Quantum Mechanical and Molecular Mechanical Methods for Iron-Sulfur Proteins
EMSL Project ID
38793
Abstract
Iron-sulfur proteins are essential in bioenergetics, including respiration, photosynthesis, nitrogen fixation, and hydrogen production and thus are prime candidates for bioengineering or biomimetic efforts in environmental bioremediation and biofuel production. In addition, a wealth of experimental information exists on both iron-sulfur cluster analogs and proteins. Determining the factors that tune the reduction potentials of these proteins is crucial for understanding their structure-function relationships and thus for potentially engineering these proteins for bioremediation of the environment and biofuel production. However, separating electronic versus electrostatic factors is difficult because of the complexity of the protein environment. Previously, our broken-symmetry density functional theory calculations of iron-sulfur protein analogs in conjunction with the experimental findings by Xuebin Wang and Lai-Sheng Wang at EMSL have given a detailed understanding of the electronic, hydrogen bonding, and electrostatic factors arising from the ligands of iron-sulfur clusters. The collaboration with the EMSL group has led to 12 publications in peer-reviewed, high-quality journals. The electron detachment energies from experimental techniques coupling electrospray with photoelectron spectroscopy (PES) are essential because they allow direct comparisons of theory and experiment for clusters in the gas phase, with no approximations for the environment. Moreover, the EMSL computing facilities and the NWChem/Ecce software packages are essential because of the complexity of the quantum mechanical calculations of iron-sulfur clusters. The proposed research builds on this work by extending our combined computational and experimental studies to proteins, specifically by optimizing Combined quantum mechanical and molecular mechanical (QM/MM) methods for calculations of chemical and physical properties of iron-sulfur proteins. The specific aims are:(1) Calibration of QM/MM using PES detachment energies of Fe-S analogs.
(2) Comparison of QM/MM redox potentials of Fe-S proteins against experiment.
(3) Comparison of electron transfer rates in Fe-S proteins against experiment.
Project Details
Project type
Exploratory Research
Start Date
2010-02-18
End Date
2011-02-20
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
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