2. Overview
Background
p3d overview
example ATP binding site
Fufezan, C. and Specht M. (2009) BMC Bioinformatics 10, 258
http://p3d.fufezan.net
http://github.com/fu/p3d
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
clone us - fork us!
6. Background
carbon
nitrogen
oxygen
chain(s) of amino acids ...
N D R P A
I
M K
... form proteins
and some bind cofactors
e.g. ATP
Adenosin-tri-phosphate
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
7. Background
knowledge based approaches to elucidate
structural factors that are essential for co-factor
binding
- protein engineering
proteins
- protein folding
- co-factor tuning
Proteins_c1_sp_Ob.qxp
9/11/08
4:14 PM
Page 1
proteins
STRUCTURE O FUNCTION O BIOINFORMATICS
V O LU M E
7 3 ,
N U M B E R
3 ,
N OV E M B E R
1 5 ,
V O LU M E
7 3 ,
N U M B E R
3 ,
N OV E M B E R
1 5 ,
2 0 0 8
PAG E S
Morozov et al. (2004) PNAS, 101, 6946Huang et al.(2004) PNAS, 101, 5536Fufezan et al. (2008) Proteins, 73, 690Negron et al. (2009) Proteins, 74, 400Fufezan (2010) Proteins, in press
5 2 7 – 7 9 4
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
A PDB Survey of Heme Ligands in Proteins
2 0 0 8
9. p3d overview
Fufezan, C. and Specht M. (2009) BMC Bioinformatics 10, 258
http://p3d.fufezan.net
Python module that allows
to access and manipulate protein structure files
rapid development of new screening tools
easily incorporate complex queries
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
10. chain
atom
AA
resid
type
x y z user
idx
ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
beta
or
temperature
factor
O
C
N
CA
CB
CG1
CG2
18. Tree Object
query( Vector1, radius )
ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
19. Tree Object
query( Vector1, radius )
ATOM Object
idx
atype
aa
chain
x
y
z
user
beta
protein-object
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
Vectors
do not have to
be atoms!!
20. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
alpha
residues
protein
not protein
21. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
alpha
residues
protein
not protein
Query function using human readable syntax
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
22. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
residues
protein
not protein
23. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
residues
protein
not protein
24. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)
residues
protein
not protein
25. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)
residues
pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )
protein
not protein
26. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)
residues
pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )
protein
not protein
for residueName in pdb.hash[non-aa-resname]:
27. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)
residues
pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )
protein
not protein
for residueName in pdb.hash[non-aa-resname]:
targets = pdb.query(' protein and within 4 of
28. Protein class
List of atom
objects (vectors)
sets (hashes)
oxygen
BSP Tree
O1
FME A
1
CA
PHE A
2
backbone
Query function using human readable syntax
alpha
e.g.: pdb.query(‘backbone and resid 5..12 and within 5 of resname FME’)
pdb.query(‘resname HOH and within 4 of resname ASP’)
pdb.query(‘oxygen and not protein’)
residues
pdb.query(‘ protein and within 4 of ’, p3d.vector.Vector(x,y,z) )
protein
not protein
for residueName in pdb.hash[non-aa-resname]:
targets = pdb.query(' protein and within 4 of
( resname 'residueName' and oxygen )' )
29. Example ATP binding
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
30. The ATP binding sites
Adenosine-tri-phosphate
ΔG˚' = -30 kJ mol-1
40 kg / day
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
31. The ATP binding sites
non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
32. The ATP binding sites
non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
33. The ATP binding sites
non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
34. The ATP binding sites
non. redundant set of proteins
24 binding sites
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
36. The ATP binding site
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
37. The ATP binding site
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
38. The ATP binding site
+4.5
hydropathy
index
Observations
10
0
1
-4.5
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
non. redundant set of proteins
24 binding sites
39. Summary
p3d allows to develop quickly Python
scripts to screen Protein structures
combines Vectors, sets and BSPTree
p3d allows flexible and complex queries
using human readable language
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
40. Acknowledgements
M. Specht
Prof. Dr. M. Hippler
founding by the DFG and
Alexander von Humboldt Stiftung
Dr. C. Fufezan
Institute for Biochemistry and Biotechnology of Plants (IBBP)
