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A robust pipeline for rapid production of versatile nanobody repertoires

Peter C Fridy, Yinyin Li, Sarah Keegan, Mary K Thompson, Ilona Nudelman, Johannes F Scheid, Marlene Oeffinger, Michel C Nussenzweig, David Fenyö, Brian T Chait, Michael P Rout
2014 Nature Methods  
All LaG binding-site residues are listed in Supplementary Table 2 Peter C Fridy 1,8 , Yinyin Li 2,8 , Sarah Keegan 3 , Mary K Thompson 1 , Ilona Nudelman 1 , Johannes F Scheid 4 , Marlene Oeffinger  ... 
doi:10.1038/nmeth.3170 pmid:25362362 pmcid:PMC4272012 fatcat:e46oxwznvbhbtbiee65c7be6wy

Intermolecular Interactions in a 44 kDa Interferon−Receptor Complex Detected by Asymmetric Reverse-Protonation and Two-Dimensional NOESY

Ilona Nudelman, Sabine R. Akabayov, Einat Schnur, Zohar Biron, Rina Levy, Yingqi Xu, Daiwen Yang, Jacob Anglister
2010 Biochemistry  
Type I Interferons (IFNs) are a family of homologous helical cytokines initiating strong anti-viral and anti-proliferative activity. All type I IFNs bind to a common cell surface receptor consisting of two subunits, IFNAR1 and IFNAR2, associating upon binding of interferon. We studied intermolecular interactions between IFNAR2-EC and IFNα2 using asymmetric reverse-protonation of the different complex components and 2D homonuclear NOESY. This new approach revealed with excellent signal-to-noise
more » ... atio 24 new intermolecular NOEs between the two molecules despite the low concentration of the complex (0.25 mM) and its high molecular weight (44 kDA). Sequential and side-chain assignment of IFNAR2-EC and IFNα2 in their binary complex helped assign the inter-molecular NOEs to the corresponding protons. A docking model of the IFNAR2-EC/IFNα2 complex was calculated based on the inter-molecular interactions found in the present study as well as four double mutant cycle constraints, previously observed NOEs between a single pair of residues and the NMR mapping of the binding sites on IFNAR2-EC and IFNα2. Our docking model doubles the buried surface area of the previous model and significantly increases the number of inter-molecular hydrogen bonds, salt bridges and Van der-Waals interactions. Furthermore, the current model reveals participation of several new regions in the binding site such as the N-terminus and A-helix of IFNα2 and the C-domain of IFNAR2-EC. As a result of these additions, the orientation of IFNAR2-EC relative to IFNα2 has changed by 30° in comparison with a previously calculated model that was based on NMR mapping of the binding sites and double mutant cycle constraints. In addition, the new model strongly supports the recently proposed allosteric changes in IFNα2 upon IFNAR1-EC binding to the binary IFNα2/ IFNAR2-EC complex. Type I IFNs are a major component of the innate immune system protecting against viral infection.
doi:10.1021/bi100041f pmid:20496919 pmcid:PMC2901802 fatcat:p6nrhmuz7jec5alkbiwpnxrmoi

Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex [article]

Christopher Akey, Digvijay Singh, Christina Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M Varberg, Zuliin Yu, Fei Fang, Yi Shi, Junjie Wang, Daniel Saltzberg, Kankang Song (+11 others)
2021 bioRxiv   pre-print
Nuclear Pore Complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the yeast NPC in which the inner ring is resolved by cryo-EM at ɑ-helical resolution to show how flexible connectors tie together different structural and functional layers in the spoke. These connectors are targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and karyopherins have similar interaction motifs,
more » ... h suggests an evolutionary and mechanistic link between assembly and transport. We also provide evidence for three major NPC variants that foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies to provide a comprehensive model of the in situ NPC with a radially-expanded inner ring. Our model reveals novel features of the central transporter and nuclear basket, suggests a role for the lumenal ring in restricting dilation and highlights the structural plasticity required for transport by the NPC.
doi:10.1101/2021.10.29.466335 fatcat:pexgamrkejdh3fks55s7t74tue

