KALODIMOS GROUP HOME PAGE
Structural & Mechanistic Biology -
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Publications

T. Saleh & C.G. Kalodimos (2017) "Enzymes at work are enzymes in motion" Science, in press.

C. Huang, P. Rossi, T. Saio & C.G. Kalodimos (2016) "Structural basis for the antifolding activity of a molecular chaperone" Nature, 537, 202-206.

N. Khanra, P. Rossi, A. Economou & C.G. Kalodimos (2016) "Recognition and targeting mechanisms by chaperones in flagellum assembly and operation" Proceedings of the National Academy of Sciences USA, 113, 9798-9803.

T. Saleh, W. Jankowski, G. Sriram, P. Rossi,S. Shah, K.B. Lee, L.A. Cruz, A.J. Rodriguez, R.B. Birge & C.G. Kalodimos (2016) "Cyclophilin A promotes cell migration via the Abl-Crk signaling pathway" Nature Chemical Biology, 12, 117-123.

Y. Monneau, Y. Ishida, P. Rossi, T. Saio, S.R Tzeng, M. Inouye & C.G. Kalodimos (2016) “Exploiting E. coli auxotrophs for leucine, valine, and threonine specific methyl labeling of large proteins for NMR applications” Journal of Biomolecular NMR, 65, 99-108.

T. Xie & C.G. Kalodimos (2015) "NMR illuminates the pathways to ALS" Elife, 4, e08679.

G. Sriram, W. Jankowski, C. Kasikara, C. Reichman, T. Saleh, K. Nguyen, J. Li, P. Hornbeck, K. Machida, T. Liu, H. Li, C.G. Kalodimos, R.B. Birge (2015) "Iterative tyrosine phosphorylation controls non-canonical domain utilization in Crk" Oncogene, 34, 4260-4269.

T. Saio, X. Guan, P. Rossi, A. Economou & C.G. Kalodimos (2014) "Structural basis for protein anti-aggregation activity of the Trigger Factor chaperone" Science, 344, 1250494.

H-S. Tzeng & C.G. Kalodimos (2013) "Allosteric inhibition through suppression of transient conformational states" Nature Chemical Biology, 9, 462-465.

C.E. Tinberg, S.D. Khare, J. Dou , L. Doyle , J.W. Nelson, W. Jankowski, C.G. Kalodimos, K. Johnsson, B.L. Stoddard & D. Baker (2013) "Computational design of ligand-binding proteins with high affinity and selectivity" Nature, 501, 212-216.

L. Chen, X. Ai, A. Portaliou, D. Remeta, C. Menetti, A. Economou & C.G. Kalodimos (2013) "Substrate-activated conformational switch on chaperones encodes a targeting signal in type III secretion" Cell Reports, 3, 709-715.

T. Saio & C.G. Kalodimos (2013) "NMR disentangles a dynamic disaggregase machinery" Nature Structural & Molecular Biology, 20, 409-410.

H-S. Tzeng & C.G. Kalodimos (2012) "Protein activity regulation by conformational entropy" Nature, 488, 236-240.

W. Jankowski,T. Saleh, M.-T. Pai, S. Ganapathy, R. B. Birge & C.G. Kalodimos (2012) "Domain organization differences explain Bcr-Abl's preference for CrkL over CrkII" Nature Chemical Biology, 8, 590-596.

C.G. Kalodimos (2012) "Protein function and allostery: a dynamic relationship" Annals of New York Academy of Sciences, 1260, 81-86.

H-S.Tzeng, M.T. Pai & C.G. Kalodimos (2012) "NMR studies of large protein systems" Methods Molecular Biology, 831,133-40

L. Chen, V. Balabanidou, D. Remeta, C. Menetti, A. Economou & C.G. Kalodimos (2011) "Structural instability tuning as a regulatory mechanism in protein-protein interactions" Molecular Cell, 44, 734-744.

P. Sarkar, T. Saleh, H-S. Tzeng, R.B. Birge & C.G. Kalodimos (2011) "Structural basis for regulation of the Crk signaling protein by a proline switch" Nature Chemical Biology, 7, 51-57.

