Senior Research Staff
Material and Molecular Simulation Center
California Institute of Technology
Mail Stop 139-74
Pasadena, CA 91125, USA
- Biomacromolecular simulations
- Constrained MD algorithms
for fast and long time MD simulations
- NEIMO algorithm developed for doing large timestep long time
MD simulations for very large (order of millions of atoms)
systems. NEIMO dynamics.
- Structure Prediction for Membrane
- As a part of MURI on structure prediction for odor
receptors we are trying to optimize the
helix packing in a seven transmembrane helix odor receptor
- Another part of the structure for membrane proteins is in collaboration
with the Los Angeles Children's Hospital in characterizing the
binding determinants for the binding of NAG dimers to the Outer membrane
protein A. One of the critical steps in the bacterial meningitis
is the binding of the NAG oligomers in the glycoproteins
of Brain Microvascular Endothelial Cells(BMEC) to the Outer Membrane
Protein (OmpA) of the E.coli.
- HEIRARCHICAL NEIMO for studying
large scale motions in proteins
- NEIMO algorithm developed for doing long timescale
MD simulations for very large proteins systems. This
captures catalytically active conformations.
Shown below is the enzyme phospho glycerate kinase going from open to
closed domain conformation
- Protein Folding
- NEIMO dynamics has been succesfully applied to folding of an
extended polyalanine (Ala)20 to a alfa helix from various starting conformations.
- It has been used to measure the helix propensities of various aminoacids
Below is a trajectory with leucine substituted in the middle of polyalanine chain
showing a transition through a beta sheet.
- Large Scale Simulations on the
Rhinovirus - 14
- Using MPSim code on the massively parallel computers we are trying to
understand the uncoating mechanism of the rhinovirus-14 with and
without the WIN drugs.