Összes szerző

Perahia David

az alábbi absztraktok szerzői között szerepel:

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

Aug 30 - szerda

15:30 – 17:00

II. Poszterszekció

P39

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

Janka Czigleczki¹, Pedro Tulio de Resende Lara², Balint Dudas^1,3,4, Hyunbum Jang⁵, David Perahia⁴, Ruth Nussinov ^5,6and 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

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) domain and a C-terminal region, which is bound to the G-domain in the inactive, GDP-bound states. 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. Here, by using molecular dynamics (MD) and MDeNM (Molecular Dynamics with excited Normal Modes) simulation methods, 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.

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

Tóth Dániel
Substrate selectivity of Sulfotransferase Isoenzymes, results based on Molecular Dynamics and Ensemble Docking

Aug 30 - szerda

15:30 – 17:00

II. Poszterszekció

P58

Substrate selectivity of Sulfotransferase Isoenzymes, results based on Molecular Dynamics and Ensemble Docking

Dániel Toth^1,2 , Bálint Dudas^2,3, David Perahia³, Erika Balog¹, Maria A. Miteva² 

¹Department of Biophysics and Radiation Biology, Semmelweis University, Hungary

²Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS - Université Paris Cité, France

³Laboratoire de biologie et pharmacologie appliquee, Ecole Normale Superieure Paris-Saclay, France

Sulfotransferase enzymes (SULTs) are a family of cytosolic globular proteins in the chain of metabolism. By catalysing a sulfate transfer from their co-factor, 3′-Phosphoadenosine 5′-Phosphosulfate (PAPS), they eliminate a large variety of small molecules like drugs, hormones and neurotransmitters. Even though the tertiary structure across the family is very similar, their substrates vary considerably in size and complexity. The aim of our project is to better understand the reasons of selectivity between the different SULT isoenzymes, by comparing the broad targeting hepatic detoxifier SULT1A1, and the ileum located, dopamine selective SULT1A3.

Based on our previous results and Molecular Dynamics (MD) and Molecular Dynamics with excited Normal Modes (MDeNM), an extended conformational space of the PAPS-bound SULT1A1 was explored. Further developments of our method utilising ensemble docking with categorised ligands, a method known as Virtual Screening was achieved. Moreover, we have broadened our scope to use the same approach for the SULT1A3.

Based on our new results, we identified the key differences, that are responsible for changing the protein dynamics and binding mechanisms, by opening the binding pocket to an unfavourable conformation for the most common ligands of 1A1, thus acting as efficient selectors. These results can be helpful in the future to develop an algorithm for machine learning, that could differentiate and even predict new substrates of the different isoforms, thus helping in the development of ADME-Tox profiling of novel drug candidates and xenobiotics.

Acknowledgment

TKP2021 EGA 23, Ministry for Innovation and Technology in Hungary,

2021-0143339, Ministére francais de l’Europe et des Affaires Etrangéres

Tét-Balaton project „drug-drug interactions of sulfotransferases” ( 2019-2.1.11-TÉT-2020-00096 )