de novo Protein Design
Presented by
Alison Fraser, Christine Lee,
Pradhuman Jhala, Corban Rivera
Outline
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Introduction
Computational methods used for sequence
and structure
Biophysical and structural characteristics
of novel protein
Conclusion
Introduction
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Number of protein folds
Computational methods for identifying
amino acid sequences compatible with
target structure – not for protein creation
Side Chains as Templates
New protein design => more rigorous test
of current force fields and optimization
methodology than redesign of naturally
occurring proteins
Introduction (continued)
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Search of nearby conformational space
and sequence space
2 methods of protein redesign (variation
of backbone conformation and amino acid
sequence)
Development of procedure for identifying
low free energy sequence-structure pairs
that iterates between sequence
optimization and structure prediction
Result: 93 residue protein with topology
not in PDB
Structure to Sequence
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RosettaDesign predicts a amino acid
sequence from a desired structure.
Input and Output
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Input a structure you would like to create
Output a amino acid sequence that will
produce the structure with low free energy
Sequence to Structure
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RosettaDesign is used to predict protein
structure from protein residue sequence.
Input and Output
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Input Amino Acid sequence
Output a Predicted near minimum free energy
structure
How does Top7 compare to
proteins in nature?
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Folding
Stability
Structure
Stability
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Thermally stable
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CD Spectrum at 98˚C
is nearly
indistinguishable from
that at 25˚C
Folding of Top7
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At intermediate
concentrations (~5 M) of
guanidine hydrochloride
(GuHCl) Top7 unfolds
cooperatively
Steep transition in
chemical denaturation is
characteristic of the twostate unfolding expected
for small, two-state,
monomeric single-domain
protein
Structure
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Nuclear Overhauser
effect spectroscopy
(NOESY) and
heteronuclear single
quantum coherence
(HSQC) exhibit
features characteristic
of protein with
substantial beta-sheet
content
Comparing Top7 to model
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Crystallization
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Top7 yielded crystals that diffracted to 2.5 Å
Strong molecular replacement (MR) solution
to phase problem
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This suggest design model very close to true
structure
Top7 crystal like the model was also
judged to be a novel topology by TOPS
server
Comparison of model (blue) and
the solved x-ray structure (red)
Implications
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Atomic Level Accuracy
(RMSD = 1.17 oA) in de
novo Protein Design
Validation of Accuracy of
Potential Functions
Reasons
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Optimization of Sequence and Structure
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No Functional Constraints
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Extensive Optimization
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No kinetics
Possible Future Impacts
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Synthetic proteins
Protein Therapeutics and Molecular
Mechanics