@article{kojetin_mclaughlin_thompson_venters_rance_cavanagh_2007, title={NMR assignment of the N-terminal repeat domain of Bacillus subtilis ClpC}, volume={1}, ISSN={["1874-2718"]}, DOI={10.1007/s12104-007-9046-8}, abstractNote={The HSP100/AAA+ superfamily protein ClpC is a key regulator of cell development in Bacillus subtilis. We present here the backbone and side-chain assignments of the N-terminal repeat domain (residues 1-145) of ClpC from Bacillus subtilis.}, number={2}, journal={BIOMOLECULAR NMR ASSIGNMENTS}, author={Kojetin, Douglas J. and McLaughlin, Patrick D. and Thompson, Richele J. and Venters, Ronald A. and Rance, Mark and Cavanagh, John}, year={2007}, month={Dec}, pages={163–165} }
 @article{kojetin_venters_kordys_thompson_kumar_cavanagh_2006, title={Structure, binding interface and hydrophobic transitions of Ca2+-loaded calbindin-D-28K}, volume={13}, DOI={10.1038/nsmb1112d}, number={7}, journal={Nature Structural & Molecular Biology}, author={Kojetin, D. J. and Venters, R. A. and Kordys, D. R. and Thompson, R. J. and Kumar, R. and Cavanagh, J.}, year={2006}, pages={641–647} }
 @article{venters_coggins_kojetin_cavanagh_zhou_2005, title={(4,2)D projection-reconstruction experiments for protein backbone assignment: Application to human carbonic anhydrase II and calbindin D-28K}, volume={127}, ISSN={["0002-7863"]}, DOI={10.1021/ja0509580}, abstractNote={Projection-reconstruction NMR experiments have been shown to significantly reduce the acquisition time required to obtain protein backbone assignment data. To date, this concept has only been applied to smaller (15)N/(13)C-labeled proteins. Here, we show that projection-reconstruction NMR techniques can be extended to larger protonated and perdeuterated proteins. We present a suite of (4,2)D triple-resonance experiments for protein backbone assignment and a Hybrid Backprojection/Lower-Value algorithm for reconstructing data with relatively weak signal-to-noise ratios. In addition, we propose a sampling theorem and discuss its implication on the choice of projection angles. We demonstrate the efficacy of this approach using the 29 kDa protein, human carbonic anhydrase II and the 30 kDa protein, calbindin D(28K).}, number={24}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Venters, RA and Coggins, BE and Kojetin, D and Cavanagh, J and Zhou, P}, year={2005}, month={Jun}, pages={8785–8795} }
 @article{ulrich_kojetin_bassler_cavanagh_loria_2005, title={Solution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing}, volume={347}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2005.01.039}, abstractNote={The marine bacterium Vibrio harveyi controls its bioluminescence by a process known as quorum sensing. In this process, autoinducer molecules are detected by membrane-bound sensor kinase/response regulator proteins (LuxN and LuxQ) that relay a signal via a series of protein phosphorylation reactions to another response regulator protein, LuxO. Phosphorylated LuxO indirectly represses the expression of the proteins responsible for bioluminescence. Integral to this quorum sensing process is the function of the phosphotransferase protein, LuxU. LuxU acts to shuttle the phosphate from the membrane-bound proteins, LuxN and LuxQ, to LuxO. LuxU is a 114 amino acid residue monomeric protein. Solution NMR was used to determine the three-dimensional structure of LuxU. LuxU contains a four-helix bundle topology with the active-site histidine residue (His58) located on α-helix C and exposed to solution. The active site represents a cluster of positively charged residues located on an otherwise hydrophobic protein face. NMR spin-relaxation experiments identify a collection of flexible residues localized on the same region of LuxU as His58. The studies described here represent the first structural characterization of an isolated, monomeric bacterial phosphotransferase protein.}, number={2}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Ulrich, DL and Kojetin, D and Bassler, BL and Cavanagh, J and Loria, JP}, year={2005}, month={Mar}, pages={297–307} }
 @article{kojetin_thompson_benson_naylor_waterman_davies_opperman_stephenson_hoch_cavanagh_2005, title={Structural analysis of divalent metals binding to the Bacillus subtilis response regulator Spo0F: the possibility for In vitro metalloregulation in the initiation of sporulation}, volume={18}, ISSN={["1572-8773"]}, DOI={10.1007/s10534-005-4303-8}, abstractNote={The presence of a divalent metal ion in a negatively charged aspartic acid pocket is essential for phosphorylation of response regulator proteins. Here, we present metal binding studies of the Bacillus subtilis response regulator Spo0F using NMR and microESI-MS. NMR studies show that the divalent metals Ca(2+), Mg(2+) and Mn(2+) primarily bind, as expected, in the Asp pocket phosphorylation site. However, identical studies with Cu(2+) show distinct binding effects in three specific locations: (i) the Asp pocket, (ii) a grouping of charged residues at a site opposite of the Asp pocket, and (iii) on the beta 4-alpha 4 loop and the beta 5/alpha 5 interface, particularly around and including H101. microESI-MS studies stoichiometrically confirm the NMR studies and demonstrate that most divalent metal ions bind to Spo0F primarily in a 1:1 ratio. Again, in the case of Cu(2+), multiple metal-bound species are observed. Subsequent experiments reveal that Mg(2+) supports phosphotransfer between KinA and Spo0F, while Cu(2+) fails to support KinA phosphotransfer. Additionally, the presence of Cu(2+) at non-lethal concentrations in sporulation media for B. subtilis and the related organism Pasteuria penetrans was found to inhibit spore formation while continuing to permit vegetative growth. Depending on the type of divalent metal ion present, in vitro phosphorylation of Spo0F by its cognate kinase KinA can be inhibited.}, number={5}, journal={BIOMETALS}, author={Kojetin, DJ and Thompson, RJ and Benson, LM and Naylor, S and Waterman, J and Davies, KG and Opperman, CH and Stephenson, K and Hoch, JA and Cavanagh, J}, year={2005}, month={Oct}, pages={449–466} }
