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Quick Link: | Text Books | Transition State Regulators | Response Regulators | Calicum Binding Proteins

| Competence | Protein Dynamics | NMR Methods | Mass Spectrometry Methods | Miscellaneous

Title	Author	Year	Options
Text Books
Protein NMR Spectroscopy: Principles & Practice (Second Edition)	J. Cavanagh, W.J. Fairbrother, A.G. Palmer III, Mark Rance & N.J. Skelton Academic Press Inc., San Diego	2006
Protein NMR Spectroscopy: Principles & Practice (First Edition)	J. Cavanagh, W.J. Fairbrother, A.G. Palmer III & N.J. Skelton Academic Press Inc., San Diego	1996
Transition State Regulators - DNA Binding Proteins
Title	Author	Year	Options
Tandem mass spectrometry acquisition approaches to enhance identifcation of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents. Rapid Communications in Mass Spec. (2007) 21: 3395-3408	Soderblom E.J., Bobay B.G., Cavanagh J., Goshe M.B.	2007
Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. Journal of Bacteriology (2007)	Strauch MA, Bobay BG, Cavanagh J, Yao F, Wilson A, Breton YL.	2007
NMR Structure of AbhN and Comparison with AbrBN: First Insights into to DNA Binding Promiscuity and Specficity of AbrB-like Transition State Regulator Proteins. JBC (2006) 281, 30: 21399-21409	Bobay BG, Mueller GA, Thompson RJ, Murzin AG, Venters RA, Strauch MA, & and Cavanagh J	2006
Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. FEBS Letters (2005) 579, 25: 5669-5674	Bobay BG, Andreeva A, Mueller GA, Cavanagh J, & Murzin AG.	2005
Evaluation of the DNA binding tendencies of the transition state regulator AbrB. Biochemistry (2004) 43, 51: 16106-16118	Bobay BG, Benson L, Naylor S, Feeney B, Clark AC, Goshe MB, Strauch MA, Thompson R, & Cavanagh J.	2004
Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry. Anal Biochem (2002) 306, 2: 222-7	Benson LM, Vaughn JL, Strauch MA, Bobay BG, Thompson R, Naylor S, & Cavanagh J.	2002
Stoichiometries of protein-protein/DNA binding and conformational changes for the transition-state regulator AbrB measured by pseudo cell-size exclusion chromatography-mass spectrometry. Biochemistry (2002) 41, 25: 7859-65	Cavanagh J, Thompson R, Bobay B, Benson LM, & Naylor S.	2002
The DNA-binding domain in the Bacillus subtilis transition-state regulator AbrB employs significant motion for promiscuous DNA recognition. J Mol Biol (2001) 305, 3: 429-39	Vaughn JL, Feher VA, Bracken C, & Cavanagh J.	2001
Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB. Nat Struct Biol (2000) 7, 12: 1139-46	Vaughn JL, Feher V, Naylor S, Strauch MA, & Cavanagh J.	2000
Response Regulators
Title	Author	Year	Options
Classification of Response Regulators based on their surface properities. Methods in Enzymology (2007) 422, : 141-169	Kojetin DJ, Sullivan DM, Thompson RT, & Cavanagh J.	2007
Predominatly buried residues in the response regulator Spo0F influence specific sensor kinase recognition. FEBS Letters (2007) 581, : 1425-1429	McLaughlin PD, Bobay BG, Regel EJ, Thompson RJ, Hoch JA, & Cavanagh J.	2007
Measurement of multisite oxidation kinetics reveals an active site conformational change in Spo0F as a result of protein oxidation. Biochemistry (2006) 45, 20: 6260-6	Sharp JS, Sullivan DM, Cavanagh J, & Tomer KB.	2006
