| Research Interests |
Physical
Chemistry & Biophysics
Our
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. |
| Recent
Publications |
Park, I.
Y., Eidsness, M. K., Lin, I.-J., Gebel, E. B., Youn,
B., Harley, J. L., Machonkin, T. E., Frederick,
R. O., Markley, J. L., Smith, E. T., Ichiye, T., and
Kang, C., Crystallographic studies of
V44 mutants of Clostridium pasteurianum rubredoxin:
Effects of side chain size on reduction
potential. Proteins: Struc. Func. Bioinf., 2004. 9:
423.
Yang, X., Niu, S., Ichiye, T., and Wang, L.-S., Direct
measurement of the hydrogen-bonding effect
on the intrinsic redox potentials of [4Fe-4S] cubane
complexes. J. Am. Chem. Soc., 2004. 126:
15790.
Tan, M.-L., Dolan, E. A., and Ichiye, T., Understanding
intramolecular electron transfer in ferredoxin:
A molecular dynamics study. J. Phys. Chem. B, 2004.
108: 20435.
Fu,
Y.-J., Niu, S., Ichiye, T., and Wang, L.-S., The
electronic structure and intrinsic redox properties
of the [2Fe-2S]+ clusters with tri- and tetra-coordinate
iron sites. Inorg. Chem., 2005.
44:
1202.
Ergenekan,
C. E., Tan, M.-L., and Ichiye, T., Effects
of environment on the structure of Pyrococcus
furiosus rubredoxin: A molecular dynamics study.
Proteins:
Struc. Func. Bioinf., 2005.
in press.
[complete list] |
Toshiko
Ichiye