Advances in Protein Science Powered by Massively Parallel Molecular Dynamics Software       

Medical, Health Informatics and Computational Biology Accomplishment | 2015

IBM researchers
Ruhong Zhou, Seung-gu Kang, Bruce Berne, Payel Das, Binquan Luan, Tien Huynh, Ajay K Royyuru, Jeffrey K Weber, Jed W Pitera, William Swope, Alessandro Curioni

Where the work was done: IBM T.J. Watson Research Center, IBM Research Almaden and IBM Research Zurick

What we accomplished: Over the past years, we have illuminated fundamental principles governing a myriad of biological processes in protein folding/misfolding/aggregation and at the bio-nano interface by combining experimental and theoretical approaches. In a paradigm-shifting fashion, we have:

(1) Demonstrated the potential for nanoscale dewetting during protein folding.

(2) Revealed how a single mutation induces protein misfolding and aggregation in proteins related to Alzheimer's disease.

(3) Resolved the mechanism underlying UV radiation-induced gamma-crystallin polymerization implicated in cataract formation.

(4) Illustrated the potential effects of nanoparticles on biomolecules in the sphere of nanotoxicity plus nanomedicine.

(5) Performed the largest set of mutations ever configured for free energy perturbation calculation to identify potential tastants for IBM clients.

Our state-of-the-art simulations based on massively parallel molecular dynamics software helped alter the landscape of the molecular modeling field, transforming molecular dynamics from a largely theoretical toy into a technique well-suited for direct comparison with experiments. These works have resulted in over 20 patents, 2 books and over 100 publications in peer reviewed journals including high impacts ones such as Nature, Science, Cell, PNAS, PLoS Medicine, JACS, ACS Nano and Angewandte Chemie.

In addition, techniques and tools developed for these projects have helped to land funded projects from some top Fortune 500 companies to conduct research related to their core businesses.

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Image credit: IBM Research