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Computational design of protein function
Loren Looger Hellinga lab
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1. Allowable structures for proteins, DNA, small molecules
Progesterone
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2. Pseudo-geometric potential
electrostatics H-bonds sterics solvation
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Pretty much like CHARMM...
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Hydrogen bonds, too... anchor r H A D -8 · { }
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Area-based solvation energy
P P P = polar H = hydrophobic H H H
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Electrostatic potential
is a function of atom-type pair & protein environment. Parameterized to fit experimental data.
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3. Algorithm for choosing best structure(s) from all available
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Protein (PBP) scaffolds
Complementary Surface Construction: Ligand coordinates Protein Poly-alanine PCS Rotational ligand ensemble Docking grid Force field Placed Fixed ligand Side-chain rotamers Evolved Ranked PCS Experiments Periplasmic Binding Protein (PBP) scaffolds Molten zone Evolving zone Fixed zone
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Metabolites Neurotransmitters Drugs Kd = 2 µM Kd = 6 µM Kd = 2 nM
[L-lactate] (µM) 0.5 1 40 80 F x Kd = 2 µM 52.5 100 Kd = 6 µM [serotonin] (µM) 12.5 25 Kd = 2 nM [TNT] (nM) 150 300 Kd = 4 nM [5-fluorouracil] (nM) 50 [MTBE] (µM) 0.25 Kd = 45 nM [PMPA] (µM) TNT RDX MTBE D-lactate L-lactate 5-fluorouracil ibuprofen PMPA~soman serotonin dopamine & Pollutants Explosives Chemical Threats
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QSAR Results for binding affinities for L-lactate & TNT Receptors
-8 -6 log Kd (obs) -4 -2
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L-lactate designs GBP QBP RBP 1 100µM 10 100mM 0.1 HBP ABP
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The use of QSARs in the predictions improves the designs: D-lactate
GBP QBP RBP 1 100µM 10 100mM 0.1 HBP ABP
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Construction of biological sentinels for chemical threats and pollutants
modulation binary expression [inducer]
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Unicellular sentinels for chemical threats and pollutants
TNT Ribose Lactate MTBE 5 Fluoro-uracil
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Dose Response of TNTa Signaling
IPTG 0 mM TNT 100 mM 2,4-DNT 100 mM 2,6-DNT 100 mM mM mM mM mM mM [TNT]
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Optically pure enantiomers
Absorbance 210nm L D Kdlactate D L none none 200µM 3µM 0.8µM 10µM Racemic mix Optically pure enantiomers Wt Gbp Immobilized receptors L-Lac.G1 D-Lac.G1 Fraction #
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Computational design of ligand-binding sites Strategy #2: predefined geometries
{ l, w1, w2, q1, q2, q3 }n geometrical description of essential features in the complementary surface Complementary surface construction ( rotamers) Site 1 Site 2 +... Calculation #2 Complementary surface construction (PCS + SCS) +... Site 1 Site 2 Combinatorial search (108 sequence 1012 rotamers) Calculation #1 Initial placement of PCS on scaffold backbone Design scaffold coordinates side-chain rotamer library Pairwise of atomic interactions
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Triose phosphate isomerase chemistry
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Acknowledgements Mary Dwyer Jeff Smith Shahir Rizk
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