 @article{kojetin_thompson_cavanagh_2004, title={Sub-classification of response regulators using the surface characteristics of their receiver domains (FEBS 27785) (vol 554, pg 231, 2003)}, volume={560}, ISSN={["1873-3468"]}, DOI={10.1016/s0014-5793(04)00063-8}, number={1-3}, journal={FEBS LETTERS}, author={Kojetin, DJ and Thompson, RJ and Cavanagh, J}, year={2004}, month={Feb}, pages={227–228} }
 @article{lutz_frank_craig_thompson_venters_kojetin_cavanagh_kumar_2003, title={Calbindin D-28K interacts with Ran-binding protein M: identification of interacting domains by NMR spectroscopy}, volume={303}, ISSN={["0006-291X"]}, DOI={10.1016/S0006-291X(03)00499-6}, abstractNote={Calbindin D28K is an EF-hand containing protein that plays a vital role in neurological function. We now show that calcium-loaded calbindin D28K interacts with Ran-binding protein M, a protein known to play a role in microtubule function. Using NMR methods, we show that a peptide, LASIKNR, derived from Ran-binding protein M, interacts with several regions of the calcium-loaded protein including the amino terminus and two other regions that exhibit conformational exchange on the NMR timescale. We suggest that the interaction between calbindin D28K and Ran-binding protein M may be important in calbindin D28K function.}, number={4}, journal={BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS}, author={Lutz, W and Frank, EM and Craig, TA and Thompson, R and Venters, RA and Kojetin, D and Cavanagh, J and Kumar, R}, year={2003}, month={Apr}, pages={1186–1192} }
 @article{kojetin_thompson_cavanagh_2003, title={Sub-classification of response regulators using the surface characteristics of their receiver domains}, volume={554}, ISSN={["0014-5793"]}, DOI={10.1016/S0014-5793(03)01167-0}, abstractNote={The omnipresent bacterial switch known as a two‐component system is comprised of a response regulator and a sensor kinase with which it interacts. Sensor kinases have been classified and further sub‐classified into groups based on their sequence similarity, loop lengths and domain organization. Response regulators have been classified predominantly by the identity and function of their output domains. Here, comparative based homology modeling of the receiver domains of the OmpR sub‐family of response regulators in Bacillus subtilis and Escherichia coli suggests further sub‐classification is possible. A color‐coded scale is used to show trends in surface hydrophobicity. For the OmpR receiver domains modeled these trends allow further sub‐classification. The specific surface regions used for this sub‐classification procedure correlate with clusters of residues that are important for interaction with cognate four helix bundle HisKA/Hpt domains.}, number={3}, journal={FEBS LETTERS}, author={Kojetin, DJ and Thompson, RJ and Cavanagh, J}, year={2003}, month={Nov}, pages={231–236} }
 @article{helton_kojetin_cavanagh_horne_2002, title={Alternative splicing of a beta(4) subunit proline-rich motif regulates voltage-dependent gating and toxin block of Ca(v)2.1 Ca2+ channels}, volume={22}, DOI={10.1523/jneurosci.22-21-09331.2002}, abstractNote={Ca2+ channel β subunits modify α1 subunit gating properties through direct interactions with intracellular linker domains. In a previous report (Helton and Horne, 2002), we showed that alternative splicing of the β4 subunit had α1 subunit subtype-specific effects on Ca2+ channel activation and fast inactivation. We extend these findings in the present report to include effects on slow inactivation and block by the peptide toxin ω-conotoxin (CTx)-MVIIC. N-terminal deletion and site-directed mutagenesis experiments revealed that the effects of alternative splicing on toxin block and all aspects of gating could be attributed to a proline-rich motif found within N-terminal β4b amino acids 10–20. Interestingly, this motif is conserved within the third postsynaptic density-95 (PSD-95)/Discs large/zona occludens-1 domain of the distantly related membrane-associated guanylate kinase homolog, PSD-95. Sequence identity of ∼30% made possible the building of β4a and β4bthree-dimensional structural models using PSD-95 as the target sequence. The models (1) reveal that alternative splicing of the β4 N terminus results in dramatic differences in surface charge distribution and (2) localize the proline-rich motif of β4b to an extended arm structure that flanks what would be the equivalent of a highly modified PSD-95 carboxylate binding loop. Northern blot analysis revealed a markedly different pattern of distribution for β4a versus β4bin the human CNS. Whereas β4a is distributed throughout evolutionarily older regions of the CNS, β4b is concentrated heavily in the forebrain. These results raise interesting questions about the functional role that alternative splicing of the β4 subunit has played in the evolution of complex neural networks.}, number={21}, journal={Journal of Neuroscience}, author={Helton, T. D. and Kojetin, D. J. and Cavanagh, J. and Horne, W. A.}, year={2002}, pages={9331–9339} }