Folding Proteins at the Speed of Life
Prof. Antti Niemi
Uppsala University, Sweden & CNRS, France

Despite impressive progress in the development of all-atom force fields and special purpose computers it would still take around 1000 years or more to fold a relatively simple protein such as myoglobin from a random chain to the native state, at all atom level. To computationally model how proteins fold and move, a new paradigm is needed. Accordingly, we propose to use techniques of modern theoretical physics including symmetry principles and a combination of geometry with the concept of integrability, to derive an energy function that governs proteins and their dynamics in the limit of slow spatial variations, in an essentially unique fashion. We observe that this energy function supports topological solitons as classical solutions, and explain how the solitons can be identified as the modular building blocks from which all folded proteins are composed. We show how crystallographic protein structures are modeled in terms of these building blocks, with experimental precision. As an example we consider myoglobin,  we are able to reach the native state within a couple of seconds, using an ordinary laptop computer with a folding pathway that fully matches the experimental observations how myoglobin folds.

About the Speaker

Prof. Niemi got his PhD from MIT in theoretical particle physics, after that he spent several years in US including Institute for Advance study in Princeton, UC Berkeley and Ohio State where he had faculty position. Then he moved to Finland, where he headed theoretical particle physics group at the Research Institute for Theoretical Physics, and were director of Institute of Particle Physics, and had lots of involvement in experimental particle physics at CERN. He has been in Sweden as a chaired professor of theoretical physics at Uppsala University since 1992, and Directeur de Recherche at CNRS in France since 2005. He has also been Chang Jiang professor at Chern Institute of Mathematics in Tianjin 2003-2008, and Qian Ren professor (part-time) at Beijing Institute of Technology since 2012.

2016-03-08 3:30 PM
Room: A203 Meeting Room
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