Cellular-Structural Biology Lab

Summary

We focus on understanding how the physicochemical and biological properties of cells modulate protein structure and function. The intracellular environment differs substantially from the conditions of high protein concentration and purity which are normally used to perform in vitro structural biology studies. Macromolecular crowding, excluded volume effects, viscosity, and intermolecular interactions with metabolites, lipids, proteins or nucleic acids, modulate the structure and activity of proteins. In addition, the composition and physicochemical properties of the cells are dynamic and change in response to biological processes such as cell cycle or the presence of different types of stress. Therefore, to understand the behavior of a given protein it is necessary to study it in vivo and with high resolution. Currently, the only technique that allows obtaining this type of information with atomic resolution is In-cell NMR.

In-cell NMR is based on the property that most of the heteronuclei found in vivo are invisible to the NMR spectrometer. Therefore, one can enrich a particular protein with NMR-active atoms and observe it within living cells. The resulting sample only displays NMR signals from the labeled species, filtering out the rest of the cellular biomass. In that way, biologically relevant interactions such as ligand-binding, post-translational modifications or structural rearrangements resulting in changes of the NMR observables of the protein can be directly quantified with high-resolution in a non-destructive manner.

We use In-cell NMR to characterize the intracellular structural properties and activity of redox proteins involved in cardiac and neuronal diseases. We are interested in the Methionine Sulfoxide Reductase (MSR) protein family. Protein methionine oxidation has traditionally been perceived as oxidative stress damage and associated with pathological processes. This view changed recently with the discovery that methionine oxidation to sulfoxide and its enzymatic reduction by MSRs acted as a main regulatory switch for central cellular processes such as remodeling of the actin cytoskeleton, synaptic transmission or cardiac muscle cell contraction. In our group we seek to understand how the intracellular environment modulates the conformational properties of MSRs, their substrate binding specificity and their enzymatic activity.

 

Selected Publications

  1. Theillet F-X.*, Binolfi A.*, Bekei B.*., Martorana A., Rose H. M., Stuiver M., Verzini S., Lorenz D., van Rossum M., Goldfarb D., Selenko P. (2016) Structural disorder of monomeric α-synuclein persists in mammalian cells. Nature, 530, 45-50. *Igual contribución.

 

  1. Binolfi A., Limatola A., Verzini S., Kosten J., Theillet F-X., Rose H. M., Bekei B., Stuiver M., van Rossum M., Selenko P. (2016) Intracellular repair of oxidation-damaged alpha-synuclein fails to target C-terminal modification sites. Nature Communications, 7, 10251.

 

  1. Danielsson J., Mu X., Lang L., Wang H., Binolfi A., Theillet F-X., Bekei B., Logan D. T., Selenko P., Wennerström H., Oliveberg M. (2015) Thermodynamics of protein destabilization in live cells. Proceedings of the National Academic of Sciences U. S. A., 112, 12402-12407.

 

  1. Smith M. J., Marshall C. B., Theillet F-X., Binolfi A., Selenko P., Ikura M. (2015) Real-time NMR monitoring of biological activities in complex physiological environments. Current Opinion in Structural Biology, 32C, 39-47.

 

  1. Lombardo V.A.*, Otten C.*, Abdelilah-Seyfried S. (2015). Large-scale zebrafish embryonic heart dissection for transcriptional analysis. Journal of Visual Experiments, (95), e52087. * Igual contribución.

 

  1. Lombardo V.A.*, Dietrich A.*, Abdelilah-Seyfried S. (2014). Blood flow and Bmp control endocardial chamber morphogenesis. Developmental Cell, 30:367–377. *Igual contribución.

 

  1. Kosten J.*, Binolfi A.*, Stuiver M., Verzini S., Theillet F-X., Bekei B., van Rossum M., Selenko P. (2014) Efficient modification of alpha-synuclein serine 129 by protein kinase CK1 requires phosphorylation of tyrosine 125 as a priming event. ACS Chemical Neuroscience, 5, 1203-1208. *Igual contribución.

 

  1. Theillet F-X.*, Binolfi A.*, Frembgen-Kesner T., Hingorani K., Sarkar M., Kyne C., Li C., Crowley P., Gierasch L., Pielak G., Elcock A. H., Gershenson A., Selenko P. (2014) Physicochemical and biological properties of cells and their effects on IDPs. Chemical Reviews, 114, 6661-6714. *Igual contribución.

 

  1. Theillet F.-X., Rose H. M., Liokatis S., Binolfi A., Thongwichian R., Stuiver M., Selenko P. (2013) Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts. Nature Protocols, 8, 1416.

 

  1. Binolfi A., Theillet F-X., Selenko, P. (2012) Bacterial in-cell NMR of human a-synuclein: a disordered monomer by nature? Biochemical Society Transactions. 40, 950-954.

 

  1. Lombardo V.A., Sporbert A., Abdelilah-Seyfried S. (2012). Cell tracking using photoconvertible proteins during zebrafish development. Journal of Visual Experiments, (67), e4350.

Collaborators

  • Alejandro J. Vila (IBR-CONICET, Rosario)
  • Bruno Manta Porteiro (Harvard Medical School, Boston)
  • Darío Krapf (IBR-CONICET, Rosario)
  • Diego de Mendoza (IBR-CONICET, Rosario)
  • Nora Calcaterra (IBR-CONICET, Rosario)
  • Pablo Armas (IBR-CONICET, Rosario)
  • Philipp Selenko (FMP, Berlin)

Director

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Andrés Binolfi
Core CCT
Email: binolfi@ibr-conicet.gov.ar
Phone: +54 341 4237070
Office Extension: 649
Laboratory Extension: 614

Researchers

Dra. Verónica Lombardo

Postdoctoral fellows

Dra. Magda Carolina Sánchez López

Undergraduate Students

Natalia Labadie

Imágenes

Reducción de sulfóxidos de metionina en proteínas catalizada por MSRs celulares. Binolfi et al. Nat. Commun. 2016, 7, 10251.

Microscopía confocal de un corazón de pez cebra.

Interacciones entre una proteína y su entorno en el interior celular. Theillet, Binolfi and Bekei et al, Nature, 530, 45-50.