Protein DNA Interactions From interactions to function prediction Sue Jones

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Protein DNA InteractionsFrom interactions to
function prediction Sue Jones

• Department of Biochemistry
• University of Sussex
• 20th Sept 2004
• EMBL Lecture Course

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Outline

• Protein-DNA Interactions importance
• Structural Data
• Predicting DNA Binding Function
• Alternative Method New Perspectives

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Protein-DNA Interactions Importance

• Gene expression
• Transcription initiation (TATA binding protein)
• RNA synthesis (RNA polymerase)
• Transcription regulation (MAX protein)
• DNA repair (DNA glycosylase oxidative DNA
  damage)

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Protein-DNA Interactions Importance

• DNA packaging (Histone H2A.e)
• DNA replication (Polymerases, Ligases, single
  stranded binding proteins)

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Outline

• Protein-DNA Interactions importance
• Structural Data
• Predicting DNA Binding Function
• Alternative Method New Perspectives

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DNA

• DNA has structural flexibility
• Structure described by Watson Crick B-form

Feature B A
Type of helix RH RH
Diameter 2.37 2.55
Rise per bp 0.34 0.29
bp per turn 10 11
Major groove Wide, deep Narrow, deep
Minor groove Narrow, shallow Wide, shallow
B A Z
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Structural Data

• NDB assemble and distribute structural
  information about nucleic acids
• 2490 structures (25/08/04)

Protein-DNA Complex Number
Double Helix 593
Single Strand 57
http//ndbserver.rutgers.edu Berman et al., 1992.
Biophys J 63 p751
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Protein-DNA Interactions Structure
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Protein-DNA Interactions characteristics

• Major and minor groove binding
• DNA-binding motifs
• Positively charged surface areas
• Size ASA 618Å2 - 2833Å2
• Conformational changes
• DNA bending
• domain movements, quaternary changes

• Nadassy et al., 1999 Biochemistry 38 p1999
• Jones et al., 1999 J.Mol.Biol. 287 p877

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Outline

• Protein-DNA Interactions importance
• Structural Data
• Predicting DNA Binding Function
• New Perspectives

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Predicting DNA Binding Function

• Knowing a proteins function is essential in
  understanding
• cellular location
• interactions
• biochemical pathways
• potential as drug targets
• Prediction of protein DNA binding site given
  unbound protein structure
• electrostatic patches
• motifs

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Predicting Function from Structure

• Structural genomics filling in the gaps of
  protein structure space
• Structures solved that have low sequence identity
  (lt 30 sequence identity)
• Potentially little or no fold similarity to any
  currently in the PDB
• Require algorithms to make fast reliable
  function predictions

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Predicting DNA Binding Function

• Easy to make matches between globally homologous
  structures
• Method aims to identify remote matches based on
  local homology of a specific motif
• Helix-Turn-Helix (HTH)
• C-terminal helix - major groove binding
• 1/3 DNA-binding protein families (16/54)

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HTH Motif Proteins
Hin Recombinase (1hcr)
Catabolic Activator Protein (1j59)
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HTH Motif Dataflow
120 HTH PDB Chains
NDB
PDB
Literature
PFAM
SMART
26 Hidden Markov Models
PDB
SAM-T99
Literature
Rasmol
349 HTH Chains
227 HTH Proteins
28 HMMs
3D-Templates
29 SREPS
7 HREPS
84 NI Proteins
86 NI Proteins
232 HTH Chains
30 SREPS
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HTH Template Library
1ais
1hcr
1b9m
1eto
1hcrA160-181 1b9mA32-56 1etoA73-95 1aisB1267-1293
1jhgA68-91 1lmb331-53 1orc016-36
1jhg
1lmb
1orc
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Template Scanning

• Scanning template library against 3D structures
• One template T (length n) scanned against protein
  P of length m, calculated optimal gapless
  superposition at each m-n1 possible positions in
  P using RMSD
• Based on Kabsch (1976) Acta Cryst A. 32 p922

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RMSD Distributions
1.6Å
Frequency
RMSD
368/8266 3.5 false positives
5/84 1.4 false negatives
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Improving Template Specificity

• Extending templates
• Assessing motif accessible surface area (ASA)
• 2 templates 61/8264 0.7 false positives
• ASA threshold (990Å2) 38/8264 0.5 false
  positives
• 3 false positives were actually real HTH
  proteins not previously annotated

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New HTH Motif 1

• DNA Methyltransferase (MGMT)
• 110-129 C-terminal domain
• d and e helices
• Site directed mutagenesis

1mgtA
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New HTH Motif 2
1fy7A

• Histone acetyltransferase
• 368-388 C-terminal domain
• zinc finger N-terminal domain
• protein-protein interactions
• SCOP winged helix

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New HTH Motif 3
1taq
1tau

• Polymerase I
• 673-700 fingers subdomain
• DNA contacts O helix
• New HTH precedes O helix

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Generic Templates
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Generic Templates
Sequence Full sequence HMMs (0.001)
Structure RMSD lt 1.6
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Structural Genomics Targets

• Scanned template library against 30 target
  structures from MCSG

Isocitrate lyase regulator transcription factor.
(Zhang et al., J. Biol. Chem. 2002)
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Summary

• Method combined structural data from NDB and PDB
  with sequence data from PFAM and SMART
• Structural template library of 7 HTH motifs
• RMSD threshold from optimal superposition
• Hit rate of 88 false positive rate of 0.5
• Recognition across families
• Template method independent of global fold
  similarity
• Potential to identify new DNA binding HTH motifs

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Online Function Prediction
http//www.ebi.ac.uk/thornton-srv/databases/PDNA-p
red
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Outline

• Protein-DNA Interactions importance
• Structural Data
• Predicting DNA Binding Function
• Alternative Method New Perspectives

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Alternative Statistical Model
Statistical Models for discerning protein
structures containing the DNA-binding HTH motif.
Mclaughlin and Berman, J. Mol. Biol. 2003 p43.

• Decision tree model to identify key structural
  features
• geometric measurements of recognition helix (RH)
  helices beta sheets preceding and following
• Key features
• High solvent accessibility of RH
• Hydrophobic interaction between RH 2nd helix
  preceding
• Predicting HTH motifs within the PDB
• 98 accuracy 0.7 false positive rate
• Predicted new HTH motifs

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Future Perspectives

• Extend method to other DNA binding motifs HLH,
  HhH, ?-ribbon
• Using electrostatic potentials with motifs to
  improve method
• Spatial templates for proteins that dont use
  discrete motifs for DNA recognition

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Acknowledgements

• Janet
• Thornton

• Jonathan
• Barker

• Helen
• Berman

• Hugh
• Shanahan

Mario Garcia Carles Ferrer

• Department of Energy USA
• European Bioinformatics Institute
• Rutgers The State University