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


 Publications
  1. 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
  2. Chen K., Eargle J., Sarkar K., Gruebele M., Luthey-Schulten Z.,
    "The functional role of ribosomal signatures,"
    Biophys. J., 99, 3930-3940, 2010
  3. 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
  4. Black A., Eargle J., Sethi A., Luthey-Schulten Z.,
    "Exit strategies for charged tRNA from GluRS,"
    JMB, 397, 1350-1371, 2010
  5. Alexander R., Eargle J., Luthey-Schulten Z.,
    "Experimental and computational determination of tRNA dynamics,"
    FEBS Letters, 584, 376-386, 2010
  6. Sethi A., Eargle J., Black A., Luthey-Schulten Z.,
    "Dynamical networks in tRNA:protein complexes,"
    PNAS, 106, 6620-6625, 2009
  7. 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
  8. Roberts E., Eargle J., Wright D., Luthey-Schulten Z.,
    "MultiSeq: unifying sequence and structure data for evolutionary analysis,"
    BMC Bioinformatics, 7, 382, 2006
  9. Eargle J. and Luthey-Schulten Z.,
    "Visualizing the dual space of biological molecules,"
    Computational Biology and Chemistry, 30, 219-226, 2006
  10. Eargle J., Wright D., Luthey-Schulten Z.,
    "Multiple Alignment of protein structures and sequences for VMD,"
    Bioinformatics, 22, 504-506, 2006


 Links