De novo Protein Design

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De novo Protein Design

• III. Coiled-coil designs

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What is a coiled coil?

• Ubiquitous protein-folding protein-protein
  interaction motif
• 5 of all DNA sequences
• Wide variety of functions
• BUT
• A common and simplesequence motif
• Ideal for design studies

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Coiled Coils Helical Wheels
HPPHPPPHPPHPPP abcdefgabcdefg
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EarlyDesign Attempts

• Hodges(LEALEGK)n3-5dimer?
• DeGrado (LEALEXK)3.5XSer Coiled Serine(1COS)

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Dimers, trimers, tetramers pentamers
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Coiled Coils Helical Nets
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Knobs-into-holes packing
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Oligomer-state Selection - Harbury
pLI
pII
pIL
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Structural Rationale
Leu _at_ d
Val/Ile _at_ a
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Rules for oligomer selection
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Partner selection?
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A simple coiled-coil designTemplate-a
abcdefg abcdefg abcdefg abcd Ac-YGC
VAALEQK IAALEQK KAALEQK IAAL C-Am
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Helicity Stability byCircular Dichroism (CD)
Spectroscopy
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Oligomer State byAnalytical Ultracentrifugation
(AUC)
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Designs achieved so far

• Parallel homo-dimers, trimers tetramers
• Parallel hetero-dimers trimers
• Synthetic partners for natural CC sequences
• Self-replicating peptides
• Anti-parallel dimers
• Peptides that switch state (e.g. LZ to amyloid)
• Protein fibres from dimeric (and pentameric)
  building blocks

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Hetero-oligomeric coiled coils?
g abcdefg abcdefg abcdefg abcdef Acid E
IAALEQE IAALEQE NAALEQE IAALEQ Base K IAALKQK
IAALKQK NAALKQK IAALKQ
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Examples of successful hetero-oligomeric
coiled-coil designs

• Peptide VELCRO hetero-dimerOShea et al.(1993)
  Current Biology 3 658-667Acid Base peptides
  only fold when mixed.
• ABC hetero-trimerNautiyal et al. (1995)
  Biochemistry 34 11645Nautiyal Alber (1999)
  Protein Science 8 843 different coiled-coil
  peptides assembleX-ray structure
  (1BB1.pdb/ABC.pdb)

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The ABC heterotrimer (1BB1)
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More-exotic examples targets TolC
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?-cylinders
Example TolC (1ek9)
2001 PFF paper