John Eargle

I'm a postdoctoral researcher in Zan Luthey-Schulten's lab using evolutionary analysis and molecular dynamics to investigate RNA:protein complexes involved in translation.

 Research Interests

My research has mostly revolved around molecules involved in protein synthesis: transfer RNA, aminoacyl-tRNA synthetases, elongation factor Tu, and the ribosome. These RNAs and proteins predate the root of the universal phylogenetic tree so they provide a window deep into our evolutionary past.

I am interested in the evolution of the structure and function of these RNA and protein molecules so the first stages of my projects begin with evolutionary analyses of available sequence and structure data. To make the whole process of creating and editing multiple sequence/structure alignments easier, I helped develop the bioinformatics analysis environment MultiSeq, which is a plugin to the molecular visualization program VMD.

Recently, I've started using network techniques to analyze biomolecular structure and dynamics.

C.V. pdf

Resume pdf

  1. VanWart A., Eargle J., Luthey-Schulten Z., Amaro R.,
    "Exploring residue component contributions to dynamical network models of allostery,"
    J. Chem. Theory Comp., in press
  2. Eargle J. and Luthey-Schulten Z.,
    "NetworkView: 3D display and analysis of dynamic structure networks,"
    Bioinformatics, in press
  3. Eargle J. and Luthey-Schulten Z.,
    "Molecular dynamics simulations and visualization of dynamics in RNA:protein complexes,"
    Leontis N. and Westhof E. eds.,
    RNA 3D Structure Analysis and Prediction, 213-238, 2012
  4. Chen K., Eargle J., Lai J., Kim H., Abeysirigunawardena S., Mayerle M., Woodson S., Ha T., Luthey-Schulten Z.,
    "Assembly of the Five-Way Junction in the Ribosomal Small Subunit Using Hybrid MD-Go Simulations,"
    J. Phys. Chem. B, 116, 6819-6831, 2012
  5. Bolser D.M., Chibon P.Y., Palopoli N., Gong S., Jacob D., Angel V.D., Swan D., Bassi S., González V., Suravajhala P., Hwang S., Romano P., Edwards R., Bishop B., Eargle J., Shtatland T., Provart N.J., Clements D., Renfro D.P., Bhak D., Bhak J.,
    "MetaBase--the wiki-database of biological databases,"
    NAR, 40, D1250-D1254, 2012
  6. Chen K., Eargle J., Sarkar K., Gruebele M., Luthey-Schulten Z.,
    "The functional role of ribosomal signatures,"
    Biophys. J., 99, 3930-3940, 2010
  7. Trabuco L., Schreiner E., Eargle J., Cornish P., Ha T.J., Luthey-Schulten Z., Schulten K.,
    "The role of L1 stalk:tRNA interaction in the ribosome elongation cycle,"
    JMB, 402, 741-760, 2010
  8. Black A., Eargle J., Sethi A., Luthey-Schulten Z.,
    "Exit strategies for charged tRNA from GluRS,"
    JMB, 397, 1350-1371, 2010
  9. Alexander R., Eargle J., Luthey-Schulten Z.,
    "Experimental and computational determination of tRNA dynamics,"
    FEBS Letters, 584, 376-386, 2010
  10. Sethi A., Eargle J., Black A., Luthey-Schulten Z.,
    "Dynamical networks in tRNA:protein complexes,"
    PNAS, 106, 6620-6625, 2009
  11. Eargle J., Black A., Sethi A., Trabuco L., Luthey-Schulten Z.,
    "Dynamics of recognition between tRNA and elongation factor Tu,"
    JMB, 377, 1382-1405, 2008
  12. Roberts E., Eargle J., Wright D., Luthey-Schulten Z.,
    "MultiSeq: unifying sequence and structure data for evolutionary analysis,"
    BMC Bioinf., 7, 382, 2006
  13. Eargle J. and Luthey-Schulten Z.,
    "Visualizing the dual space of biological molecules,"
    Comp. Biol. and Chem., 30, 219-226, 2006
  14. Eargle J., Wright D., Luthey-Schulten Z.,
    "Multiple Alignment of protein structures and sequences for VMD,"
    Bioinformatics, 22, 504-506, 2006