The overall goals of this project are to develop a molecular mechanics force field for the iron-sulfur cluster based class of proteins that are ubiquitous in biological systems. These proteins serve as dioxygen, carbon monoxide and nitric oxide sensors, act as electron transfer and redox agents and serve some proton transfer functions. The force field parameters will be established for a series of iron-sulfur cluster based proteins with well established crystal structures; additional model compounds will be examined as well, again with literature structural information available. High level calculations will be conducted to gain good theoretical structures that agree with the crystallographic data. We will first attempt to use density functional theory (DFT) methods for these calculations, due to the good balance between sophistication and speed (even for large molecular systems) offered by these calculations. The data from the x-ray structures and the calculations will provide ample data for the extraction of bond length, angle and torsional force constants, the Lennard-Jones parameters, and the charge distribution among the atoms of the system. These components make up the potential function used in the AMBER force field. Initially, we will seek to augment this force field in coming up with a parameterized set suitable for conducting molecular mechanics calculators on iron-sulfur based proteins. We will test the efficacy of this molecular mechanics force field, checking for both interpolative and predictive value in structurally similar and dissimilar iron-sulfur cluster proteins. We will compare the results of the molecular mechanics calculations with x-ray structures as well as literature heats of formation, dipole moments, bond dissociation energies and ionization potentials. Finally, with the new force field capabilities in hand we will study important biological structure and function questions regarding iron-sulfur proteins using long timescale molecular dynamics simulations in explicit water. This is appealing as this approach has not been generally applied to iron-sulfur systems to due lack of adequate force field parameters.
The development of fast and reliable methods for simulating protein structure and reactivity is a crucial tool for studying these biologically important molecules. This work will aim to develop a computational approach suitable for describing the geometry of iron-sulfur based proteins. Defects in iron-sulfur cluster containing molecules are known to be associated with mitochondrial diseases, and the ability to better model these systems may lend new insight into diseases such as Parkinson's. ? ? ?
| Weaver, Michael N; Merz Jr, Kenneth M (2009) Assessment of the CCSD and CCSD(T) Coupled-Cluster Methods in Calculating Heats of Formation for Cu Complexes. Mol Phys 107:1251-1259 |
| Weaver, Michael N; Yang, Yue; Merz Jr, Kenneth M (2009) Assessment of the CCSD and CCSD(T) coupled-cluster methods in calculating heats of formation for Zn complexes. J Phys Chem A 113:10081-8 |
| Yang, Yue; Weaver, Michael N; Merz Jr, Kenneth M (2009) Assessment of the ""6-31+G** + LANL2DZ"" mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionization potentials for first-row-transition-metal complexes. J Phys Chem A 113:9843-51 |
