Progress in analyzing protein-protein interactions

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Progress in analyzing protein-protein
interactions Chia Jer-ming Prasanna R Kolatkar
LinKui(BNU)
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Structure guys

• Paaventhan Palasingam
• Jeremiah S Joseph

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Protein Functional Dbase Protein
Interactions Rosetta Stone Text
Information/Dbase MS/yeast two-hybrid
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Value of Kleisli/K1
Data doesnt have to be re-stored locally in a
specific format Efficient Flexible
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Protein-Protein Interaction Database (PPiDB v
1.0)                                            
                                                  
           
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•    Protein-Protein Interaction Queries
•    Query Interactions
• by Species 
• by Protein
• by Text Search engine.

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• P V PROTEIN KINASE 1 PKGA lt-
  P34101Also called EC 2.7.1.-, FRAGMENT.From
  Dictyostelium discoideum.Interacting domain
  Eukaryotic protein kinase domain.

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•    Information of Eukaryotic protein kinase
  domain
•    DB links Pfam PubMed Swissprot PDB
  Genbank DIP
•    Interacting with 55 domains
• Actin
• Adenylate and Guanylate cyclase catalytic domain
• Ank repeat
• BTK motif
• C2 domain
• CNH domain
• Cadherin domain
• Cyclic nucleotide-binding domain
• Death domain
• DnaJ domain
• Double-stranded RNA binding motif
• EF hand
• EGF-like domain
• F5/8 type C domain
• FHA domain

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•    Interacting domains Eukaryotic protein
  kinase domain ltgt Death domain
•    Shared proteins
• death-associated protein kinase 1, also EC
  2.7.1.-, DAP KINASE 1, from Homo sapiens
• probable serine/threonine protein kinase pelle,
  also EC 2.7.1.37, from Drosophila melanogaster
• serine/threonine protein kinase rip, also EC
  2.7.1.-, CELL DEATH PROTEIN RIP, RECEPTOR
  INTERACTING PROTEIN, from Mus musculus
• serine/threonine protein kinase rip, also EC
  2.7.1.-, CELL DEATH PROTEIN RIP, RECEPTOR
  INTERACTING PROTEIN, from Homo sapiens
•    Protein pairs
• Species Bovine - Bos taurus
• activin receptor type i precursor ltgt fasl
  receptor precursor
• activin receptor type ii precursor ltgt fasl
  receptor precursor
• angiopoietin 1 receptor precursor ltgt fasl
  receptor precursor

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• P V PROTEIN KINASE 1 PKGA lt-
  P34101Also called EC 2.7.1.-, FRAGMENT.From
  Dictyostelium discoideum.Interacting domain
  Eukaryotic protein kinase domain.

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•    Interactions
• P34101protein kinase 1
• ltgt Q021581-phosphatidylinositol-4,5-bisphosphate
  phosphodiesterase
• ltgt P05987camp-dependent protein kinase
  regulatory chain
• ltgt P08796contact site a protein precursor
• ltgt P34125myosin heavy chain kinase
• ltgt P42527myosin heavy chain kinase a
• ltgt P90648myosin heavy chain kinase b
• ltgt P22467myosin ia heavy chain
• ltgt P34092myosin ib heavy chain
• ltgt P42522myosin ic heavy chain
• ltgt P34109myosin id heavy chain
• ltgt Q03479myosin ie heavy chain
• ltgt P54695myosin if heavy chain
• ltgt P54696myosin ih heavy chain
• ltgt P08799myosin ii heavy chain, non muscle
• ltgt P54697myosin ij heavy chain
• ltgt P13833myosin regulatory light chain

•    Interactions
• P34101protein kinase 1
• ltgt Q021581-phosphatidylinositol-4,5-bisphosphate
  phosphodiesterase
• ltgt P05987camp-dependent protein kinase
  regulatory chain
• ltgt P08796contact site a protein precursor
• ltgt P34125myosin heavy chain kinase
• ltgt P42527myosin heavy chain kinase a
• ltgt P90648myosin heavy chain kinase b
• ltgt P22467myosin ia heavy chain
• ltgt P34092myosin ib heavy chain
• ltgt P42522myosin ic heavy chain
• ltgt P34109myosin id heavy chain
• ltgt Q03479myosin ie heavy chain
• ltgt P54695myosin if heavy chain
• ltgt P54696myosin ih heavy chain
• ltgt P08799myosin ii heavy chain, non muscle
• ltgt P54697myosin ij heavy chain
• ltgt P13833myosin regulatory light chain

• Interactions
• P34101protein kinase 1
• ltgt Q021581-phosphatidylinositol-4,5-bisphosphate
  phosphodiesterase
• ltgt P05987camp-dependent protein kinase
  regulatory chain
• ltgt P08796contact site a protein precursor
• ltgt P34125myosin heavy chain kinase
• ltgt P42527myosin heavy chain kinase a
• ltgt P90648myosin heavy chain kinase b
• ltgt P22467myosin ia heavy chain
• ltgt P34092myosin ib heavy chain
• ltgt P42522myosin ic heavy chain
• ltgt P34109myosin id heavy chain
• ltgt Q03479myosin ie heavy chain
• ltgt P54695myosin if heavy chain
• ltgt P54696myosin ih heavy chain
• ltgt P08799myosin ii heavy chain, non muscle
• ltgt P54697myosin ij heavy chain
• ltgt P13833myosin regulatory light chain

