Predicting protein structure and function

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Predicting protein structure and function
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Protein function
Genome/DNA Transcriptome/mRNA Proteome Metabolo
me Physiome
Transcription factors
Ribosomal proteins Chaperonins
Enzymes
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Protein function
Not all proteins are enzymes ?-crystallin eye
lens protein needs to stay stable and
transparent for a lifetime (very little turnover
in the eye lens)
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What can happen to protein function through
evolution

• Proteins can have multiple functions (and
  sometimes many -- Ig).
• Enzyme function is defined by specificity and
  activity
• Through evolution
• Function and specificity can stay the same
• Function stays same but specificity changes
• Change to some similar function (e.g. somewhere
  else in metabolic system)
• Change to completely new function

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How to arrive at a given function

• Divergent evolution homologous proteins
  proteins have same structure and same-ish
  function
• Convergent evolution analogous proteins
  different structure but same function
• Question can homologous proteins change
  structure (and function)?

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How to evolve

• Important distinction
• Orthologues homologous proteins in different
  species (all deriving from same ancestor)
• Paralogues homologous proteins in same species
  (internal gene duplication)
• In practice to recognise orthology,
  bi-directional best hit is used in conjunction
  with database search program

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How to evolve

• By addition of domains (at either end of protein
  sequence) Lesk book page 108
• Often through gene duplication followed by
  divergence

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Structural domain organisation can be nasty
Pyruvate kinase Phosphotransferase
b barrel regulatory domain a/b barrel catalytic
substrate binding domain a/b nucleotide binding
domain
1 continuous 2 discontinuous domains
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• The DEATH Domain
• Present in a variety of Eukaryotic proteins
  involved with cell death.
• Six helices enclose a tightly packed hydrophobic
  core.
• Some DEATH domains form homotypic and
  heterotypic dimers.

http//www.mshri.on.ca/pawson
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How to predict function

• Sequence information Homology searching
• Sequence-structure information Fold recognition
  (Threading)
• Structure-structure information structure
  superpositioning

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Flavodoxin fold
5(??) fold
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Rules of thumb when looking at a multiple
alignment (MA)

• Hydrophobic residues are internal
• Gly (Thr, Ser) in loops
• MA hydrophobic block -gt internal ?-strand
• MA alternating (1-1) hydrophobic/hydrophilic gt
  edge ?-strand
• MA alternating 2-2 (or 3-1) periodicity gt
  ?-helix
• MA gaps in loops
• MA Conserved column gt functional? gt active
  site

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Rules of thumb when looking at a multiple
alignment (MA)

• Active site residues are together in 3D structure
• Helices often cover up core of strands
• Helices less extended than strands gt more
  residues to cross protein
• ?-?-? motif is right-handed in gt95 of cases
  (with parallel strands)
• MA inconsistent alignment columns and match
  errors!
• Secondary structures have local anomalies, e.g.
  ?-bulges

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Burried and Edge strands
Parallel ?-sheet
Anti-parallel ?-sheet
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Periodicity patterns
Burried ?-strand Edge ?-strand ?-helix