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	Charalampos (Babis) Kalodimos Associate Professor Email
	Contact   Links Phone: (732) 445-4500 x6209 Fax: (732) 445-3753 Mail: Chemistry & Chemical Biology Biomedical Engineering, 599 Taylor Rd, Piscataway, NJ 08854 Lab web page Biochemistry

The main research interests of the lab have been focused on the elucidation of the molecular and mechanistic basis of a wide range of important biological phenomena. Our current and future efforts are directed towards understanding how central biological processes, such as transcription regulation, protein translocation and secretion, cell signaling, and protein folding take place. We strongly believe that a detailed characterization of biomolecular interactions necessarily involves investigation of the inter-relationship between function, structure, dynamics, kinetics and energetics of a system. Towards this challenging goal, we employ state-of-the-art NMR spectroscopy methodologies complemented by many other biochemical and biophysical techniques. NMR spectroscopy in particular is a very powerful methodology that allows the study of the three-dimensional structure of biomolecules in semi-physiological conditions. Furthermore, NMR spectroscopy can provide a unique insight into the dynamic aspects of the macromolecules and their interaction with ligands over time. Application of these methodologies in our lab has already resulted in very exciting and novel information.



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.

Transcription regulation
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).

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.

1. Gelis I, Bonvin A, Keramisanou D, Economou A. Kalodimos CG (2007) Structural basis for signal sequence recognition by the 204-kDa translocase motor SecA determined by NMR. Cell. 131:756-769.
2. Sarkar P, Reichman C, Saleh T, Birge RB, C.G. Kalodimos CG (2007) Proline cis-trans isomerization controls autoinhibition of a signaling protein. Molecular Cell. 25: 413-426.
3. Popovych N, Sun S, Ebright RH, Kalodimos CG (2006) Dynamically driven protein allosteric cooperativity. Nature Structural & Molecular Biology. 13: 831-838.
4. Keramisanou D, Biris N, Gelis I, Sianidis G, Karamanou S, Economou A, Kalodimos CG (2006) Disorder-order transitions underlie catalysis of the helicase motor of SecA. Nature Structural & Molecular Biology. 13: 594-602.
5. Kalodimos CG, Biris N, Bonvin A, Levandoski M, Guennuegues M, Boelens R, Kaptein R (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science. 305: 386-389.
6. Kalodimos CG, Bonvin A, Salinas R, Weschelberger R, Boelens R, Kaptein R (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.
7. Kalodimos CG, Boelens R, Kaptein R (2002) A residue-specific view of the association and dissociation pathway in protein-DNA recognition. Nature Structural Biology. 9: 193-197.
8. Kalodimos CG, Folkers G, Boelens R, Kaptein R (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.

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