Structural analysis of divalent metals binding to the Bacillus subtilis response regulator Spo0F: the possibility for in vitro metalloregulation in the initiation of sporulation. Biometals (2005) 18, 5: 449-66	Kojetin DJ, Thompson RJ, Benson LM, Naylor S, Waterman J, Davies KG, Opperman CH, Stephenson K, Hoch JA, & Cavanagh J.	2005
Solution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing. J Mol Biol (2005) 347, 2: 297-307	Ulrich DL, Kojetin D, Bassler BL, Cavanagh J, & Loria JP.	2005
¹H, ¹⁵N, and ¹³C chemical shift assignments of the Vibrio harveyi histidine phosphotransferase protein LuxU. J Biomol NMR (2004) 29, 4: 551-552	Ulrich DL, Thompson R, Bassler B, Cavanagh J, & Loria JP.	2004
Sub-classification of response regulators using the surface characteristics of their receiver domains. FEBS Lett (2003) 554, 3: 231-236	Kojetin DJ, Thompson RJ, & Cavanagh J.	2003
Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F. Nature (1999) 400, 6741: 289-93	Feher VA & Cavanagh J.	1999
Characterization of interactions between a two-component response regulator, Spo0F, and its phosphatase, RapB. Biochemistry (1998) 37, 47: 16538-45	Tzeng YL, Feher VA, Cavanagh J, Perego M, & Hoch JA.	1998
Identification of communication networks in Spo0F: a model for phosphorylation-induced conformational change and implications for activation of multiple domain bacterial response regulators. FEBS Lett (1998) 425, 1: 1-6	Feher VA, Tzeng YL, Hoch JA, & Cavanagh J.	1998
High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition. Biochemistry (1997) 36, 33: 10015-25	Feher VA, Zapf JW, Hoch JA, Whiteley JM, McIntosh LP, Rance M, Skelton NJ, Dahlquist FW, & Cavanagh J.	1997
¹H, ¹⁵N, and ¹³C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR. Protein Sci (1995) 4, 9: 1801-14	Feher VA, Zapf JW, Hoch JA, Dahlquist FW, Whiteley JM, & Cavanagh J.	1995
Functional implications of the structure of the bacterial response regulator Spo0F. J Cell Biochem (1995) , : 25-25	Feher VA, Zapf J, Hoch JA, Whiteley JM, Cavanagh J, & Dahlquist FW.	1995
Altered Folding of a Bacillus subtilis Protein Initiated by Genetic Deletion of an N-terminal Methionine. Faseb J (1995) 9, 6: A1243-A1243	Zapf JW, Feher VA, Djavakhishvili T, Cavanagh J, Dahlquist FW, Hoch JA, & Whiteley JM.	1995
Aspartyl phosphates in the regulatory control of bacterial response. Amino Acids (1994) 6, 2: 131-140	Cavanagh J, Zapf J, Hoch JA, Feher V, Dahlquist FW, & Whiteley JM.	1994
NMR structural investigations of Spo0F - a regulatory protein from Bacillus subtilis. Faseb J (1993) 7, 7: A1238-A1238	Cavanagh J, Feher V, Zapf J, Hoch JA, & Whiteley JM.	1993
Calicum Binding Proteins
Title	Author	Year	Options
Peptide binding proclivities of calcium loaded calbindin-D28k. FEBS Letters (2007) 581, : 4778-4782	Kordys DR, Bobay BG, Thompson RJ, Venters RA, Cavanagh J.	2007
Structure, binding interface and hydrophobic transitions of Ca²⁺-loaded calbindin-D28K. NSMB (2006) 13, : 641-647	Kojetin DJ, Venters RA, Kordys DR, Thompson RJ, & Kumar R & Cavanagh J.	2006
Calbindin D28K interacts with Ran-binding protein M: identification of interacting domains by NMR spectroscopy. Biochem Biophys Res Commun (2003) 303, 4: 1186-92	Lutz W, Frank EM, Craig TA, Thompson R, Venters RA, Kojetin D, Cavanagh J, & Kumar R.	2003