Observation of Intermolecular Interactions in Large Protein Complexes by 2D-Double Difference Nuclear Overhauser Enhancement Spectroscopy: Application to the 44 kDa Interferon–Receptor Complex

Ilona Nudelman, Sabine R. Akabayov, Tali Scherf, Jacob Anglister
2011 Journal of the American Chemical Society  
NMR detection of intermolecular interactions between protons in large protein complexes is very challenging since it is difficult to distinguish between weak NOEs from intermolecular interactions and the much larger number of strong intramolecular NOEs. This challenging task is exacerbated by the decrease in signal-to-noise ratio in the often used isotope-edited and isotopefiltered experiments as a result of enhanced T 2 relaxation. Here we calculate a double difference spectrum that shows
more » ... sively intermolecular NOEs and manifests the good signal-to-noise ratio in 2D homonuclear NOESY spectra even for large proteins. The method is straightforward and results in a complete picture of all intermolecular interactions involving non exchangeable protons. Ninety seven such 1 H-1 H NOEs were assigned for the 44 KDa interferon-α2/IFNAR2 complex and used for docking these two proteins. The symmetry of the difference spectrum, its superb resolution and unprecedented signal-to-noise ratio in this large protein/receptor complex suggest that this method is generally applicable to study large biopolymeric complexes.
doi:10.1021/ja205480v pmid:21819146 pmcid:PMC3173517 fatcat:oifp3qzft5elthg6hl3be4sx5e

Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform

Javier Fernandez-Martinez, Seung Joong Kim, Yi Shi, Paula Upla, Riccardo Pellarin, Michael Gagnon, Ilan E. Chemmama, Junjie Wang, Ilona Nudelman, Wenzhu Zhang, Rosemary Williams, William J. Rice (+5 others)
2016 Cell  
The last steps in mRNA export and remodeling are performed by the Nup82 complex, a large conserved assembly at the cytoplasmic face of the nuclear pore complex (NPC). By integrating diverse structural data, we have determined the molecular architecture of the native Nup82 complex at subnanometer precision. The complex consists of two compositionally identical multiprotein subunits that adopt different configurations. The Nup82 complex fits into the NPC through the outer ring Nup84 complex. Our
more » ... ap shows that this entire 14 MDa Nup82-Nup84 complex assembly positions the cytoplasmic mRNA export factor docking sites and mRNP remodeling machinery right over the NPC's central channel, rather than on distal cytoplasmic filaments as previously supposed. We suggest that this configuration efficiently captures and remodels exporting mRNP particles immediately upon reaching the cytoplasmic side of the NPC. Graphical abstract Fernandez-Martinez et al.
doi:10.1016/j.cell.2016.10.028 pmid:27839866 pmcid:PMC5130164 fatcat:uqc6jafqhnee3nxemv7gyvigny

Integrative structure and functional anatomy of a nuclear pore complex

Seung Joong Kim, Javier Fernandez-Martinez, Ilona Nudelman, Yi Shi, Wenzhu Zhang, Barak Raveh, Thurston Herricks, Brian D. Slaughter, Joanna A. Hogan, Paula Upla, Ilan E. Chemmama, Riccardo Pellarin (+20 others)
2018 Nature  
0 0 M o n t h 2 0 1 8 | V o L 0 0 0 | n A t U R E | 1 ARticLE Nuclear pore complexes (NPCs) are large proteinaceous assemblies studded through the nuclear envelope, the double-membraned barrier that surrounds the nucleus; NPCs are the sole mediators of macromolecular transport between the nucleus and the cytoplasm, and carry key regulatory platforms for numerous nuclear processes 1 . NPCs are also major targets for viral manipulation and defects in this transport machine are directly linked to
more » ... uman diseases, including cancers 2 . Each NPC is an eight-fold symmetric, cylindrical assembly consisting of approximately 550 copies of about 30 different proteins of the nucleoporin family (Nups). These Nups assemble into sub-complexes that form higher-order structures called spokes. Eight spokes assemble into even larger modules: coaxial outer and inner rings form a symmetric core scaffold, which is connected to a membrane ring, a nuclear basket and cytoplasmic RNA export complexes 3 . The scaffold surrounds a central channel that is formed in part by multiple intrinsically disordered Phe-Gly (FG) repeat motifs that extend from nucleoporins termed FG Nups. These FG motifs mediate selective nucleocytoplasmic transport through specific interactions with nuclear transport factors (NTFs), which carry their cognate macromolecular cargoes 4 . It has also previously been suggested that the central channel contains a feature called the central transporter 5 . Although partial structures have previously been described 3,6,7 , a complete, high-resolution structure for the entire NPC in any organism has hitherto been lacking, leaving open key questions as to how the NPC is organized and functions, and how it evolved. To address these questions, we have determined an integrative structure of the yeast NPC at sub-nanometre precision. Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.
doi:10.1038/nature26003 pmid:29539637 fatcat:y5o267xpkfhk3e4fagdjuycjzm

