B.S. Yale University 1990
Ph.D. MIT, 1995
Post-Doctoral Fellowship, 1995-1999, Univ. of Colorado, Boulder
Our laboratory is interested in biological molecules that structurally rearrange as part of their normal activity.
Non-coding RNAs and the proteins with which
they interact. Non-coding RNAs (ncRNAs) are
involved in a variety of regulatory processes
associated with mRNA stability and post-transcriptional
gene regulation. We are using a variety
of methodologies including structure mapping,
CD spectroscopy, fluorescence, and
microcalorimetry to probe the structural
changes associated with the biology of ncRNAs.
One system under study is DsrA, a ncRNA from
E. coli involved in the cold shock response.
Together with Hfq (Figure 1), a bacterial
homolog of the Sm- and Lsm proteins,
DsrA regulates RpoS
translation. We have probed
the different faces of Hfq and
shown that they both bind
RNAs but with different specificities. Hfq also interacts with a variety of proteins.
We are looking at the way in which the RNAs bound to Hfq help to specify
the protein components in this dynamic RNA-protein particle.
Thermodynamics of RNA Folding. RNA folding and RNA structural rearrangements
are important determinants of the biological activity. We use CD,
isothermal titration calorimetry (ITC) and differential scanning calorimetry
(DSC) to probe these structural changes and the fundamental thermodynamics
of RNA folding transitions. We have been looking extensively at heat capacity
changes (ΔCP), the temperature dependence of the ΔH. We are exploring
the fundamental properties of this thermodynamic parameter, such as its
physical origin in RNA folding, its dependence on oligonucleotide length and
sequence, its dependence on ion condensation and water interactions, and
the way it responds to divalent ion binding. We have found that the ΔCP can
be used, among other things, to reveal information about the residual structures
in the “unfolded” state. Such structures have a major impact on isothermal
Mechanistic Analysis of the Large Clostridial Cytotoxins. The laboratory is also
investigating the mechanistic enzymology and biophysics of toxins A and B
from Clostridium difficile, a common enteric bacterium. Infection with this
organism is the primary cause of antibiotic-associated diarrhea (a condition
that afflicts >3 million patients annually). Toxins A and B catalyze mono-glucosylation
of the RhoA sub-family of small G-proteins, inducing apoptosis in the
afflicted cells. We have cloned and expressed both the 66kD glucosyltransferase
domain as well as the intact 300 kD holotoxin. We are using these materials
to explore structural transitions required for translocation across cellular
membranes during pathogenesis and substrate recognition.
Figure 1. Hfq hexamerizes to form a very stable toroidal structure. The top and bottom faces both bind RNAs but the sites have different specificities and functions.
C. difficile Toxin:
Swett, R., Cisneros, G. A., Feig, A. L. (2012) Conformational Analysis of Clostridium difficile Toxin B and its Implications for Substrate Recognition. PLOS One. 7(7): e41518. doi:10.1371/journal.pone.0041518
Kern, S. M. and Feig, A. L. (2011) Adaptation of Clostridium difficile toxin A for use as a protein translocation system. Biochem. Biophys. Res. Commun.405(4) 570-574. doi:10.1016/j.bbrc.2011.01.070.
Abdeen, S. J., Swett, R. J., and Feig, A. L. (2010) Peptide inhibitors targeting Clostridium difficile toxins A and B, ACS Chem Biol 5, 1097-1103.
RNA Biochemistry and Biophysics:
Salim, N.N., Faner, M.A., Philip, J., and Feig, A. L. (2012) Requirement of Upstream Hfq Binding (ARN)x Elements in glmS and the Hfq C-Terminal Region for GlmS Up-regulation by sRNAs GlmZ and GlmY. Nucl. Acids Res. 40, 8021-32. doi:10.1093/nar/gks392
Salim, N. Lamichhane, Zhao, R. Banerjee, T. R. Rueda, D and Feig, AL. (2012) Thermodynamic and Kinetic
Analysis of an RNA Kissing Interaction and its Resolution into an Extended Duplex. Biophys. J.102, 1097-1107. doi:10.1016/j.bpj.2011.12.052
Salim NN, Feig AL. (2010) An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction. PLoS One. 2010 Sep 28;5(9). pii: e13028. PMID: 20927406
Mikulecky, PJ and Feig, AL. (2006) Heat Capacity Changes Associated with Nucleic Acid Folding. Biopolymers, 82, 38-58.