Quantum Mechanical and Molecular Mechanical Methods for Iron-Sulfur Proteins
EMSL Project ID
39962
Abstract
Iron-sulfur proteins are an important class of electron carriers and redox sites in a wide variety of electron transport and enzymatic processes, including photosynthesis, respiration, nitrogen fixation, and hydrogen production. Determining the factors that tune reduction potentials of these proteins is crucial for understanding their structure-function relationships, which can be used in engineering the functions by either mutations in the protein or metal substitution in the cluster for bioengineering or biomimetic efforts in environmental bioremediation and biofuel production. Our previous broken-symmetry (BS) density functional theory (DFT) studies of for iron-sulfur protein analogs, in conjunction with findings from photoelectron spectroscopy (PES), collision-induced dissociation, and sulfur K-edge X-ray absorption spectroscopy (XAS), have led to fundamental understanding of the structure, energetics, and reactivity of Fe-S clusters. Meanwhile, our preliminary results from BS-DFT calculations of gas-phase analogs and the environmental contribution of the surrounding protein plus solvent from Poisson-Boltzmann continuum electrostatics calculations of crystal structures of proteins using partial charges for the cluster from the BS-DFT calculations have given remarkably good agreement with experiments. The proposed research is to optimize combined quantum mechanical and molecular mechanical (QM/MM) methods for calculations of chemical and physical properties of iron-sulfur proteins utilizing the EMSL computing facilities and NWChem/Ecce software packages. The specific aims are:(1) Calibration of QM/MM using PES detachment energies and S K-edge XAS Fe-S covalencies of Fe-S analogs.
(2) Comparison of QM/MM redox potentials and Fe-S covalencies of Fe-S proteins against experiment.
(3) Comparison of electron transfer rates in Fe-S proteins against experiment.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2010-10-01
End Date
2012-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Luo Y, S Niu, and T Ichiye. 2012. "Understanding Rubredoxin Redox Sites by Density Functional Theory Studies of Analogues." Journal of Physical Chemistry A 116(35):8918–8924. doi:10.1021/jp3057509
Niu S, and T Ichiye. 2011. "Density Functional Theory Calculations of Redox Properties of Iron–Sulphur Protein Analogues." Molecular Simulation 37(7):572-590. doi:10.1080/08927022.2011.582111
Niu S, DL Huang, PD Dau, HT Liu, LS Wang, and T Ichiye. 2014. "Assessment of Quantum Mechanical Methods for Copper and Iron Complexes by Photoelectron Spectroscopy." Journal of Chemical Theory and Computation 10(3):1283-1291. doi:10.1021/ct400842p
Niu S, M Tan, and T Ichiye. 2011. "The Large Quadrupole of Water Molecules ." Journal of Chemical Physics 134(13):134501. doi:10.1063/1.3569563
Perrin BS, S Niu, and T Ichiye. 2013. "Calculating Standard Reduction Potentials of [4Fe–4S] Proteins." Journal of Computational Chemistry 34(7):576–582. doi:10.1002/jcc.23169