Metalloenzymes are important but challenging targets for computational studies because a reliable and computationally efficient potential function for the metal site is not straightforward to obtain. The challenges are particularly severe for metalloenzymes that feature structurally flexible active sites and/or dynamical metal coordination spheres, for which good examples include metalloenzymes with open active sites and thus promiscuous catalytic activities and proteins whose metal coordination sphere undergoes major redox/pH-coupled changes. Here we propose to develop novel QM/MM methods based on the latest formulation of density functional tight binding (DFTB3) approach to strike the proper balance of computational efficiency and accuracy for metalloenzymes.
The specific aims are: 1. Parameterize DFTB3 for closed-shell systems (Mg, Zn, P and S) to facilitate the study of reactivity in flexible metalloenzymes that employ Mg and Zn as co-factors. Refine a novel DFTB3-MM interaction Hamiltonian and a multi-level QM/MM free energy framework that judiciously combines DFTB3/MM and high-level QM/MM potentials. The methods will be carefully benchmarked with both small molecule and metalloenzyme systems. 2. As an application to closed-shell metalloenzymes, dissect the catalytic mechanism of AP superfamily enzymes with both cognate and non-cognate substrates. Test the hypothesis that the remarkable catalytic promiscuity observed for the AP superfamily members is due to the significant structural flexibilities of the bi-metallic active site, which is able to recognize trasition states of distinct nature for different substrates. Test the computational results by comparing relevant observables (linear free energy relations, kinetic isotope effects, mutation and thio-effects) to experiments. 3. Introduce orbital angular momentum dependence of the Hubbard parameters into spin-polarized DFTB approach for the description of open-shell species. We will focus on the parameterization for copper and the method will be systematically tested and refined by comparing structural and energetic (e.g., reduction potential and pKa) properties of small molecules and copper proteins. Apply the approach to resolve several outstanding questions regarding the pH dependence of redox properties in blue copper proteins, setting the stage for applications to more complex problems, such as the binding of copper to proteins implicated in neurodegenerative diseases.

Public Health Relevance

The computational methods we develop will greatly facilitate mechanistic studies of metalloenzymes/metalloproteins implicated in key biological processes such as phosphoryl transfers, electron transfers and bioenergy transduction, which are often perturbed in devastating human conditions such as cancer and neurodegenerative diseases. Therefore, our research will have major long-term impacts on our ability to design novel strategies that combat these diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM106443-02
Application #
8725702
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Anderson, Vernon
Project Start
2013-09-01
Project End
2017-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Wisconsin Madison
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
City
Madison
State
WI
Country
United States
Zip Code
53715
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Gruden, Maja; Andjeklovi?, Ljubica; Jissy, Akkarapattiakal Kuriappan et al. (2017) Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules. J Comput Chem 38:2171-2185
Roston, Daniel; Demapan, Darren; Cui, Qiang (2016) Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site. J Am Chem Soc 138:7386-94
Jin, Haiyun; Goyal, Puja; Das, Akshaya Kumar et al. (2016) Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations. J Phys Chem B 120:1894-910
Roston, Daniel; Cui, Qiang (2016) Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. J Am Chem Soc 138:11946-57
Roston, D; Cui, Q (2016) QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes. Methods Enzymol 577:213-50
Christensen, Anders S; Kuba?, Tomáš; Cui, Qiang et al. (2016) Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 116:5301-37
Cui, Qiang (2016) Perspective: Quantum mechanical methods in biochemistry and biophysics. J Chem Phys 145:140901
Lu, Xiya; Fang, Dong; Ito, Shingo et al. (2016) QM/MM free energy simulations: recent progress and challenges. Mol Simul 42:1056-1078

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