H-S. Tzeng & C.G. Kalodimos (2011) “Protein dynamics and allostery: an NMR view” Current Opinion in Structural Biology, 21, 62-67.

C.G. Kalodimos (2011) “NMR reveals novel mechanisms of protein activity regulation” Protein Science, 20, 73-82.

M.T. Pai & C. G. Kalodimos (2011) "Dynamic fluctuations lubricate the circadian clock" Proceedings of the National Academy of Sciences of USA, 108, 14377-14378.

G. Sriram, C. Reichman, A. Tunceroglu, N. Causal, T. Saleh, K. Machida, B. Mayer, Q. Ge, J. Li, P. Hornbeck, C.G. Kalodimos & R.B. Birge (2011) “Phosphorylation of Crk on tyrosine 251 in the RT loop of the SH3C domain promotes Abl kinase transactivation” Oncogene, 30, 4645-4655.

H-S. Tzeng & C.G. Kalodimos (2009) "Dynamic activation of an allosteric regulatory protein" Nature, 462, 368-372.

G. Gouridis, S. Karamanou, I. Gelis, C.G. Kalodimos & A. Economou (2009) "Signal peptides are allosteric activators of the protein translocase" Nature, 462, 363-367.

N. Popovych, H-S. Tseng, M. Tonelli, R.H. Ebright & C.G. Kalodimos (2009) "Structural basis for cAMP-mediated allosteric transition in the catabolite activator protein" Proceedings of the National Academy of Sciences USA, 106, 6927-6932.

R.B. Birge, C.G. Kalodimos, F. Inagaki, S. Tanaka (2009) "Crk and CrkL adaptor proteins: networks for physiological and pathological signaling" Cell Communication Signaling, 7, 13.

S. Karamanou, A. Bariami, E. Papanikou, C.G. Kalodimos, A. Economou (2008) "Assembly of the translocase motor onto the preprotein-conducting channel" Molecular Microbiology, 70, 311-322.

I. Gelis, A. Bonvin, D. Keramisanou, S. Karamanou, A. Economou & C.G. Kalodimos (2007) "Structural basis for signal sequence recognition by the 204-kDa SecA motor ATPase" Cell, 131, 756-769.

P. Sarkar, C. Reichman, T. Saleh, R.B. Birge & C.G. Kalodimos (2007) "Proline cis-trans isomerization controls autoinhibition of a signaling molecule" Molecular Cell, 25, 413-426.

S. Karamanou, G. Gouridis, E. Papanikou, G. Sianidis, I. Gelis, D. Keramisanou, E. Vrontou, C.G. Kalodimos, A. Economou (2007) "Preprotein-controlled catalysis in the helicase motor of SecA" The EMBO Journal, 26, 2904-2914.

N. Popovych, S. Sun, R.H. Ebright & C.G. Kalodimos (2006) "Dynamically driven protein allostery" Nature Structural & Molecular Biology, 13, 831-838.

D. Keramisanou, N. Biris, I. Gelis, S. Karamanou, G. Sianidis, A. Economou & C.G. Kalodimos (2006) "Disorder-order folding transitions underlie catalysis in the helicase motor of SecA" Nature Structural & Molecular Biology, 13, 594-602.

E. Papanikou, S. Karamanou, C. Baud, M. Frank, G. Sianidis, D. Keramisanou, C.G. Kalodimos, A. Kuhn, A. Economou (2005) "Identification of the preprotein binding domain of SecA" Journal of Biological Chemistry, 280, 43209-43217.

C. G. Kalodimos, N. Biris, A.M.J.J. Bonvin, M.M. Levandoski, M. Guennuegues, R. Boelens & R. Kaptein (2004) "Structure and flexibility adaptation between nonspecific and specific protein-DNA complexes" Science, 305, 386-389.

C. G. Kalodimos, R. Boelens & R. Kaptein (2004) "Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the Lac repressor system" Chemical Reviews, 104, 3567-3586.