The effects of Ca²⁺ binding on the conformation of calbindin D28K: A nuclear magnetic resonance and microelectrospray mass spectrometry study. Anal Biochem (2003) 317, 1: 59-66	Venters RA, Benson LM, Craig TA, Paul KH, Kordys DR, Thompson R, Naylor S, Kumar R, & Cavanagh J.	2003
Competence
Title	Author	Year	Options
NMR assignment of the N-terminal repeat domain of Bacillus subtilis ClpC J Bio NMR (2007)	Kojetin D.J., McLaughlin P.D., Thompson R.J., Venters R.A, Rance M., Cavanagh J.	2007
Protein Dynamics
Title	Author	Year	Options
Solution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing. J Mol Biol (2005) 347, 2: 297-307	Ulrich DL, Kojetin D, Bassler BL, Cavanagh J, & Loria JP.	2005
Protein dynamic studies move to a new time slot. Nat Struct Biol (2001) 8, 11: 912-4	Cavanagh J & Venters RA.	2001
The DNA-binding domain in the Bacillus subtilis transition-state regulator AbrB employs significant motion for promiscuous DNA recognition. J Mol Biol (2001) 305, 3: 429-39	Vaughn JL, Feher VA, Bracken C, & Cavanagh J.	2001
May the driving force be with you - whatever it is. Nat Struct Biol (2000) 7, 1: 11-3	Cavanagh J & Akke M.	2000
Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F. Nature (1999) 400, 6741: 289-93	Feher VA & Cavanagh J.	1999
Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA. J Mol Biol (1999) 285, 5: 2133-46	Bracken C, Carr PA, Cavanagh J, & Palmer AG III.	1999
Identification of communication networks in Spo0F: a model for phosphorylation-induced conformational change and implications for activation of multiple domain bacterial response regulators. FEBS Lett (1998) 425, 1: 1-6	Feher VA, Tzeng YL, Hoch JA, & Cavanagh J.	1998
Pervasive conformational fluctuations on microsecond time scales in a fibronectin type III domain. Nat Struct Biol (1998) 5, 1: 55-9	Akke M, Liu J, Cavanagh J, Erickson HP, & Palmer AG III.	1998
High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition. Biochemistry (1997) 36, 33: 10015-25	Feher VA, Zapf JW, Hoch JA, Whiteley JM, McIntosh LP, Rance M, Skelton NJ, Dahlquist FW, & Cavanagh J.	1997
NMR Methods
Title	Author	Year	Options
(4,2)D Projection--reconstruction experiments for protein backbone assignment: application to human carbonic anhydrase II and calbindin D(28K). J Am Chem Soc (2005) 127, 24: 8785-95	Venters RA, Coggins BE, Kojetin D, Cavanagh J, & Zhou P.	2005
Current approaches for the study of large proteins by NMR. J Mol Struct (2002) 602-603, : 275-292	Venters RA, Thompson R, & Cavanagh J.	2002
Two-dimensional relayed-rotating-frame overhauser spectroscopy ¹H NMR experiments for the selective identification of 1,2-glycosidic linkages in polysaccharides. Anal Biochem (2000) 278, 1: 52-8	Cipollo JF, Trimble RB, Rance M, & Cavanagh J.	2000
CO_H(N)CACB experiments for assigning backbone resonances in ¹³C/¹⁵N-labeled proteins. J Biomol NMR (1998) 11, 4: 451-6	Astrof N, Bracken C, Cavanagh J, & Palmer AG III.	1998
(H)N(COCA)NH and HN(COCA)NH experiments for ¹H-¹⁵N backbone assignments in ¹³C/¹⁵N-labeled proteins. J Biomol NMR (1997) 9, 1: 94-100	Bracken C, Palmer AG III , & Cavanagh J.	1997
Sensitivity enhanced NMR Techniques for the study of biomolecules. Ann. Rep. NMR (1993) 27, : 1	Cavanagh J & Rance M.	1993
