The Prediction of Protein pKas

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The Prediction of Protein pKas Jan H.
Jensen Department of Chemistry http//www.uiowa.
edu/quantum
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Protein pKas Motivation
Fundamental Chemical Reaction PH ? P H pKa
DGrxn/1.36 Protein Structure/Function
Relationships Molecular Determinants of
pKas Protein Engineering Improved Activity /
Stability at extreme pH New Catalysts
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Lysozyme Catalysis requires on pKa gap
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Current State-of-the-Art Bashford and Karplus 1990
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Lysozyme (Nielsen Vriend 2001)
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Challenges
PH ? P H pKa DGrxn/1.36 Target maximum
error 0.5 pH units or 0.7 kcal/mol System
size Solvent effects Long-range interactions
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QM/MM Scope and Challenges
Prediction of Select pKas Other Protonation
States from Standard Models or Experiment Is
QM Prediction of pKas Possible?
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Ab Initio Prediction of pKas
-?Gs(AH)
Li, Hains, Everts, Robertson Jensen J. Phys.
Chem. B 2002 Case, Noodleman Int. J. Quant. Chem.
1997 Schuurmann, Tomasi J. Phys. Chem. A
1998, da Silva et al. J. Phys. Chem. A 1999,
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Polarized Continuum Model of Bulk
Solvation Tomasi and co-workers
Bandyophayay, Gordon, Mennucci, Tomasi J. Chem.
Phys. 2002 Li, Pomelli Jensen Theo. Chem. Acc.
2003
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Computed
Experimental
O
4.6
4.8
9.8
10.6
9.8
10.0
7.0
N
6.2
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QM/EFP Approach
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Kairys Jensen J. Phys. Chem. A 2000
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Buffer Construction
EFP Construction

Error kcal/mol 0.1 0.2
Molina, Li Jensen J. Comp. Chem. in press
Minikis, Kairys, Jensen J. Phys. Chem. A 2001
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Proof-of-Concept
Turkey Ovomucoid Third Domain
Lys55 11.4 vs 11.1
Li, Hains, Everts, Robertson Jensen J. Phys.
Chem. B 2002
Molina, Li Jensen J. Comp. Chem. in press
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Lysine 55 pKa
Combined EFP/ Force Fields
Exp 11.1 EFP 11.4 AMBER 10.9 CHARMM 10.9 OPLS-A
A 10.9
Molina, Li Jensen J. Comp. Chem. in press
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Lysine 55 pKa
Benchmarking Force Fields
Exp 11.1 EFP 11.4 AMBER 9.7 CHARMM
9.6 OPLS-AA 9.8
Molina, Li Jensen J. Comp. Chem. in press
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Lysine 55 pKa
14 Å EFP
Exp 11.1 EFP 10.9
A minimal model for pKa predictions?
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OMTKY3 Carboxyl pKas
A minimal theoretical model
IEF-PCM (UAHF) RHF/6-31G(d)
MP2/6-31G(2d,p)// RHF/6-31G(d)
Li, Robertson Jensen Proteins, submitted
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OMTKY3 Carboxyl pKas
A minimal structural model
Li, Robertson Jensen Proteins, submitted
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Li, Robertson Jensen Proteins, submitted
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OMTKY3 Carboxyl pKas
The minimal model is accurate
Li, Robertson Jensen Proteins, submitted
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OMTKY3 Carboxyl pKas
Simpler model easier analysis
Li, Robertson Jensen Proteins, submitted
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OMTKY3 Carboxyl pKas
Molecular Determinants Hydrogen bonding source
of pKa-lowering Desolvation important for
Asp27 Charge-Charge interactions 0.5 pH
units pKa determined by local protein structure
Li, Robertson Jensen Proteins, submitted
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Current / Future Directions Molecular
Determinants of pKas Carboxyl pKas Hui Li
(ubiquitin) Mor Naor (xylanase) Pablo Molina
(helix N-termini) Cysteine pKas Mor
Naor Histidine pKas Su Chen NMR Chemical
Shifts and Hydrogen Bonding Serine proteases
Pablo Moloina Backbone amides Laura
Parker Redox Potentials Blue Copper Proteins
Hui Li Methodology Stable PCM gradients
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Acknowledgments
Current Group Hui Li Mor Naor Su Chen Laura
Parker Former Group Members Pablo
Molina Visvaldas Kairys Ryan Minikis Alex
Hains Josh Everts Collaborators Mark Gordon
Iowa State U.Walt Stevens DOE Cristian Pomelli
Pisa Andrew Robertson UI

