Research overview
We are interested in exploring mechanisms in chemistry and
biology. In particular, we are interested in uncovering physical principles
that govern the conformational transitions of proteins
and nucleic acids. How do proteins fold? Do all proteins adopt unique
three-dimensional structures? What are the energetic and entropic
determinants for preferred folding pathways? How do environmental
factors influence the folding pathways and intermediate states?
In recent years, misfolded proteins and structured aggregates have been
implicated in a class of disorders, such as Alzheimer’s, Parkinson’s and
mad cow diseases, underscoring the need for molecular- and atomic-level
understanding of protein folding. While advances in protein engineering
and other experimental techniques have been leading the way in mapping
folding pathways of proteins, significant progress has also been made in
theoretical investigations. Notably, the folding funnel theory has
enabled theoretical predictions of protein folding pathways using
native-state based coarse-grained models. High performance computing
power combined with implicit solvent models and advanced conformational
sampling methods have allowed in silico folding of small proteins at
atomic resolution.
Guided by classical, statistical and quantum mechanical theories, we are
developing theoretical methods and physical models, and implementing
them into computer simulations to elucidate molecular mechanisms in
biological processes. Some of our current projects include metal-ion
binding to proteins; pH effects in protein folding and amyloid
formation; conformational dynamics of RNA; methods for accelerated
molecular simulations.
News & Highlights
Feb 2009 - Students from the CCB class
participate in
the first
worldwide competition of pKa prediction
Sept 2008 -
Research from University of Oklahoma in enzyme research provides new
insights
Feb 2008 -
"Exceptional" paper, evaluation on "Faculty of 1000 Biology"
Oct 2007 -
Papers of the week: A new alternative "endosomic" amyloid hypothesis
Oct 2007 -
The Goldilocks Scenario