Professor of Biochemistry & Biophysics, UNC-CH Director, Center for Computational and Systems Biology, UNC-CH Graduate Director, Program in Cellular and Molecular Biophysics, UNC-CH PHD - Boston University (click for Full Publication List)

HONORS & AWARDS

• March of Dimes Basil O'Connor Starter Scholar Research Award, 2004-2006

RESEARCH

Summary:

My laboratory has developed novel approaches to molecular structural modeling and dynamic simulations, allowing studies of structure and dynamics of biological molecules at time scales relevant to biological systems (Core Techniques). These approaches have enabled us to (i) perform rapid and accurate virtual drug screening, as highlighted by the recent Critical Assessment of Structure-Activity Relationship (CSAR) competition and the identification of two ligands for cystic fibrosis transmembrane regulator (CFTR) and for mu-opioid receptor (MOR); (ii) build structures of the dynein head unit and MOR and its variants prior to the release of their solved structures; and (iii) develop allosteric approaches to protein activity control. Most of our efforts are directed toward understanding etiologies of human diseases, among which are the protein misfolding diseases cystic fibrosis and amyotrophic lateral sclerosis.

Mechanisms of Protein Misfolding and Aggregation. Protein misfolding underlies many diverse human diseases, such as cystic fibrosis, amyotrophic lateral sclerosis (ALS), and Parkinson’s disease. Protein misfolding results either in a loss of function (e.g. the loss of CFTR protein in cystic fibrosis) or in a toxic gain of function (e.g. formation of amyloid fibrils in ALS). The fundamental significance of protein misfolding is difficult to over-estimate, yet little is known about the molecular mechanisms that result in protein misfolding at the atomic level. The process downstream from misfolding is aggregation. Specifically, the formation of amyloid fibril, the insoluble aggregate of usually solvable proteins or polypeptides, has been associated with over 16 types of human diseases, such as Alzheimer’s Disease, light-chain amyloidosis, spongiform encephalopathies, and ALS. Although many advances have been made in the structural characterization of amyloid fibrils and their mechanisms of formation, many aspects of this process remain unclear. Understanding protein misfolding and aggregation processes will greatly impact modern medicine and biology and will allow the development of novel pharmaceutical strategies.

We use a multidisciplinary approach that uniquely combines biophysics, biochemistry, and structural and computational biology to uncover the mechanisms of protein misfolding and aggregation. We then use our knowledge of these mechanisms to uncover the etiologies of human diseases and to develop novel therapeutic strategies. We have also developed approaches (described below) for virtual drug screening that have resulted in lead compounds to fight cystic fibrosis and also an agonist of mu-opioid receptor (provisional patents filed) that has been shown to be responsible for pain sensitivity.

Core Techniques:

• Medusa - a computational platform for molecular modeling, which includes a physics-based force field to evaluate the energetics of given conformations of molecules and molecular complexes, as well as rapid algorithms to search conformational space
• Eris - a computational tool for accurately predicting mutation-induced protein stability changes and for protein design
• πDMD – parallel discrete molecular dynamics (DMD) simulation package that allows long time scale sampling of molecular conformational space
• MedusaDock - a novel methodology that performs fully flexible docking of both the ligand and protein target and accurately evaluates protein-ligand binding
• Surface matching through fingerprints -a novel approach to match protein surfaces that allows identification of candidate interacting proteins and ligands based only on their three-dimensional geometry
• CryoEM fitting - an algorithm that can rapidly screen hundreds of thousands of structures and identify those that best fit a given cryoEM density
• Structural filters and high-resolution structure refinement - a set of filters to assess the quality of a structural model or a low-resolution structure
• Loop modeling and grafting – an applicationthat allows the building of loop structures using DMD simulations, as well as their grafting into a host protein (used in protein design)

