Institute for Protein Design

Frank DiMaio, PhD

Assistant Professor

Dr. Frank DiMaio is an Assistant Professor in the UW Department of Biochemistry (see DiMaio lab page).  His research is focused on protein structure determination from sparse and noisy experimental data.  By combining ideas from protein structure prediction with data-guided conformational sampling, we may uniquely determine a protein’s structure to atomic accuracy in cases where neither data nor prediction alone is sufficient.  The methods Frank has developed include tools for solving difficult molecular replacement problems, elucidating more than a dozen structures previously unsolved in the laboratories of expert crystallographers [1,2,3].  He has also developed a new approach for low-resolution crystal refinement; this method outperforms state-of-the-art refinement packages, making it possible to infer detailed atomic interactions from low-resolution crystal data [4,5].  Frank is further interested in developing tools for de novo structure determination from low-resolution data, as well as extending these approaches to other sources of data.  Additionally, he is more generally interested in structure prediction, developing methods for improving conformational sampling [6,7], protein forcefield development [8], and modeling (and design) of symmetric protein assemblies [9].  Improvements to structure prediction – both sampling methods and forcefields – are critical to designing proteins with novel function.

Frank DiMaio, PhD
Assistant Professor
Department of Biochemistry
University of Washington
J575, Health Sciences Building, Box 357370
Seattle, WA 98195-7370
 
Phone: (206) 221-5283
Email: dimaio@u.washington.edu
 
References:

[1] F. DiMaio, T. Terwilliger, R. Read, A. Wlodawer, G. Oberdorfer, E. Valkov, A. Alon, D. Fass, H. Axelrod, D. Das, S. Vorobiev, H. Iwai, P. Pokkuluri and D. Baker (2011). Improving molecular replacement by density- and energy- guided protein structure optimization. Nature. 473:540-3.

[2] A. Alon, I. Grossman, Y. Gat, V. Kodali, F. DiMaio, T. Mehlman, G. Haran, D. Baker, C. Thorpe, D. Fass (2012). The dynamic disulphide relay of quiescin sulphydryl oxidase. Nature 488:414-8.

[3] E. Valkov, A. Stamp, F. DiMaio, D. Baker, B. Verstak, P. Roversi, S. Kellie, M.J. Sweet, A. Mansell, N.J. Gay, J.L. Martin, and B. Kobe (2011). Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection. Proceedings of the National Academy of Sciences. 108:14879-84.

[4] F. DiMaio*, N. Echols*, J. Headd, T. Terwilliger, P. Adams, D. Baker (2013). Improved protein crystal structures at low resolution by integrated refinement with Phenix and Rosetta. Nature Methods (in press).

[5] T.I. Brelidze, E.C. Gianulis, F. DiMaio, M.C. Trudeau, W.N. Zagotta (2013). Structure of the C-terminal region of an ERG channel and functional implications. Proceedings of the National Academy of Sciences. 110:11648-53.

[6] Y. Song*, F. DiMaio*, R. Y.-R. Wang, D. Kim, C. Miles, T.J. Brunette, J. Thompson and D. Baker (2013) High resolution comparative modeling with RosettaCM. Structure (in press).

[7] D. Kim*, F. DiMaio*, R. Y.-R. Wang, Y. Song, D. Baker (2013). One contact for every twelve residues is sufficient for accurate topology-level protein structure modeling. Proteins (in press).

[8] P. Conway*, M. Tyka*, F. DiMaio*, D. Konerding and D. Baker (2013). Relaxation of backbone bond geometry improves protein energy landscape modeling.  Protein Science (in press).

[9] F. DiMaio, A. Leaver-Fay, P. Bradley, D. Baker, I. André. (2011) Modeling symmetric macromolecular structures in Rosetta3. PLoS One. 6:e20450.