TCBG Seminar

Electronic Structure of Proteins Solvated in Explicit Water: Insights from Ab Initio Molecular Dynamics Calculations on Graphical Processing Units (GPU)

Mr. Ivan Ufimtsev
Department of Chemistry
Stanford University
Stanford, CA

Monday, January 25, 2010
3:00 pm (CT)
3269 Beckman Institute


It has been long recognized that water plays an important role in protein structure and dynamics by stabilizing surface residues through polarization, charge transfer, and other types of protein-water interactions. Despite this fact, solvated proteins have almost exclusively been studied by means of classical molecular mechanics with fixed charges. Ab initio treatment of solvated proteins is obviously highly desirable; however, this has been computationally prohibitive for large systems on conventional computational hardware. On the other hand, graphical processing units (GPUs) (essentially consumer graphics cards) manufactured by Nvidia have recently emerged as a powerful alternative to commodity processors, with a high density of arithmetic units on each chip and large memory bandwidth to support these arithmetic units. We have redesigned electronic structure algorithms for the GPU architecture and demonstrated accelerations of more than 100x compared to a popular electronic structure program running on traditional hardware. This talk will focus on our recent ab initio molecular dynamics simulations of solvated Bovine pancreatic trypsin inhibitor (BPTI) protein. Fittingly, BPTI was the first protein ever studied with force-field based molecular dynamics and now it is one of the first proteins to be studied with ab initio molecular dynamics. Population analysis of the electronic charge density reveals a significant amount of charge (2.6e) transferred from BPTI to the solvent. Half of the charge is transferred from charged residues and the rest is transferred from neutral and polar residues in approximately equal amounts. In the gas phase, BPTI demonstrates high intra-protein polarization between neutral and polar residues which vanishes upon solvation.

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