Structure and Function of Proteins

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Structure and Function of Proteins
19-20 Oct 2009
Winter 2009/10

• Lecturer Dr. Ora Furman

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Introduction

• Exercises outline
• Molecules visualization getting to know
  Deep-View.
• Illustrative examples of concepts learnt in each
  lesson.
• Some basic bioinformatic skills.

• Grades policy
• 2/3 exam
• 1/3 exercise grades 10 exercises, 8
  compulsory.
• Exercises are done in pairs and handed as hard
  copies.

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

• Protein structure Coordinates (the coordinates
  are used by Deep-View to display
• the structure on your screen)
• number of atom
• atom type
• residue type
• name of chain
• number of residue
• x-coordinates
• y-coordinates
• z-coordinates
• 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

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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

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Website Information
Exercises website address http//courses.md.huji
.ac.il/81817 Lectures website address (EDU
portal) https//eduportal.ekmd.huji.ac.il/defaul
t.aspx (course 81817) sPDBv path (from EKMD
terminal desktop) Applications for students gt
Bioinformatics gt sPDBv
exercises website
open 2 windows
Software
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How to open an EKMD account ?
Open this website
http//agcc.ekmd.huji.ac.il/ekmd.asp

• Youll need
• The 1st 8 digits of your ID number
• 4 digit code
• Follow the instructions