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Nicholas M. Luscombe and Janet M. Thornton JMB (2002) 320, 991-1009

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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Nicholas M. Luscombe and Janet M. Thornton JMB (2002) 320, 991-1009

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  1. 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

  2. Outline • Background • Methods and Tools • Results • Discussions

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. Results • Main conclusion: 3 classes

  10. Result Statistics

  11. Results (Aligned Positions)

  12. 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

  13. Results (Conservation)

  14. 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.

  15. 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

  16. “Universal” Code (Preferences)

  17. 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.

  18. 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

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