Vijay Pande
Abstract
Alzheimer's Disease (AD) is believed to be caused by the aggregation of Abeta peptides. In particular, recent evidence suggests that the small molecular weight oligomers -- intermediate states in the kinetic pathway for aggregation -- are the toxic element in AD. Using massively parallel simulation within the Petascale Folding@home distributed computing project and novel data mining methodology, we have simulated the misfolding and aggregation of Abeta peptides in all-atom detail, including an atomistic representation of the solvent on experimentally relevant timescales. This level of detail allows us to make specific predictions for the nature of small molecular weight (2-4 chains) oligomers of Abeta. In addition to presenting these predictions, I will also discuss recent experimental validation of these predictions, as well as subsequent experiments motivated by these simulation results.
Biography
Prof. Pande’s current research centers on the development and application of novel grid computing simulation techniques to address problems in chemical biology.
In particular, he has pioneered novel distributed computing methodology to break fundamental barriers in the simulation of kinetics and thermodynamics of proteins
and nucleic acids. As director of the Folding@Home project (http://folding.stanford.edu), Prof. Pande has, for the first time, directly simulated protein folding
dynamics with quantitative comparisons with experiment, often considered a “holy grail” of computational biology. His current research also includes novel
simulation methods for high accuracy drug binding affinity calculations, protein misfolding, and related diseases such as Alzheimer’s Disease.
Prof. Pande received a BA in Physics from Princeton University in 1992. There, he was first introduced to biophysical questions, especially in his undergraduate
thesis research with Prof. Philip Anderson, a Nobel Laureate in physics. In 1995, he received his PhD in physics from MIT, studying as a NSF Fellow under Profs.
Toyoichi Tanaka and Alexander Grosberg. At MIT, Prof. Pande’s research centered on statistical mechanical models of protein folding and design, suggesting novel
ways to design protein sequences to have the desired stability and folding properties. As a Miller Fellow working with Prof. Daniel Rokhsar at UC Berkeley, Prof.
Pande extended this methodology to examine atomistic protein models, laying the foundations for his later work at Stanford University.
Prof. Pande has won numerous awards, including APS Fellow (2008), the Irving Sigal Young Investigator Award from the Protein Society (2006), the MIT Indus Global
Technovator’s Award (2004), a Henry and Camile Dreyfus Teacher-Scholar award (2003), being named to MIT’s TR100 (2002), and named a Frederick E. Terman Fellow (2002).
Prof. Pande is currently an Associate Professor of Chemistry and (by courtesy) of Structural Biology at Stanford University.