PhD Scientific Days 2023

Budapest, 22-23 June 2023

Pharmaceutical Sciences - Posters E

Functionally important C-terminus of small GTPase Ran: exploring its nucleotide-specific conformational surface

Janka Czigleczki1, Pedro Tulio de Resende Lara2, Balint Dudas1,3,4, Hyunbum Jang5, David Perahia4, Ruth Nussinov5,6 and Erika Balog1

1Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
2Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas—UNICAMP, Campinas, Brazil
3Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS—Université Paris Cité, Paris, France
4Laboratoire et Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
5Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
6Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel

Text of the abstract

As a member of the Ras superfamily of small GTPases, Ran (Ras-related Nuclear protein) is the main regulator of the nucleo-cytoplasmic transport through the nuclear core complex. It functions as a molecular switch cycling between the GDP-bound inactive or “off” and GTP-bound active or “on” state. Since deregulation of Ran is linked to numerous cancers from the stage of cancer initiation to metastasis, understanding the complexity of its interaction, especially the regulatory mechanism, is critical for drug discovery. Ran consists of a globular (G) or GTP binding domain (residue 1–172) and a C-terminal region (residue 173–216) which terminates in a unique acidic tail (DEDDDL), which is bound to the G-domain in the inactive, GDP-bound states. The standalone full-length Ran-GTP structure has not
been determined but it has been crystalized in complex forms. The crystal structures of the GTP-bound active form complexed with Ran binding proteins (RanBP) show that the C-terminus undergoes a large conformational change, embracing Ran binding domains (RanBD), whereas in the crystal structures of macromolecular complexes not containing RanBDs the structure of the C-terminal segment remains unresolved, indicating its large conformational flexibility. This movement could not have been followed either by experimental or simulation methods. Using simulations, our goal is to study potential conformational structures of the GTP-bound active forms and compare them to the inactive form.

Based on the results of molecular dynamics (MD) and MDeNM (Molecular Dynamics with excited Normal Modes), we present how rigid the C-terminal region is in the inactive RanGDP form and for the first time in the literature, we were able to follow its conformational flexibility in the GTP-bound form. This conformational mapping allows us to envisage how the C-terminus can embrace RanBDs during the function of Ran.

This project was partially funded by the TKP2021-EGA-23 provided by the Ministry of Innovation and Technology of Hungary; by federal funds from the National Cancer Institute, National Institutes of Health, under contract HHSN261201500003I and by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.

The simulations were carried out by JC, and were analyzed and interpreted by JC, PR, BD, HJ, RN, DP, and EB.