BioNMR Publications

Recent publications using the METACyt Biomolecular NMR Facilitiy:


SifR is an Rrf2-family quinone sensor associated with iron-catechol uptake in Streptococcus pneumoniae D39
Zhang, Y., Martin, J. E., Edmonds, K. A., Winkler, M. E., and GIEDROC, D. P. (2022)
J. Biol Chem, in the press (doi: 10.1016/j.jbc.2022.102046). *Editor’s pick
View: PubMed

The effect of ligands and transducers on the Neurotensin receptor 1 (NTS1) conformational ensemble.
Dixon, A.D., Inoue, A., Robson, S.A., Culhane,  K.J., Trinidad, J.C., Sivaramakrishnan, S., Bumbak, F. &  J.J. Ziarek. JACS. 2022, 144(23):10241-10250. View: Pubmed

Zn regulated GTPase metalloprotein activator 1 (ZNG1) regulates zinc homeostasis in vertebrates
Weiss, A., Murdoch, C. C., Edmonds K. A., Jordan, M. R., Monteith, A. J., Perera, Y. R.,
Rodríguez Nassif, A. M., Petoletti, A. M., Beavers, W. N., Krystofiak, E. S., Thalluri, K., Wu, H., DiMarchi, R. D., Chazin, W. J., *GIEDROC, D. P., and *Skaar E. P. (2022)
Cell, 185, 1-16 (doi: 10.1016/j.cell.2022.04.011) View: PubMed


Functional asymmetry and chemical reactivity of CsoR family persulfide sensors.
Fakhoury JN, Zhang Y, Edmonds KA, Bringas M, Luebke JL, Gonzalez-Gutierrez G, Capdevila DA, Giedroc DP. Nucleic Acids Res. 2021 Dec 2;49(21):12556-12576. View: Pubmed

TRACT revisited: An Algebraic Solution for Determining Overall Rotational Correlation Times from Cross-Correlated Relaxation Rates.
Robson, S.A., Dağ, Ç., Wu, H. & J.J. Ziarek.  Journal of Biomolecular NMR. 2021 Sep;75(8-9):293-302. View: Pubmed


The Pneumococcal Iron Uptake Protein A (PiuA) Specifically Recognizes Tetradentate FeIIIbis- and Mono-Catechol Complexes.
Zhang Y, Edmonds KA, Raines DJ, Murphy BA, Wu H, Guo C, Nolan EM, VanNieuwenhze MS, Duhme-Klair AK, Giedroc DP. J Mol Biol. 2020 Sep 4;432(19):5390-5410. View: Pubmed

1H, 13C, 15N backbone resonance assignments of the apo and holo forms of the ABC transporter solute binding protein PiuA from Streptococcus pneumoniae.
Edmonds KA, Zhang Y, Raines DJ, Duhme-Klair AK, Giedroc DP. Biomol NMR Assign. 2020 Jun 3. doi: 10.1007/s12104-020-09952-9.View: Pubmed


Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae.
Rued BE, Alcorlo M, Edmonds KA, Martínez-Caballero S, Straume D, Fu Y, Bruce KE, Wu H, Håvarstein LS, Hermoso JA, Winkler ME, Giedroc DP. mBio. 2019 Jan 29;10(1):e02622-18. doi: 10.1128/mBio.02622-18. View: Pubmed


Tuning site-specific dynamics to drive allosteric activation in a pneumococcal zinc uptake regulator
Capdevila, D. A., Huerta, F., Edmonds, K. A, Le, M. T., Wu, H. & GIEDROC, D. P. (2018)
eLife 7,e37268 (doi: 10.7554/eLife.37268)
View: Pubmed

Functional role of solvent entropy and conformational entropy of metal binding in dynamically driven allosteric system
Capdevila, D. A., Edmonds, K. A, Campanello, G. C., Wu, H., Gonzalez-Gutierrez G,. & GIEDROC, D. P. (2018) J Am. Chem. Soc. 140, 9108-9119 (doi: 0.1021/jacs.8b02129)
View: Pubmed

