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3DM: Protein engineering Super-family platforms
1. Find the best starting enzyme
2. Find the hotspots
3. Select the best mutations at these hotspots
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
Hexokinases
Glucokinases
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
Allowed amino acids at pos. 64 (46 in alignment) = A,G,P,S,C
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3DM: Protein engineering Super-family platforms
HexokinasesGlucokinases
Allowed amino acids:
A,G,P,S
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
Can we change a hexokinase into a glucokinase?
With a smart library (size 32) targeted at these correlating positions -> 10 fold increase of glycokinase activity.
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3DM: Protein engineering Super-family platforms
Cupin superfamily
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platformsWT = P27Y28 Y28GP27A -> 200% control P27A -> 15% Y28GP27E -> 85% Y28GP27R -> 80%
Y28G -> 10%
G28 -> P,A -> no act.
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3DM: Protein engineering Super-family platformsY28DP27G -> 300% Y28RP27N -> 200% all others less active as wild type
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3DM: Protein engineering Super-family platforms
Inhibitor Design
The ICL-like superfamily:
* OAH is a member
* Used by fungi produce oxalate (toxic)
The most conserved residues ( >97% )
Correlating positions
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3DM: Protein engineering Super-family platforms
ICL:OH
O-
OHHO
O-
HOO-
O O-
OH
HOO-
OAH:OH O-
OH
HO
O- OHOH
O- Glu(100%)
Inhibitor Design
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
OAH:
Ser157 -> A, P or T : Km = 1200, 600, 800 x WT
kcat = 0.2, 0.3, 0.4 X WT
ICL:
Pro157 -> S: Km = 50 x WT,
kcat = equal to wildtypeOAH:
Ser157Pro: Changed specificity. Increased the affinity of OAH for a isocitrate like compound
Petal death protein:
Ser157Pro: Selectively removed OAH activity
Inhibitor Design
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3DM: Protein engineering Super-family platforms
OH O-
F
F
O- OH
Inhibitor Design
OH O-
OH
HO
O- OH
100% Diol
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3DM: Protein engineering Super-family platforms
Correlating different data types:
Correlation between fungi that are known oxalic acid producers and the amino acids in the alignment. -> make subset
Select all amino acids that are conserved within this group and a different residue in the rest of the alignment.
The best scoring amino acid = S157!!!!!
Subsets and data comparison
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
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3DM: Protein engineering Super-family platforms
Enantioselectivity:
Select all mutations from articles that are known to have effect on enantioselectivity and plot these in the protein of interest.
Design library at these positions taking high # of positions with low # of different aa.
Thermostability:
Select positions that are flexible in the structure (B-FIT values/RMSD) excluding parts that move to perform the function
Introduce the most common residues at these positions
Smart library design
Selectivity:
Select mutations from articles that are known to have effect on specificity and/or use correlated mutation data.
Always think!!!!
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3DM: Protein engineering Super-family platforms
Thank you for your attention