, B 58, D 17, 1HHK 174FTNOTE 1 D 194, D 196, E 48, AND E 58 ARE DISORDERED, AND HAVE 1HHK 175FTNOTE 1 OCCUPANCIES EQUAL TO ZERO IN THIS ENTRY. 1HHK 176

Definition of secondary structure and disulfide bonds : Definition of secondary structure and disulfide bonds : HELIX 1 H1 ALA A 49 GLU A 53 1 1HHK 184HELIX 2 H2 PRO A 57 TYR A 84 1 1HHK 185...SHEET 1 SA 8 GLU A 46 PRO A 47 0 1HHK 196SHEET 2 SA 8 THR A 31 ASP A 37 -1 O ARG A 35 N GLU A 46 1HHK 197...

PDB Files (iv)PDB Files (iv)

Protein structure: Coordinates (the coordinates are used by Protein structure: Coordinates (the coordinates are used by Deep-View to displayDeep-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 273ATOM 2 CA GLY A 1 15.736 -5.423 12.197 1.00 28.36 1HHK 274ATOM 3 C GLY A 1 15.249 -3.991 12.170 1.00 26.32 1HHK 275ATOM 4 O GLY A 1 14.679 -3.545 13.170 1.00 26.79 1HHK 276ATOM 5 N SER A 2 15.443 -3.339 11.045 1.00 24.58 1HHK 277ATOM 6 CA SER A 2 15.070 -1.952 10.856 1.00 22.79 1HHK 278

Technical RemarksTechnical 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”

Website InformationWebsite 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

How to open an EKMD account?

http://agcc.ekmd.huji.ac.il/ekmd.asp Open this website:

You’ll need

The 1st 8 digits of your ID number

4 digit code

Follow the instructions…