Metal-dependent allosteric activation and inhibition on the same molecular scaffold: The copper sensor CopY from Streptococcus pneumoniae
Glauninger, H., Zhang, Y., Higgins, K. A., Jacobs, A. D., Martin, J. E., Fu, Y., H. Coyne, J. 3rd, Bruce, K. E., Maroney, M. J., Clemmer, D. E., Capdevila, D. A., & GIEDROC, D. P. Chem Sci. 2018 Jan 7;9(1):105-118. View: Pubmed


Entropy redistribution controls allostery in a zinc metalloregulatory protein
Capdevila, D. A., Braymer, J. J., Edmonds, K. A., Wu, H., & GIEDROC, D. P. (2017)
Proc. Natl Acad. Sci. USA
114, 4424-4429 (doi: 10.1073/pnas.1620665114) 
View: Pubmed


Resolution of Site-Specific Conformational Heterogeneity in Proline-Rich Molecular Recognition by Src Homology 3 Domains
Horness RE, Basom EJ, Mayer JP, and Thielges MC. J. Am. Chem. Soc. 2016, 138, 1130-1133.DOI: 10.1021/jacs.5b11999

The S2 Cu(I) site in CupA from Streptococcus pneumoniae is required for cellular copper resistance
Fu, Y., Bruce, K., Wu, H. & GIEDROC, D. P. 2015, Metallomics. 2016, 8, 61-70. View: PDF


1H, 13C, 15N resonance assignments of the extracellular loop 1 domain (ECL1) of Streptococcus pneumoniae D39 FtsX, an essential cell division protein.
Fu Y, Bruce KE, Rued B, Winkler ME, Giedroc DP. Biomol NMR Assign. 2015.

A new class of orthosteric uPAR·uPA small-molecule antagonists are allosteric inhibitors of the uPAR·vitronectin interaction.
Liu D, Zhou D, Wang B, Knabe WE, Meroueh SO. ACS Chem Biol. 2015, 10(6):1521-34.

Electrostatic occlusion and quaternary structural ion pairing are key determinants of Cu(I)-mediated allostery in the copper-sensing operon repressor (CsoR)
Chang, F.-M.J., Martin, J.E. & GIEDROC, D. P. 2015, Biochemistry 54, 2462-2473 View: PubMed


Cu(I)-mediated allosteric switching in a copper-sensing operon repressor (CsoR).
Chang FM, Coyne HJ, Cubillas C, Vinuesa P, Fang X, Ma Z, Ma D, Helmann JD, García-de los Santos A, Wang YX, Dann CE 3rd, Giedroc DP. J Biol Chem. 2014 Jul 4;289(27):19204-17.

¹H, ¹³C, ¹⁵N resonance assignments of murine hepatitis virus nonstructural protein 3a.
Keane SC, Giedroc DP. Biomol NMR Assign. 2014 Apr;8(1):15-7.

Backbone and sterospecific methyl side chain resonance assignments of the homodimeric zinc sensor AdcR (32 kDa) in the apo- and Zn(II)-bound states.
Guerra AJ, Giedroc DP. Biomol NMR Assign. 2014 Apr;8(1):11-4.


Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.
Chakravorty, D. K, Wang, B., Lee, C. W., Guerra, A .J., GIEDROC, D. P., & Merz, K. M. Jr. (2013) J. Biomol. NMR 56, 125-137. View: PubMed

A new structural paradigm in copper resistance in Streptococcus  pneumoniae.
Fu, Y., Tsui, H .-C., Bruce, K. E., Sham, L. T., Higgins, K. A., Lisher, J .P., Kazmierczak, K. M., Maroney, M. J., Dann, C. E. 3rd, Winkler, M. E., & GIEDROC, D. P. (2013)
Nat. Chem. Biol. 9, 177-183. View: PubMed

Allosteric inhibition of a zinc-sensing transcriptional repressor: Insights into the arsenic repressor (ArsR) family.
Campanello, G. C., Ma, Z., Grossoehme, N. E., Guerra, A. J., Ward, B. P., Dimarchi, R. D., Ye, Y,, Dann, C. E., 3rd, & GIEDROC, D. P. (2013) J. Mol. Biol. 425, 1143-1157.
View: PubMed

