Chromatin structure and architecture. DNA within the cell nucleus is packaged into chromatin and, at present, a variety of models describe the structure of the condensed 30 nm chromatin fiber observed in vitro. However, evidence for a 30 nm chromatin structure in vivo is currently lacking, except in specialized cells such as mature avian erythrocytes in which all of the chromatin is essentially inactive. We are specifically interested in understanding the organization of DNA within condensed chromatin in vivo, as well as the topological constraints imposed on its higher order imposed by organizing proteins such as CTCF and cohesin. Accordingly, we are developing high resolution chromosome capture conformation assays utilizing native chromatin fragments, such as the previously studied condensed heterochromatin flanked by the developmentally regulated folate receptor and beta-globin genes. These studies will allow us to better understand the structure of the chromatin fiber in vivo, thus providing insight in the relations between chromatin structure and essential processes such as gene expression and DNA replication. Macromolecular assemblies. Macromolecular assemblies have been characterized in terms of their shape, stoichiometry and affinity of interaction using hydrodynamic methods. These studies form an integral part of current biochemical, structural and physiological investigations as evidenced by recently published work carried out in collaboration with Dr. Clore. E. coli enzyme I represents the first component of the bacterial phosphotransferase system, a pathway coupling the phosphorylation and active transport of sugars across the cell membrane. Enzyme I autophosphorylation by phosphoenolpyruvate (PEP) is the first step of this process and previous studies have shown that alpha-ketoglutarate (aKG) inhibits enzyme I. We have provided a structural basis for enzyme I inhibition by alpha-ketoglutarate and shown that it not only binds to the active site of enzyme I but also acts as a competitive inhibitor for PEP. A characterization of the self-association of enzyme I in the presence of both PEP and aKG was necessary for a determination of the structure and elucidation of this mechanism, which now provides a direct regulatory link between carbon and nitrogen metabolism in E. coli (Venditti et al., ACS Chemical Biology, 2013). Furthermore, in collaboration with colleagues on the NIH campus and at UT Southwestern, we improved upon analytical ultracentrifugation methodology, one of the primary tools used in the studies mentioned above. This methodology leads to more accurate hydrodynamic parameters and accounts for variations previously observed across different instruments. This is not only important for hydrodynamic modeling that routinely requires the highest accuracy, but also in the context of regulatory issues for biologics (Ghirlando et al., Analytical Biochemistry, 2013).

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Zhao, Huaying; Ghirlando, Rodolfo; Piszczek, Grzegorz et al. (2013) Recorded scan times can limit the accuracy of sedimentation coefficients in analytical ultracentrifugation. Anal Biochem 437:104-8
Inagaki, Sayaka; Ghirlando, Rodolfo; Grisshammer, Reinhard (2013) Biophysical characterization of membrane proteins in nanodiscs. Methods 59:287-300
Ghirlando, Rodolfo; Felsenfeld, Gary (2013) Physical chemistry of nucleic acids and their complexes. Biopolymers 99:910-5
Sugiman-Marangos, Seiji N; Peel, John K; Weiss, Yoni M et al. (2013) Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states. Nucleic Acids Res 41:9934-44
Ghirlando, Rodolfo; Balbo, Andrea; Piszczek, Grzegorz et al. (2013) Improving the thermal, radial, and temporal accuracy of the analytical ultracentrifuge through external references. Anal Biochem 440:81-95
Hong, Jingjun; Feng, Hanqiao; Zhou, Zheng et al. (2013) Identification of functionally conserved regions in the structure of the chaperone/CenH3/H4 complex. J Mol Biol 425:536-45
Ghirlando, Rodolfo; Felsenfeld, Gary (2013) Chromatin structure outside and inside the nucleus. Biopolymers 99:225-32
Phillips, Damilola D; Fattah, Rasem J; Crown, Devorah et al. (2013) Engineering anthrax toxin variants that exclusively form octamers and their application to targeting tumors. J Biol Chem 288:9058-65
Ghirlando, Rodolfo; Felsenfeld, Gary (2008) Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn. J Mol Biol 376:1417-25