Chemistry & Biophysics
research involves theoretical studies of biological
macromolecules and other condensed matter systems
at a molecular level. We are interested in problems
such as how the structure of a given protein promotes
its biological function and how solvent influences
structure and function of proteins, as well as general
problems in solution theory.
We use a variety of theoretical and computational
tools in our research. One approach is molecular dynamics
simulations, especially molecular dynamics simulations,
in which the motions of the individual atoms comprising
the molecules are modeled. This type of computer simulation
has provided insights into many physical, chemical
and biochemical problems, and is particularly useful
in studying complex biological molecules. Other tools
include electronic structure calculations, continuum
dielectrics and statistical mechanical theory.
One research area involves electron transfer, a crucial
process in both respiration and photosynthesis. We
use molecular dynamics simulations to understand at
a molecular level how the protein environment influences
the transfer process. Our focus is on the iron-sulfur
proteins, particularly rubredoxin.
Another research area is in liquid state theory, using
both statistical mechanical theories and computer simulations.
We are formulating molecular theories of solvation
for macromolecules such as proteins and DNA. This work
has ranged from studies of water and aqueous solutions
to proteins in solution. The goal of this work is to
include solvent effects efficiently into computer simulations
of proteins and nucleic acids which is currently a
major stumbling block.
Tan, M.-L.; Dolan, E. A.; Ichiye, T. Understanding intramolecular electron transfer in ferredoxin: A molecular dynamics study. J. Phys. Chem. B 2004, 108, 20435-20441.
Chowdhuri, S.; Tan, M.-L.; Ichiye, T. Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: A molecular dynamics study. J. Chem. Phys. 2006, 125, 144513-144520.
Xiao, Y.; Tan, M.-L.; Ichiye, T.; Wang, H.; Smith, M. C.; Meyer, J.; Sturhahn, W.; Alp, E. E.; Zhao, J.; Yoda, Y.; Cramer, S. P. Dynamics of Rhodobacter capsulatus [2Fe-2S] ferredoxin VI and Aquifex aeolicus ferredoxin 5 via nuclear resonance vibrational spectroscopy (NRVS) and resonance Raman spectroscopy. Biochem. 2008, 47, 6612-6627.
Niu, S.; Ichiye, T. Cleavage of [4Fe-4S]-type clusters: Breaking the symmetry. J. Phys. Chem. A, Articles ASAP April 20, 2009.
Niu, S.; Ichiye, T. Insight into environmental effects on bonding and redox properties of [4Fe-4S] clusters in proteins. J. Am. Chem. Soc., Articles ASAP April 2, 2009.