Conformational heterogeneity and DNA recognition by the morphogen bicoid

R. Adhikary, Y.X. Tan, J. Liu, J. Zimmermann, M. Holcomb, C. Yvellez, P.E. Dawson, F.E. Romesberg, Biochemistry (2017) published online 26 May.
pubpic2017AdhikaryACS Editors’ Choice: We introduce C-D bonds within different structural elements in the Drosophila transcription factor bicoid, a homeodomain protein with morphogenic activity. C-D absorptions are characterized in the free and DNA-bound states, as well as during thermal denaturation. Residues in the DNA recognition helix, but not other helices, exhibit multiple conformations, and overall the data are consistent with the existence of multiple stable conformations in the folded state.


Transparent window vibrational probes for the characterization of proteins with high structural and temporal resolution

R. Adhikary, J. Zimmermann, F.E. Romesberg, Chem. Rev. (2017) 117:1927–1969.
pubpic2017adhikaryWe review the strengths and weaknesses of the different transparent window vibrational probes, methods by which they may be site-specifically incorporated into peptides and proteins, and the physicochemical properties they may be used to study. These topics are put into context through four case studies focused on KSI, SH3, DHFR, and cyt c.


Temperature dependence of CN and SCN IR absorptions facilitates their interpretation and use as probes of proteins

R. Adhikary, J. Zimmermann, P.E. Dawson, F.E. Romesberg, Anal. Chem. (2015) 87:11561–11567.
pubpic2015badhikaryIn both model systems and the N-terminal Src homology 3 domain of Crk-II (nSH3), we show that the absorption frequency of cyano and thiocyano probes is linearly correlated with temperature and that the slope of the resulting line (frequency-temperature line slope or FTLS) reflects the nature of the probe’s microenvironment, including whether or not the probe is engaged in H-bonds.


Evidence of an unusual N-H—N hydrogen bond in proteins

R. Adhikary, J. Zimmermann, J. Liu, R. Forrest, T. Janicki, P. Dawson, S. Corcelli, F.E. Romesberg, J. Am. Chem. Soc. (2014) 136:13474-13477.
pubpic2014adhikaryWe characterize the IR stretching frequencies of deuterated variants of proline and four proline residues of an Src homology 3 domain protein. CD stretching frequencies are shifted to lower energies due to hyperconjugation with Ni electron density, and along with DFT calculations, the data reveal that the Ni+1-H–Ni interactions constitute H-bonds that may play an important role in protein folding, structure, and function.


IR probes of protein microenvironments: utility and potential for perturbation

R. Adhikary, J. Zimmermann, P.E. Dawson, F.E. Romesberg, ChemPhysChem (2014) 15:849-853.
pubpic2014adhikaryWe use IR spectroscopy to characterize nSH3 variants labeled with CN or N3 at five different positions. Like carbon-deuterium (C-D) bonds, CN and N3 can provide information about their surrounding protein environment, but unlike C-D, they tend to be perturbative and thus should be used with caution.


Experimental characterization of electrostatic and conformational heterogeneity in an SH3 domain

R. Adhikary, J. Zimmermann, J. Liu, P.E. Dawson, F.E. Romesberg, J. Phys. Chem. B, 117:13082-13089.
pubpic2013adhikaryWe use the IR absorptions of carbon-deuterium bonds site-selectively incorporated throughout the N-terminal SH3 domain from the murine adapter protein CrkII to characterize its different microenvironments with high spatial and temporal resolution.