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Nicholas M. Luscombe and Janet M. Thornton JMB (2002) 320, 991-1009 PowerPoint Presentation
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Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. Nicholas M. Luscombe and Janet M. Thornton JMB (2002) 320, 991-1009. Outline. Background Methods and Tools Results Discussions. Background.

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Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity

Nicholas M. Luscombe and Janet M. Thornton

JMB (2002) 320, 991-1009

outline
Outline
  • Background
  • Methods and Tools
  • Results
  • Discussions
background
Background
  • DNA-binding proteins have a central role in all aspects of the genetic activity within an organism:
    • transcription, packaging, rearrangement, replication and repair
  • Of great importance to understand the nature of interactions between proteins and DNA
previous methods
Previous Methods
  • Individual structure studies
  • Surveys in search for common principles of binding that apply across most, or all protein–DNA complexes
    • atomic contacts between amino acid residues and bases
    • Secondary structural elements and small structural motifs
    • whole protein structure interactions
existing conclusions
Existing Conclusions
  • There is no simple code relating amino acid sequence to the DNA sequence it binds.
  • Detailed rules for DNA-sequence recognition is best understood within the context of individual protein families
    • strong underlying trends: e.g. arginine–guanine
this paper
This Paper
  • The first global analysis of the conservation of amino acid residue sequences in DNA-binding proteins.
    • to see whether amino acid residues that interact with DNA are better conserved
    • to assess the effect that amino acid mutations have on binding specificity
methods and tools
Methods and Tools
  • 1. Select 240 protein-DNA complexes (3.0A or better) from PDB
  • 2. Classify into structural families by pairwise SSAP (54 families).
  • 3. Structural multiple alignment of family members via CORA program suite.
  • 4. Identify distinct DNA-binding domains
  • 5. Use HMMER suite to train an HMM sequence template for each structural “template”..
  • 6. Use the trained HMMS to search SWISS-PROT.
methods and tools1
Methods and Tools
  • 7. Discard non DNA-binding proteins and collapse sets with greater than 95% sequence identity
  • 8. Build multiple alignments of the selected SWISS-PROT entries via HMMER
  • 9. Score amino-acid conservation via PET91 matrix
    • [0, 100] – Unconserved - conserved
  • 10. Identify surface residues via NACCESS
  • 11. Identify DNA-binding positions via HBPLUS
results
Results
  • Main conclusion: 3 classes
results summary
Results Summary
  • The average length of a multiple alignment is 138 amino acid residue positions, including gaps.
  • Many more protein residues interact with the DNA backbone than with bases.
  • The ratios are lower for multi-specific and highly specific families—emphasis towards interactions with bases
analysis
Analysis
  • Amino acids that interact with the DNA are better conserved than those that do not.
  • Sequence-specific families place greater emphasis on interactions with DNA bases than non-specific families.
  • DNA backbone-contacting positions are well conserved in all families.
about mutations
About Mutations
  • Conservation of base-contacting positions depends on the binding class of the family.
    • For non-specific families, invariably in the minor groove.
    • For highly-specific families target-contacting positions are very conserved.
  • Fuzzy recognition allows single proteins to recognize different, but related target sequences.
  • Members of multi-specific families recognize different DNA sequences by mutating amino acids at base contacting positions
discussions
Discussions
  • First comprehensive assessment of the level of conservation in DNA-binding proteins
  • Confirms many expectations about the nature of DNA-protein complexes.
  • Interesting insight into the evolution of divergent bindings.
personal comments
Personal Comments
  • “Old”—2002
  • No silver bullet (various families)
  • No DNA side analysis yet
    • Ahmad et al,2004, Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information, Bioinformatics
    • Ahmad et al,2008, Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins, NAR
  • Thanks