M.A Durney, R.W. Wechselberger, C.G. Kalodimos, R. Kaptein,C.E. Vorgias, R. Boelens (2004) "An alternate conformation of the hyperthermostable HU protein from Thermotoga maritima has unexpectedly high flexibility" FEBS Letters, 563, 49-54.

C. G. Kalodimos, A.M.J.J. Bonvin, R. K. Salinas, R. Weschelberger, R. Boelens & R. Kaptein (2002) "Plasticity in Protein-DNA recognition: lac Repressor Recognizes its Natural Operator with Alternative Conformations of its DNA-Binding Domain" The EMBO Journal, 21, 2866-2876.

C. G. Kalodimos, R. Boelens & R. Kaptein (2002) "A Residue-Specific View of the Association and Dissociation Pathway in Protein-DNA Recognition" Nature Structural Biology, 9, 193-197.

C. G. Kalodimos, G. Folkers, R. Boelens & R. Kaptein (2001) "Strong DNA Binding by Covalently-Linked Lac Headpiece: The Crucial Role of Hinge Helices" Proceedings of the National Academy of Sciences of USA, 98, 6039-6044.

C. G. Kalodimos, I. P. Gerothanassis & R. Pierattelli (2000) "Multinuclear (13C, 17O, 57Fe) NMR Studies of Carbonmonoxy Heme Proteins and Synthetic Model Compounds " Journal of Inorganic Biochemistry, 79, 371-380.

C. G. Kalodimos, I. P. Gerothanassis, E. Rose, G. E. Hawkes & R. Pierattelli (1999) "Iron-57 Nuclear Shieldings as a Quantitative Tool for Estimating Porphyrin Ruffling in Hexacoordinated Carbonmonoxy Heme Model Compounds in Solution" Journal of the American Chemical Society, 121, 2903-2908.

C. G. Kalodimos, I. P. Gerothanassis, R. Pierattelli and B. Ancian (1999) "Carbon-13 and Oxygen-17 Chemical Shifts, (16O/18O) Isotope Effects on 13C Chemical Shifts, and Vibrational Frequencies of Carbon Monoxide in Various solvents and of the Fe-C-O Unit in Carbonmonoxy Heme Proteins and Synthetic Model Compounds" Inorganic Chemistry, 38, 4283-4293.

C. G. Kalodimos & I. P. Gerothanassis (1998) "Carbon-13 Nuclear Shieldings as a Novel Method in Estimating Porphyrin Ruffling in Superstructured Heme Model Compounds in Solution" Journal of the American Chemical Society, 120, 6407-6408.

C. G. Kalodimos, I. P. Gerothanassis & G. E. Hawkes (1998) "13C and 57Fe NMR Studies of the Fe-C-O Unit of Heme Proteins and Synthetic Model Compounds in Solution. Comparison With IR Vibrational Frequencies and X-ray Structural Data" Biospectroscopy, 4, S57-S69.

C. G. Kalodimos, I. P. Gerothanassis, G. E. Hawkes & P. Haycock (1998) "The Effects of Atropisomerism and Porphyrin Deformation on 57Fe Shieldings in Superstructured Hemoprotein Models" Journal of Magnetic Resonance, 131, 163-165.

C. G. Kalodimos, I. P. Gerothanassis, A. Troganis, B. Loock & M. Momenteau (1998) "13C Shieldings, 18O Isotope Effects on 13C Shieldings, and 57Fe-13C Spin Couplings of the Fe-C-O Unit in Superstructured Hemoprotein Models: Comparison with Hemoproteins, C-O Vibrational Frequencies, and X-ray Structural Data" Journal of Biomolecular NMR, 11, 423-435.

I. P. Gerothanassis, M. Momenteau, P. J. Barrie, C. G. Kalodimos & G. E. Hawkes (1996) "13C CP/MAS NMR Studies of Hemoprotein Models with and without Axial Hindered Base: 13C Shielding Tensors and Comparison with Hemoproteins and X-Ray Structural Data" Inorganic Chemistry, 35, 2674-2679.

I. P. Gerothanassis & C. G. Kalodimos (1996) "NMR Shielding and the Periodic Table" Journal of Chemical Education,73, 801-804

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