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Nick Leioatts' Research Profile

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My research interests include understanding how proteins allosterically transduce signal.  To this end, I am employing a variety of computational methods.  In particular, I am interested in the activation dynamics of a biomedically important class of molecules, G protein-coupled receptors.  These integral membrane proteins transduce signal across the cell membrane, but the allosteric mechanism of their activation is not fully understood.  I am applying molecular dynamics simulations and elastic network models to track structural transitions associated with activation/deactivation of a model receptor, rhodopsin.  I am also interested in the development of novel methods for tracking structural transitions and analyses that allow us to directly compare simulation data to experimental observables.  Leveraging multiple time-scale models I hope to produce a better picture of the allosteric cascade that connects the ligand-binding pocket to the protein’s active site.

 

Publications:

  1. Leioatts, N., Mertz, B., Martinez-Mayorga, K., Romo, T. D., Pitman, M. C., Feller, S. E., Grossfield, A., Brown, M. F., "Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures", Biochemistry, 2013, DOI: 10.1021/bi4013947 (pdf)
  2. Leioatts, N., and Grossfield, A., "Molecular dynamics simulations of membranes and membrane proteins", in Molecular modeling at the atomic scale - Methods and applications in quantitative biology, ed. Ruhong Zhou, Taylor and Francis, to be published in 2014
  3. Seckler, J. M., Leioatts, N., Miao, H., and Grossfield, A. "The interplay of structure and dynamics in the function of HIV-1 reverse transcriptase"Proteins: Struc. Func. Bioinf., 2013, 81, 1792-1801, (pdf)
  4. Leioatts, N., Romo, T. D., and Grossfield, A., "Elastic network models are robust to variations in formalism", J. Chem. Theor. Comput., 2012, DOI:10.1021/ct3000316, (pdf)