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Scoring System
Computational Identification Weak Same keywords
Moderate Experimental evidence from DIP or
elsewhere Good References in literature
relating names of proteins Good More than 1
support Strong
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PPDB Current Status Putative Filtered 753508
350819
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Christian von Mering, Roland Krause, Berend
Snel, Michael Cornell, Stephen G. Oliver,
Stanley Fields Peer Bork NATURE VOL 417 23
MAY 2002
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Evolutionary Relationships Functional
Relationships Putative Drug Targets
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Current BIND Database Statistics DatabaseRecord
Count Interaction Database 20000 Biomolecu
lar Pathway Database 8 Molecular Complex
Database 851 Organisms represented 12 GI
Database 4651 DI Database 0 Publication
Database 428
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BIND Interactions RAS-GTP active form of RAS
bound to GTP RAF Y2H Homo sapiens
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DIP DATABASE STATISTICS Number of
proteins 6963 Number of organisms 113 Number
of interactions 18059
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Improving Quality

• Integrating high quality structural data
• Separating interaction categories
• Decreasing false positives

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Using 3-D data

• 3-D data from PDB (Thornton,Ofran and Rost)
• Inter-domain interactions distances and
  comparison between sequence separation
• Also do for inter-protein interactions

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Better structural analysis

• Careful analysis of the structural data needed
• Transient,Permanent,homo-oligomers,hetero-oligomer
  s
• ML could be highly useful with better
  categorization

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• Sarah Teichman domains separated by 30 residues
  are the ones that have interaction

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• Testing the rule
• Need a good data set to test the rule

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X-ray crystallography

• Structural Information important for detailed and
  mechanistic understanding
• Least populated data
• Highly useful when merged with lots of functional
  information

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• PFAM/PDB
• Single chain with multiple domains including
  complexes
• Only use non-redundant chains
• calculate distances between the domains

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• Criteria
• 6A
• Number of contacts you can choose
• Between domains
• If xtal contact omit

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• What did we see with the 1273 chains
• Teichman rule basically obeyed
• Exceptions
• Binding proteins
• SH3 proteins

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Applying PPDB

• PPDB can be used to predict a set of interacting
  proteins.
• Intersection with Y2H studies and other methods
• Help direct structural genomics of complexes and
  improve PPDB

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Thermatoga structural genomics

• Great model to look at a large set of complexes
• Will be useful for looking at interactions in
  other systems
• Can be used to build a database of interacting
  motifs

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Thermatoga current state

• Crystallized several hundred and scores of
  structures
• Initial Yeast two hybrid data
• Large scale-up facilities

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Thermatoga Y2H vs PPDB

• 15 overlap
• Improving

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TFs

• Stem Cell totipotency TFs
• Hep B TFs
• ER TFs

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Support

• Mass Spec
• MA
• Structure
• Other info

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Genomic analysis

• Careful genomic data analysis can greatly
  accelerate discovery (i.e regulatory networks)

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• Pombe kinase
• What are the possible interactions?

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Pombe Yeast Score E-val Human Score E-val
BUB1 BUB1 231 2E-63 BUB1 137 2E-35
BYR1 MKK1 195 9E-53 MAP2K2 238 1E-65
BYR2 STE11 292 5E-82 MAP3K3 216 3E-59
CDC2 CDC28 377 1E-107 CDK2 390 1E-111
CDC7 CDC15 206 3E-56 MAP3K8 192 7E-52
CDR1 KCC4 229 5E-63 BRSK2 201 1E-54
CDR2 HSL1 246 5E-68 BRSK1 255 5E-71
CDS1 RAD53 228 9E-63 CHK2 174 1E-46
CEK1 RIM15 209 6E-57 MAST3 160 2E-42
CHK1 CHK1 218 1E-59 CHK1 189 3E-51
CKA1 CKA2 361 1E-103 CK2a1 390 1E-111
CKI1 YCK1 395 1E-113 CK1g2 344 1E-97
CKI2 YCK2 405 1E-116 CK1g3 338 6E-96
CKI3 YCK3 342 5E-97 CK1g1 331 8E-94
CMK1 CMK1 217 2E-59 CaMK1a 244 1E-67
CMK2 RCK1 245 8E-68 CaMK1d 210 2E-57
CRK1 KIN28 317 2E-89 CDK7 304 1E-85
DSK1 SKY1 230 5E-63 MSSK1 205 2E-55
FIN1 KIN3 231 2E-63 NEK2 229 4E-63
HHP1 HRR25 424 1E-122 CK1e 440 1E-126
KIN1 KIN2 331 1E-93 MARK3 233 3E-64
KSG1 PKH1 294 1E-82 PDK1 294 1E-82
LKH1 KNS1 273 5E-76 CLK2 296 3E-83
MEK1 MEK1 181 1E-48 DCAMKL3 170 2E-45
MKH1 BCK1 326 2E-92 MAP3K2 187 2E-50
MPH1 MPS1 233 2E-64 TTK 238 7E-66
NAK1 KIC1 282 4E-79 MST3 234 2E-64
ORB6 CBK1 448 1E-129 NDR2 374 1E-106
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Which way is right?

• Strong et al Eisenberg Dec 15 NAR Functional
  linkage M. Tuberculosis
• Giot et al.Rothberg Dec 5 Science Drosophila Y2H