REPRESENTATIVE PUBLICATIONS

Modeling

• Ding, F., Lavendar, C. A., Weeks, K. M. and Dokholyan, N. V. "Three-dimensional RNA structure refinement by hydroxyl radical probing", Nature Methods, in press (2012)
• Shirvanyants, D., Ding, F., Tsao, D., Ramachandran, S. and Dokholyan, N. V. "DMD: an efficient and versatile simulation method for fine protein characterization", Journal of Physical Chemistry B, in press (2012)
• Proctor, E. A., Yin, S., Tropsha, A., and Dokholyan, N. V. "Discrete molecular dynamics distinguishes native-like binding poses from decoys in difficult targets", Biophysical Journal, 102:144-151 (2012)
• Dagliyan, O., Proctor, E. A., D'Auria, K., Ding, F. and Dokholyan N. V. "Structural and Dynamic Determinants of Protein-peptide Recognition", Structure, 19:1837-1845 (2011)
• Ding, F., Yin, S., and Dokholyan, N. V. "Rapid flexible docking using a stochastic rotamer library of ligands", Journal of Chemical Information and Modeling, 50:1623-1632 (2010)
• Yin, S., Proctor, E. A., Lugovskoy, A. A. and Dokholyan, N. V. "Fast screening of protein surfaces using geometric invariant fingerprints", Proceedings of the National Academy of Sciences USA, 106:16622-16626 (2009)
• Yin, S., Biedermannova, L., Vondrasek, J., and Dokholyan, N. V., "MedusaScore: An accurate force-field based scoring function for virtual drug screening", Journal of Chemical Information and Modeling, 48:1656-1662 (2008)
• Ding, F., Tsao, D., Nie, H., and Dokholyan, N. V. "Ab initio folding of proteins with all-atom discrete molecular dynamics", Structure, 16:1010-1018 (2008)
• Yin, S., Ding, F., and Dokholyan, N. V. "Eris: An automated estimator of protein stability", Nature Methods, 4:466-467 (2007)

Applications

• Nakayama, T., Butler, J. S., Sehgal, A., Severgnini, M., Racie, T., Sharman J., Ding, F., Morskaya, S. S., Brodsky, J., Tchangov, L., Kosovrasti, V., Meys, M., Nechev, L., Wang, G., Peng, C. G., Fang, Y., Maier, M., Rajeev, K. G., Li, R., Hettinger, J., Barros, S., Clausen, V., Zhang, X., Wang, Q., Hutabarat, R., Dokholyan, N. V., Wolfrum, C., Manoharan, M., Kotelianski, V., Stoffel, M. and Sah, D. W. Y. "Harnessing a Physiologic Mechanism for siRNA Delivery with Mimetic Lipoprotein Particles", Molecular Therapy, in press (2012)
• Ding, F., Furukawa, Y., Nukina, N., and Dokholyan, N. V. "Local unfolding of Cu, Zn Superoxide Dismutase monomer determines the morphology of fibrillar aggregates", Journal of Molecular Biology, in press (2012)
• Redler, R. and Dokholyan, N.V. "The complex molecular biology of amyotrophic lateral sclerosis (ALS)", Progress in Molecular Biology and Translational Science, 107:215-262 (2012)
• Serohijos, A.W.R., Yin, S., Ding, F., Gauthier, J., Gibson, D., Maixner, W., Dokholyan, N. V.*, and Diatchenko, L.* "Structural basis for μ-opioid receptor binding and activation", Structure, 19:1683-1690 (2011)
• Aleksandrov, A. A., Kota, P., Aleksandrov, L. A., He, L., Jensen, T., Cui, L., Gentzsch, M., Dokholyan, N. V., and Riordan, J. R. "Regulatory insertion removal restores maturation, stability and function of ΔF508 CFTR", Journal of Molecular Biology, 401:194-210 (2010)
• Karginov, A. V., Ding, F., Kota, P., Dokholyan, N. V.*, and Hahn, K. M.* "Engineered allosteric activation of kinases in living cells", Nature Biotechnology, 28:743-748 (2010)
• Hao, J., Serohijos, A. W. R., Newton, G., Tassone, G., Wang, Z., Sgroi, D. C., Dokholyan, N. V.*, and Basilion, J. P.*, "Identification of peptide ligands to CRIP1, a novel biomarker for cancers", Public Library of Science Computational Biology, 4:e1000138 (2008)

CONTACT INFO

120 Mason Farm Rd
Campus Box # 7260
3097 Genetic Medicine Bldg
Chapel Hill, NC 27599

Office: 919-843-2513
Lab: 919-966-3137

dokh@email.unc.edu

Lab Location: 3100C-D Genetic Medicine

Dokholyan Lab Website