Practical aspects of recording multidimensional NMR spectra in water with flat baselines. J Magn Reson Ser A (1993) 103, 3: 338-348	Waltho JP & Cavanagh J.	1993
Suppression of cross-relaxation effects in TOCSY spectra via a modified dipsi-2 mixing sequence. J Magn Reson (1992) 96, 3: 670-678	Cavanagh J & Rance M.	1992
Sensitivity improvement in 3-dimensional heteronuclear correlation NMR spectroscopy. J Magn Reson (1992) 96, 2: 416-424	Palmer AG, Cavanagh J, Byrd RA, & Rance M.	1992
Improved resolution in three-dimensional constant-time triple resonance NMR spectroscopy of proteins. J Biomol NMR (1992) 2, 1: 103-8	Palmer AG III , Fairbrother WJ, Cavanagh J, Wright PE, & Rance M.	1992
Sensitivity improvement in proton-detected 2-dimensional heteronuclear correlation NMR spectroscopy. J Magn Reson (1991) 93, 1: 151-170	Palmer AG, Cavanagh J, Wright PE, & Rance M.	1991
Sensitivity improvement in proton-detected 2-dimensional heteronuclear relay spectroscopy. J Magn Reson (1991) 91, 2: 429-436	Cavanagh J, Palmer AG, Wright PE, & Rance M.	1991
Uniform labeling of a recombinant antibody Fv-fragment with ¹⁵N and ¹³C for heteronuclear NMR spectroscopy. FEBS Lett (1991) 287, 1-2: 185-8	Riechmann L, Cavanagh J, & McManus S.	1991
Sensitivity improvement in isotropic mixing (TOCSY) experiments. J Magn Reson (1990) 88, 1: 72-85	Cavanagh J & Rance M.	1990
RF phase coherence in rotating-frame NMR experiments in isotropic solutions. J Magn Reson (1990) 87, 2: 363-371	Rance M & Cavanagh J.	1990
A combined 2-dimensional relayed-NOESY TOCSY experiment. J Magn Reson (1990) 87, 2: 408-414	Cavanagh J & Rance M.	1990
The time-dependence of coherence transfer in homonuclear isotropic mixing experiments. J Magn Reson (1990) 87, 1: 110-131	Cavanagh J, Chazin WJ, & Rance M.	1990
Suppression of uninformative peaks in two-dimensional relayed-NOESY spectra. J Magn Reson (1988) 26, 12: 1093-1096	Cavanagh J, Titman JJ, & Keeler J.	1988
Aspects of molecular recognition - Use of a truncated driven pseudo-NOESY experiment to elucidate the environment of intermolecular electrostatic interactions in vancomycin. J Chem Soc Commun (1988) , 11: 707-709	Waltho JP, Cavanagh J, & Williams DH.	1988
Suppression of HOHAHA and false NOE cross peaks in camelspin spectra. J Magn Reson (1988) 80, 1: 186-194	Cavanagh J & Keeler J.	1988
Practicalities and applications of reverse heteronuclear shift correlation - porphyrin and polysaccharide examples. J Magn Reson (1988) 26, 10: 867-875	Cavanagh J, Hunter CA, Jones DNM, Keeler J, & Sanders JKM	1988
Multiplet effects in two-dimensional double-quantum-filtered zero-quantum spectroscopy. J Magn Reson (1988) 77, 3: 612-617	Cavanagh J & Keeler J.	1988
Improvement of C-13 satellite spectra by double difference spectroscopy. J Magn Reson (1988) 77, 2: 356-362	Cavanagh J & Keeler J.	1988
Semi-selective two-dimensional NMR experiments. J Magn Reson (1987) 74, 2: 386-393	Cavanagh J, Waltho JP, & Keeler J.	1987
Complete suppression of diagonal peaks in COSY spectra. J Magn Reson (1987) 71, 3: 561-567	Cavanagh J & Keeler J.	1987
Mass spectrometry Methods
Title	Author	Year	Options
Tandem mass spectrometry acquisition approaches to enhance identifcation of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents. Rapid Commun Mass Spectrom (2007) 21: 3395-3408	Soderblom E.J., Bobay B.G., Cavanagh J., Goshe M.B.	2007
