Vaidehi Nagarajan

Senior Research Staff
Material and Molecular Simulation Center
California Institute of Technology
Mail Stop 139-74
Pasadena, CA 91125, USA

----------------------------- E-mail: vaid@wag.caltech.edu

Research interests

o 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.

o Structure Prediction for Membrane Proteins

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 protein.

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. Rhinovirus Simulations
o 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

o 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.
    o 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.

    Rhinovirus Simulations