designing proteins - american scientific affiliation · designing proteins the creative potential...
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![Page 1: Designing Proteins - American Scientific Affiliation · Designing Proteins The Creative Potential of Enthalpy and Entropy Ben McFarland Department of Chemistry Seattle Pacific University](https://reader030.vdocument.in/reader030/viewer/2022021505/5aed64d27f8b9a585f90252f/html5/thumbnails/1.jpg)
Designing ProteinsThe Creative Potential of Enthalpy and Entropy
Ben McFarlandDepartment of ChemistrySeattle Pacific University
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Proteins are chemical: they have defined atomic structures accessible through
X-ray crystallography
Purify a protein Grow a crystal of it Put in X-ray beam
X-ray diffraction patterns show electron density, define atomic coordinates
http://hasylab.desy.de/user_info/available_instruments/x_ray_protein_crystallography/index_eng.htmlhttp://www.bio.ph.ic.ac.uk/pxcourse/images/diff_pattern.sq.jpghttp://prism.mit.edu/X-ray/cuanode3.jpg
hνX-ray source
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Atomic structures are beautiful and complex, proteins much more so
http://www.wellcomecollection.org/exhibitionsandevents/exhibitions/fromatomstopatterns/gallery/WTD039444.htm
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The atomic coordinates of a protein allow for chemical/computational analysis and
designProtein structure
+ computer algorithms(molecular mechanics & force fields)
understanding which atoms are most strongly interacting
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Protein chemistry’s Holy Grail:The Protein Folding Problem
• Fix amino acid sequence Find atomic coordinates
• Movie of computer simulation of villin folding
• Weeks of CPU time = a few milliseconds of a folding pathway
• Rosetta@home, Folding@home, FoldIt, etc.
• We are getting closer to the goal each year, but X-ray crystallography is still the trusted standard
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The Inverse Protein Folding Problem (design) is a little easier
• Fix atomic coordinates (of the protein backbone) Fit in amino acids inbetween
• Instead of moving a backbone through space, we are filling in the gaps with amino acids
Fewer degrees of freedom mean this problem is more computationally tractable
Also, we can “stack the deck” and search for the strongest possible interactionsDavid Baker’s Top7,
the first designed protein
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Protein chemists analyze Top7 in terms of enthalpy and entropy
ΔG = ΔH - TΔSΔG = “free energy” = negative if a reaction will
produce more products than reactants
ΔH = “enthalpy” = heat emitted or absorbed(forming strong bonds releases heat)
ΔS = “entropy” = degeneracy; isoenergeticstates accessible to a system. S = k ln Ω
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Extreme enthalpyholds Top7 together
• Rosetta optimizes good bonds, minimizes bad ones, in every location
• (Rosetta knows little of entropy beyond an implicit solvation term)
• Top7 has an excess of enthalpicstability:
It does not unfold when boiled
Must add nearly saturating concentrations of unfolding chemicals to unfold it
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enthalpy
Rough “folding funnel” = Top7 Smooth funnel = natural protein
unfoldedstate
foldedstate
entropy
Journal of Molecular Biology
Volume 338, Issue 3, 30 April 2004, Pages 573-583
The hidden costs of Top7’s stability:(i) A rough folding funnel and
(ii) persistent, dimerizing fragments
The hidden costs of Top7’s stability:(i) A rough folding funnel and
(ii) persistent, dimerizing fragments
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The hidden costs of Top7’s stability:(i) A rough folding funnel and
(ii) persistent, dimerizing fragments
Journal of Molecular BiologyVolume 362, Issue 5, 6 October 2006, Pages 1004-1024
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Michael Hecht’s Lab: All proteins need is a little stability and they can catalyze reactions surprisingly well
Pattern random polar/non-polar amino acids to produce 4 semi-stable helices
Test for activities:Heme/CO bindingPeroxidaseEsteraseLipase*
*Not peer-reviewed yet
Protein Engineering, Design & Selection vol. 17 no. 1 pp. 67±75, 2004Protein Sci. 2004 13: 1711-1723
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The potential fruitfulness of the proteome
• Hecht’s best “default” proteins are similar to the proteins observed in nature
(without even trying)
• For some activities, “worse”-structured proteins are better catalysts
• Defined structure appears to be the pre-requisite for enzymatic activity
• “Moonlighting” proteins are likely
• Creative potential: A genome pregnant with possibilities
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We can design protein-protein surfaces/interfaces as well as cores
Our proteins: MICA & NKG2D
A section of MICA is disordered until NKG2D sits down on it
Our strategy: remove an entropy barrier by stabilizing interactions beneath the interface, inside MIC-A
• Better design scores meant our 8 chosen residues fit together better (better enthalpy)Yellow = MICA
Orange = NKG2D
Green = disordered when NKG2D is not present
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The NKG2D/MICA interaction is driven by entropy as well as enthalpy
Measure thermodynamics of binding with surface plasmon resonance at different temperatures to construct van’t Hoff plots
Enthalpy = MICA forms stronger bonds to NKG2D than to water
Entropy = water can assume more configurations when it’s not next to MICA (squeezed out by NKG2D binding); Entropy makes this interaction (and others) happen
TCRTCR--MHCMHC
NKG2DNKG2D--MICAMICA
Binding E
nergyB
inding Energy
ProteinProtein--ProteinProtein
Protein-protein interaction data (n=30) taken from Stites (1997) Chem. Rev. 97: 1233-50.
