The goal of this proposal is to elucidate the nature of induced polarization in condensed biomolecular systems and to complete a first generation all-atom polarizable force field for proteins and phospholipid membranes. We have adopted and started to develop a potential function that incorporates electronic polarizability using classical Drude oscillators. We have optimized a simple water model (SWM4-DP) and are now ready to move to the next phase.
Our first aim will be to elucidate the nature of induced polarizability in condensed phases relative to the gas phase by optimizing the force field for a number of basic compounds. These initial studies will also help clarify the fundamental reduction of induced electronic polarizability in condensed systems caused by Pauli's exclusion principle and the overlap of electronic clouds.
Our second aim will be to optimize the internal portion of the force field.
Our third aim will be to assess the accuracy of the force field by performing molecular dynamics simulations of a test suite of proteins in the crystal environment. In addition, the nature of the interfacial potential of lipid membranes will be elucidated by performing a MD simulation of a fully polarizable model of a lipid bilayer and of the cation-ligand interactions giving rise to cooperative binding of calcium to the EF-hands in calbindin. It is important to emphasize that the three aims in the proposed study are linked in an iterative fashion. Upon completion of the proposed study a novel force field for proteins and lipids that includes explicit treatment of electronic polarizability will be available to the scientific community. While the proposed studies will be performed using the program CHARMM, the simplicity of the classical Drude oscillator used to treat electronic polarizability will insure that the developed force field may be readily implemented in other simulation packages.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM072558-05
Application #
7341078
Study Section
Biophysical Chemistry Study Section (BBCB)
Program Officer
Chin, Jean
Project Start
2005-02-01
Project End
2009-09-14
Budget Start
2008-02-01
Budget End
2009-09-14
Support Year
5
Fiscal Year
2008
Total Cost
$251,874
Indirect Cost
Name
University of Chicago
Department
Pediatrics
Type
Schools of Medicine
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637
Han, Kyungreem; Venable, Richard M; Bryant, Anne-Marie et al. (2018) Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions. J Phys Chem B 122:1484-1494
Lin, Fang-Yu; Lopes, Pedro E M; Harder, Edward et al. (2018) Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. J Chem Inf Model 58:993-1004
Huang, Jing; Lemkul, Justin A; Eastman, Peter K et al. (2018) Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. J Comput Chem 39:1682-1689
Villa, Francesco; MacKerell Jr, Alexander D; Roux, Benoît et al. (2018) Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2. J Phys Chem A 122:6147-6155
Aleksandrov, Alexey; Lin, Fang-Yu; Roux, Benoît et al. (2018) Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. J Comput Chem 39:1707-1719
Khan, Hanif Muhammad; MacKerell, Alexander D; Reuter, Nathalie (2018) Cation-? interactions between methylated ammonium groups and tryptophan in the CHARMM36 additive force field. J Chem Theory Comput :
Lin, Fang-Yu; MacKerell Jr, Alexander D (2018) Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields. J Chem Inf Model :
Lin, Fang-Yu; MacKerell Jr, Alexander D (2018) Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator. J Chem Theory Comput 14:1083-1098
Huang, Jing; MacKerell Jr, Alexander D (2018) Force field development and simulations of intrinsically disordered proteins. Curr Opin Struct Biol 48:40-48
Boulanger, Eliot; Huang, Lei; Rupakheti, Chetan et al. (2018) Optimized Lennard-Jones Parameters for Druglike Small Molecules. J Chem Theory Comput 14:3121-3131

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