Protein-metal ion interactions, stoichiometries and relative affinities determined by on-line size exclusion gel filtration mass spectrometry. Rapid Commun Mass Spectrom (2003) 17, 4: 267-71	Benson LM, Kumar R, Cavanagh J, & Naylor S.	2003
In-line Desalting mass spectrometry for the study of noncovalent biological complexes. Anal Chem (2003) 75, 14: 3281-3286	Cavanagh J, Benson LM, Thompson R, & Naylor S.	2003
Miscellaneous
Title	Author	Year	Options
Inhibition and dispersion of proteobacterial biofilms. Chem Commun. (2008) 1698-1700	Justin J. Richards, Robert W. Huigens III, T. Eric Ballard, Anne Basso, John Cavanagh and Christian Melander	2008
Targeting RNA with cysteine-constrained peptides. Bioorg Med Chem Lett. (2007)	Virginia A. Burns, Benjamin G. Bobay, Anne Basso, John Cavanagh, Christian Melander	2007
Structural and catalytic response to temperature and cosolvents of carboxylesterase EST1 from the extremely thermoacidophilic archaeon Sulfolobus solfataricus P1. Biotechnol Bioeng (2002) 80, 7: 784-93	Sehgal AC, Tompson R, Cavanagh J, & Kelly RM.	2002
Alternative splicing of a β subunit proline-rich motif regulates voltage-dependent gating and toxin block of Ca_v2.1 Ca²⁺ channels. J Neurosci (2002) 22, 21: 9331-9	Helton TD, Kojetin DJ, Cavanagh J, & Horne WA.	2002
Autologous biological response modification of the gonadotropin receptor. J Biol Chem (2001) 276, 15: 12410-9	Mahale SD, Cavanagh J, Schmidt A, MacColl R, & Dias JA.	2001
Novel Schizosaccharomyces pombe N-linked GalMan₉GlcNAc isomers: role of the Golgi GMA12 galactosyltransferase in core glycan galactosylation. Glycobiology (1999) 9, 5: 497-505	Ziegler FD, Cavanagh J, Lubowski C, & Trimble RB.	1999
Nuclear magnetic resonance ¹⁵N and ¹H resonance assignments and global fold of rusticyanin. Insights into the ligation and acid stability of the blue copper site. J Mol Biol (1994) 244, 4: 370-84	Hunt AH, Toy-Palmer A, Assa-Munt N, Cavanagh J, Blake RC 2nd , & Dyson HJ.	1994
¹H, ¹⁵N and ¹³C resonance assignments for the first three zinc fingers of transcription factor IIIA. J Biomol NMR (1994) 4, 3: 433-54	Liao X, Clemens K, Cavanagh J, Tennant L, & Wright PE.	1994
¹H, ¹⁵N and ¹³C resonance assignments, secondary structure, and the conformation of substrate in the binary folate complex of Escherichia coli dihydrofolate reductase. J Biomol NMR (1994) 4, 3: 349-66	Falzone CJ, Cavanagh J, Cowart M, Palmer AG 3rd , Matthews CR, Benkovic SJ, & Wright PE.	1994
Solution structure of the Bacillus subtilis glucose permease Iia domain and its interaction with another phosphocarrier protein Hpr. J Cell Biochem (1993) , : 271-271	Yuan C, Fairbrother WJ, Gippert GP, Case DA, Cavanagh J, Reizer J, Saier MH, & Wright PE.	1993
Improving the antigen affinity of an antibody Fv-fragment by protein design. J Mol Biol (1992) 224, 4: 913-8	Riechmann L, Weill M, & Cavanagh J.	1992
Polypeptide backbone resonance assignments and secondary structure of Bacillus subtilis enzyme IIIglc determined by two-dimensional and three-dimensional heteronuclear NMR spectroscopy. Biochemistry (1991) 30, 28: 6896-907	Fairbrother WJ, Cavanagh J, Dyson HJ, Palmer AG III , Sutrina SL, Reizer J, Saier MH Jr, & Wright PE.	1991