Our lab works on two main objectives: first, the determination of the structural and dynamic basis for the function and assembly of large protein machineries; and second, the determination of the role of the internal protein dynamics in regulating protein activity and allosteric interactions. Our goal to tackle large and complex systems is arguably a very challenging one. However, obtaining simultaneously structural and dynamic information on these complex systems while at work will pave the way for ultimately understanding how they function. NMR spectroscopy is best suited for providing such invaluable information; nevertheless, its application has been mostly limited to smaller size proteins. We have recently been able to push the envelope by applying NMR to large and very complex biological systems, with the promise to gain unprecedented knowledge of their sophisticated mechanisms of action.
Molecular chaperones prevent aggregation and misfolding of proteins in the cellular environment and are thus central to maintaining protein homeostasis. However, scarcity of high-resolution structural data has impeded an understanding of the recognition and anti-aggregation mechanisms of molecular chaperones. The scarcity of structural data on complexes between chaperones and unfolded client proteins is primarily due to technical challenges originating in the dynamic nature of these complexes We have recently initiated NMR structural studies aiming to determine the structure of several molecular chaperones in complex with large unfolded proteins as client substrates.
Protein translocation & secretion
The Sec translocase catalyzes the secretion of hundreds of different substrates and hence displays an astonishing degree of substrate promiscuity. It consists of the membraneous SecYEG translocon, the SecA ATPase motor, and the SecB chaperone. SecA is the main player of the translocase as it performs a dazzling array of activities by interacting with all of the components of the translocation system (signal sequence and mature of the preprotein, SecB, SecYEG, and nucleotide), it partitions between the membrane and cytosol and functions as an ATP-dependent motor. The major goal of this project is to ultimately provide the structural, dynamic and molecular basis of the assembly of the whole Sec translocase machinery.
Cell signaling and oncogenes
The major goal of this project is to ultimately provide the molecular basis of Abl oncogene transactivation by Crk. That requires that we first understand how the individual Crk and Abl proteins, both proto-oncogenes, function. Crk-family adaptors form a growing class of signal transduction proteins that mediate the timely formation of protein complexes elicited by a variety of extracellular stimuli, including various growth and differentiation factors. Crk proteins are overexpressed in many human cancers including various carcinomas and sarcomas. Despite the prominent role of Crk in cell signaling, currently the mechanistic basis for the regulation of its function remains elusive. Such an understanding is now rendered even more urgent because of the many studies highlighting the important role played by Crk proteins in mediating the action of other human oncogenes, such as the leukemia-inducing Bcr-Abl protein, as well as in the phagocytosis of apoptotic cells.
Protein dynamics and allostery
The major goal of this project is to establish the important role of protein dynamics at multiple timescales in regulating the function and activity of protein systems. NMR spectroscopy provides an extremely powerful tool because of its unique capacity to determine the motions that atoms undergo in a protein at superb resolution. Our group has been intrigued by the potential mechanisms that Nature has chosen to use to propagate information over long distances, a process termed allostery. Recently, our group demonstrated for the first time that allostery can be mediated exclusively by transmitted changes in protein motions, without a corresponding propagation of conformational changes.
The major goal of this project is to provide the structural and mechanistic basis of the assembly of the transcription initiation complex. Transcription initiation, the first step in gene expression, is the step at which most regulation of gene expression occurs. Unraveling the mechanisms that underpin transcription regulation has been a major goal of our group. We are also interested in understanding the mechanisms by which regulatory proteins discern their target sequences within the DNA genome. This requires that we also understand the properties of their complexes with nonspecific DNA. Nonspecific sites participate in the regulation of the physiological function because they complex, in vivo, most of the DNA binding protein molecules that are not bound at their regulatory functional sites. Furthermore, protein-nonspecific DNA interactions may also play an important role in the in vivo translocation of DNA binding proteins. Currently, we are studying another prototype system for understanding transcription regulation, that is, the catabolite activator protein (CAP). We wish to understand how the protein is activated and how it mediates formation of the initiation complex.
Type III protein secretion
The major goal of this project is to provide the molecular and mechanistic basis of the recognition of substrates by their cognate chaperones and their interaction with the ATPase in type III secretion system (TTSS). TTSS is an exceptional bacterial organelle that has specifically evolved to deliver bacterial proteins into eukaryotic cells. T3SSs are encoded by a large number of bacterial species that are symbiotic or pathogenic for humans, other animals including insects or nematodes, and plants. The study of these systems may lead to unique insights into not only organelle assembly and protein secretion but also mechanisms of symbiosis and pathogenesis. Our focus is one of the best characterized TTSS translocons, which is the enteropathogenic E. coli (EPEC).
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.
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.
C.E. Tinberg, S.D. Khare, J. Dou, L. Doyle, J.W. Nelson, A. Schena, 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.
H-S. Tzeng & C.G. Kalodimos (2012) “Protein activity regulation by conformational entropy” Nature, 488, 236-240.
W. Jankowski, T. Saleh, M-T. Pai, G. Sriram, 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.
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” Nature Chemical Biology, 7, 51-57.
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 sequences are allosteric activators of the protein translocase” Nature, 462, 363-367.
N. Popovych, H-S. Tzeng, M. Tonelli, R.H. Ebright & C.G. Kalodimos (2009) “Structural basis for cAMP-mediated allosteric control of the catabolite activator protein” Proceedings of the National Academy of Sciences of USA, 106, 6927-6932.
I. Gelis, A. Bonvin, D. Keramisanou, A. Economou & C.G. Kalodimos (2007) “Structural basis for signal sequence recognition by the 204-kDa translocase motor SecA determined by NMR” Cell, 131, 756-769.