Chromatin structure and architecture. DNA within the cell nucleus is packaged into chromatin and a variety of models presently describe the structure of the condensed 30 nm chromatin fiber. We are specifically interested in an understanding of the topological organization of DNA within condensed 30 nm chromatin fragments. In order to do this we are currently developing high resolution chromosome capture conformation assays utilizing both in vitro model systems, as well as 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 determine the structure of the 30 nm chromatin fiber, which will in turn provide a better understanding of the relations between chromatin structure and essential processes such as gene expression and DNA replication. Macromolecular assemblies. In collaboration with members of the Laboratory of Molecular Biology, and others, protein and protein-nucleic acid assemblies have been characterized in terms of their shape, stoichiometry and affinity of interaction using hydrodynamic methods. These studies extend current biochemical and structural investigations as exemplified by recently published studies on the monovalent lectin microvirin carried out in collaboration with Drs. G. Marius Clore and Carole Bewley. In this study, purified microvirin was shown to exist as a monodisperse monomer which binds monovalently to mannose alpha(1-2) mannose with an affinity of 50 micromolar. As this disaccharide unit terminates the arms of high mannose N-linked carbohydrate chains, microvirin is able to interact with the highly glycosylated HIV-1 surface protein gp120 and prevent HIV-1 entry into cultured cells. These biophysical and structural studies illustrate the molecular mechanism through which microvirin inhibits HIV entry (Shahzad-ul-Hussan et al., 2011).

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Chiliveri, Sai Chaitanya; Louis, John M; Ghirlando, Rodolfo et al. (2018) Tilted, Uninterrupted, Monomeric HIV-1 gp41 Transmembrane Helix from Residual Dipolar Couplings. J Am Chem Soc 140:34-37
Zhou, Bing-Rui; Jiang, Jiansheng; Ghirlando, Rodolfo et al. (2018) Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures. J Mol Biol 430:3093-3110
Nguyen, Trang T; Ghirlando, Rodolfo; Venditti, Vincenzo (2018) The oligomerization state of bacterial enzyme I (EI) determines EI's allosteric stimulation or competitive inhibition by ?-ketoglutarate. J Biol Chem 293:2631-2639
Chittori, Sagar; Hong, Jingjun; Saunders, Hayden et al. (2018) Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N. Science 359:339-343
Lusvarghi, Sabrina; Ghirlando, Rodolfo; Davison, Jack R et al. (2018) Chemical and Biophysical Approaches for Complete Characterization of Lectin-Carbohydrate Interactions. Methods Enzymol 598:3-35
Kang, Hyeog; Oka, Shinichi; Lee, Duck-Yeon et al. (2017) Sirt1 carboxyl-domain is an ATP-repressible domain that is transferrable to other proteins. Nat Commun 8:15560
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Passos, Dario Oliveira; Li, Min; Yang, Renbin et al. (2017) Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science 355:89-92
Jha, Jyoti K; Li, Mi; Ghirlando, Rodolfo et al. (2017) The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2. MBio 8:
Libich, David S; Tugarinov, Vitali; Ghirlando, Rodolfo et al. (2017) Confinement and Stabilization of Fyn SH3 Folding Intermediate Mimetics within the Cavity of the Chaperonin GroEL Demonstrated by Relaxation-Based NMR. Biochemistry 56:903-906

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