Indexes - volume 60

B Trewin
2010 Australian Meteorological and Oceanographic Journal  
Reeder and Nudelman, Ilona. A climatology of pressure jumps around the Gulf of Carpentaria, 91 Steinle,  ...  Reeder; Nudelman, Ilona and Smith, Roger K. A climatology of pressure jumps around the Gulf of Carpentaria, 91 Mills, Graham A.  ... 
doi:10.22499/2.6004.008 fatcat:bcxvsotsojfshelq6jdt25txpi

Page 429 of Psychological Abstracts Vol. 77, Issue Author Index 1-2 [page]

Psychological Abstracts  
.— See Nudelman, H. B. 17502 Herczeg, Ilona— See Bartké, Gydrgy 5458, 17929 Herd, Denise.  ... 

Pore timing: the evolutionary origins of the nucleus and nuclear pore complex

Mark C. Field, Michael P. Rout
2019 F1000Research  
Acknowledgments Our thanks to Ilona Nudelman for help with Figure 2 .  ... 
doi:10.12688/f1000research.16402.1 pmid:31001417 pmcid:PMC6449795 fatcat:nszex63g4ncglfgvbu6dzn7cge

Characterizing Light-Regulated Retinal MicroRNAs Reveals Rapid Turnover as a Common Property of Neuronal MicroRNAs

Jacek Krol, Volker Busskamp, Ilona Markiewicz, Michael B. Stadler, Sebastian Ribi, Jens Richter, Jens Duebel, Silvia Bicker, Hans Jörg Fehling, Dirk Schübeler, Thomas G. Oertner, Gerhard Schratt (+3 others)
2010 Cell  
., 2008; Nudelman et al., 2009) , and miR-132 is required for activity-dependent dendritic growth and spine formation (Wayman et al., 2008; Impey et al., 2010) .  ... 
doi:10.1016/j.cell.2010.03.039 pmid:20478254 fatcat:54xdpoeuvzfang2svgnvlkwkeq

Mapping chromatin accessibility and active regulatory elements reveals new pathological mechanisms in human gliomas [article]

Karolina Stepniak, Magdalena A Machnicka, Jakub Mieczkowski, Anna Macioszek, Bartosz Wojtas, Bartlomiej Gielniewski, Sylwia K. Krol, Rafal Guzik, Michal J Dabrowski, Michal Draminski, Marta Jardanowska, Ilona Grabowicz (+12 others)
2019 bioRxiv   pre-print
., Nudelman, G., Tsankov, A.M., Katsyv, I., Tejero, R.,Zhang, B., Walsh, M., Friedel, R.H., Zaslavsky, E., et al. (2018).  ... 
doi:10.1101/867861 fatcat:jw4iwqestbh6fmp637lfd6vghq

Synthetische und mutasynthetische Zugänge zu neuen Hsp90 Inhibitoren [article]

Jekaterina Hermane, University, My
Nudelman, J. Org. Chem. 1997, 62, 7512-7515.  ...  Die Fluor-Aminobenzoesäuren 174, 175 und 176 wurden hierfür von ILONA BULYSZKO hergestellt und zur Verfügung gestellt (Abbildung 22). 90 86 a) S. B. Rosenblum, T. Huynh, A. Afonso, H. R. Davis, J. N.  ... 
doi:10.15488/8085 fatcat:rf5kka76rbfodnz5s7gtd5itfe