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Decreasing the entropy of MIC-A didn’t help, but increasing it did help
Entropy-enthalpy compensation: we stabilized entropy, but enthalpy overcompensated
Is some MIC-A disorder necessary for binding to its receptor?
0
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0 5e-7 1e-6 2e-6 3e-6 4e-6 5e-6
MIC-A WT
RU
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M[NKG2D]
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MIC3LR
U (E
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M[NKG2D]
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MIC1Q4I6S7D8L
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0 5e-7 1e-6 2e-6 3e-6 4e-6 5e-6
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“normal”Better Design Scores Worse Design Scores
-10
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** *
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ΔΔ
H o
r -TΔΔ
S (k
cal/m
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Other examples where increasing entropy helps stabilize a protein interaction
• Increasing entropy of reactant protein: Kossiakoff’s hGHv
• Increasing entropy of product complex: Fernandez’s Cl displacing a nearby loop
• Recall Hecht’s flexible, default, multispecific proteins
Complex chemicals have complex mechanisms of interaction, and entropy can be harnessed to manipulate those mechanisms
Biochemistry 45(28): 8488-98. Mol Pharm. 2008 May-Jun;5(3):430-7.
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Reclaiming Entropy from the “Dark Side”
Entropy is consistent, lawful, predictable, manipulable, even good.
“Without some disorder nothing can be alive.”
• RJP Williams, The Natural Selection of the Chemical Elements (1996), p. 83
http://www.padawansguide.com/gifs/ghosts1.jpg (c) 1983 Lucasfilm
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An argument against “stochastophobia”(the fear of entropy)
• 2 reasons for “stochastophobia”:a.) entropy (and math: S = k ln Ω) are complex conceptsb.) it sounds like chance is the ultimate arbiter of life
• My own studies found 2 ways entropy makes good things happen:
Water molecules disordering drives protein associationWe increased MICA’s configurations and observed better binding to NKG2D = better potential therapy
• Unpredictable molecular motions lead to predictable stochastic behavior of a population of molecules
MIC-A binding NKG2D may be driven by randomness but it will always bind
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Finding that entropy is good: Entropy is a cornerstone of creation
• If randomness can be reliably used in protein chemists’ acts of sub-creation, might it also be relied upon in creation of species?
• Entropy: not a barrier, but an opportunity
“What remains indelibly remarkable, therefore, is ... the delicate blend of openness, constraint, and temporality that clothes the cosmos with drama. ... If nature is narrative, we must remark at how fortunate it is that adaptation and design are not comfortably complete.”– John F. Haught, “Is Fine-Tuning Remarkable?” Fitness of
the Cosmos for Life (Cambridge, 2008), p.45, 46.
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Thank you!
• Thanks also to:– 5 years of biochemistry student researchers
working on this project– Seattle Pacific University– Montana Research Endowment– The National Institutes of Health for funding
our research– Owen Ewald (Classics, SPU) for the accurate
translation of “stochastophobia”