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upport Research Corporation Petroleum Research
Fund University of Iowa Biosciences
Initiative Center for Biocatalysis and
Bioprocessing NSF-CRIF NSF NCI Advanced
Biomedical Computing Center
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Select EFP References http//www.uiowa.edu/quant
um
EFP Methodology Gordon, Freitag, Bandyopadhyay,
Jensen, Kairys, and Stevens, J. Phys. Chem. A
2001, 105, 293 Covalent Link Kairys and Jensen,
J. Phys. Chem. A 2000, 104, 6656 Protein EFP
Construction Minikis, Kairys, and Jensen J. Phys.
Chem. A 2001, 105, 3829 Molina, Li, and Jensen, J
Comp. Chem. in press. Partial Hessian
Vibrational Analysis Li and Jensen, Theo. Chem.
Acc., 2002, 107, 211 EFP/PCM Interface Bandyopadh
yay, Gordon, Mennucci, and Tomasi J. Chem. Phys.
, 2002, 116, 5023 Li, Pomelli, and Jensen Theo.
Chem. Acc. 2003, 109, 71 pKa Predictions Li,
Hains, Everts, Robertson, and Jensen, J. Phys.
Chem. B, 2002, 106, 3486. Li, Robertson, and
Jensen, Proteins, submitted.
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Select EFP References http//www.uiowa.edu/quant
um
EFP Methodology Gordon, Freitag, Bandyopadhyay,
Jensen, Kairys, and Stevens, J. Phys. Chem. A
2001, 105, 293 Covalent Link Kairys and Jensen,
J. Phys. Chem. A 2000, 104, 6656 Protein EFP
Construction Minikis, Kairys, and Jensen J. Phys.
Chem. A 2001, 105, 3829 Molina, Li, and Jensen, J
Comp. Chem. in press. Partial Hessian
Vibrational Analysis Li and Jensen, Theo. Chem.
Acc., 2002, 107, 211 EFP/PCM Interface Bandyopadh
yay, Gordon, Mennucci, and Tomasi J. Chem. Phys.
, 2002, 116, 5023 Li, Pomelli, and Jensen Theo.
Chem. Acc. 2003, 109, 71 pKa Predictions Li,
Hains, Everts, Robertson, and Jensen, J. Phys.
Chem. B, 2002, 106, 3486. Li, Robertson, and
Jensen, Proteins, submitted.
STOP! Do not go beyond THIS slide! Doing so may
bring down dppt!!!!
29
Select EFP References http//www.uiowa.edu/quant
um
EFP Methodology Gordon, Freitag, Bandyopadhyay,
Jensen, Kairys, and Stevens, J. Phys. Chem. A
2001, 105, 293 Covalent Link Kairys and Jensen,
J. Phys. Chem. A 2000, 104, 6656 Protein EFP
Construction Minikis, Kairys, and Jensen J. Phys.
Chem. A 2001, 105, 3829 Molina, Li, and Jensen, J
Comp. Chem. in press. Partial Hessian
Vibrational Analysis Li and Jensen, Theo. Chem.
Acc., 2002, 107, 211 EFP/PCM Interface Bandyopadh
yay, Gordon, Mennucci, and Tomasi J. Chem. Phys.
, 2002, 116, 5023 Li, Pomelli, and Jensen Theo.
Chem. Acc. 2003, 109, 71 pKa Predictions Li,
Hains, Everts, Robertson, and Jensen, J. Phys.
Chem. B, 2002, 106, 3486. Li, Robertson, and
Jensen, Proteins, submitted.
STOP! Definitely do not go beyond THIS
slide! Doing so WILL bring down dppt!!!!