Mechanistic insight into inhibition of two-component system signaling.
Francis S, Wilke KE, Brown DE, Carlson EE.
Medchemcomm. 2013;4(1):269-277. Epub 2012 Nov 21. PubMed

1H, 13C, and 15N resonance assignments of NmtR, a Ni(II)/Co(II) metalloregulatory protein of Mycobacterium tuberculosis.
Lee CW, Giedroc DP.
Biomol NMR Assign. 2013 Oct;7(2):145-8. Epub 2012 May 22. PubMed


Backbone and sterospecific methyl side chain resonance assignments of the homodimeric zinc sensor AdcR (32 kDa) in the apo- and Zn(II)-bound states.
Guerra, A. J.., & GIEDROC, D. P. (2012) Biomol. NMR Assign., published online Nov 9, 2012 View: PubMed

Backbone resonance assignments of the homotetrameric (48 kD) copper sensor CsoR from Geobacillus thermodenitrificans in the apo- and Cu(I)-bound states: insights into copper-mediated allostery.
Coyne, H. J., 3rd., & GIEDROC, D. P. (2012) Biomol. NMR Assign., published online Sept 22, 2012 View: PubMed

Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery.
Lee CW, Chakravorty DK, Chang FM, Reyes-Caballero H, Ye Y, Merz KM Jr, Giedroc DP.
Biochemistry. 2012 Mar 27;51(12):2619-29. Epub 2012 Mar 14. PubMed

Functional transcriptional regulatory sequence (TRS) RNA binding and helix destabilizing determinants of murine hepatitis virus (MHV) nucleocapsid (N) protein.
Keane SC, Liu P, Leibowitz JL, Giedroc DP.
J Biol Chem. 2012 Mar 2;287(10):7063-73. Epub 2012 Jan 12. PubMed

The transiently ordered regions in intrinsically disordered ExsE are correlated with structural elements involved in chaperone binding.
Zheng Z, Ma D, Yahr TL, Chen L.
Biochem Biophys Res Commun. 2012 Jan 6;417(1):129-34. Epub 2011 Nov 25. PubMed


Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state.
Guerra AJ, Dann CE 3rd, Giedroc DP.
J Am Chem Soc. 2011 Dec 14;133(49):19614-7. Epub 2011 Nov 21. Epub 2011 Nov 21. PubMed

Mycobacterium tuberculosis NmtR harbors a nickel sensing site with parallels to Escherichia coli RcnR.
Reyes-Caballero H, Lee CW, Giedroc DP.
Biochemistry. 2011 Sep 20;50(37):7941-52. Epub 2011 Aug 26. PubMed

The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold.
Lee CW, Li L, Giedroc DP.
FEBS Lett. 2011 Apr 6;585(7):1049-53. Epub 2011 Mar 4. PubMed


A Q63E Rhodobacter sphaeroides AppA BLUF domain mutant is locked in a
pseudo-light-excited signaling state.

Dragnea V, Arunkumar AI, Lee CW, Giedroc DP, Bauer CE.
Biochemistry. 2010 Dec 21;49(50):10682-90. Epub 2010 Nov 24. PubMed

The metalloregulatory zinc site in Streptococcus pneumoniae AdcR, a zinc-activated MarR family repressor.
Reyes-Caballero H, Guerra AJ, Jacobsen FE, Kazmierczak KM, Cowart D, Koppolu
UM, Scott RA, Winkler ME, Giedroc DP.
J Mol Biol. 2010 Oct 22;403(2):197-216. Epub 2010 Sep 8. PubMed


Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound

Arunkumar AI, Campanello GC, Giedroc DP.
Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18177-82. Epub 2009 Oct 12. PubMed

Spectroscopic studies of the AppA BLUF domain from Rhodobacter sphaeroides: addressing movement of tryptophan 104 in the signaling state.
Dragnea V, Arunkumar AI, Yuan H, Giedroc DP, Bauer CE.
Biochemistry. 2009 Oct 27;48(42):9969-79. PubMed

GroEL Recognizes an Amphipathic Helix and Binds to the Hydrophobic Side.
Li Y, Gao X, Chen L.
J Biol Chem. 2009 Feb 13;284(7):4324-31. Epub 2008 Dec 12. PubMed

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