Protein structure, folding and function


Proteins are essential for every living cell, participating in all cellular processes. The knowledge of their structure and function enables understanding the cell and living organisms’ functioning. Our group studies proteins by analyzing the relationships between their structures and functions and their possible metabolic roles in certain organisms. We use widely distributed protein models relevant to physiological processes in all living organisms, such as flavoproteins, molecular chaperones, and proteases. We analyze their expression, folding, stability, structure, catalytic functions, and degradation. This information allows us to discover their role and design bacterial enzyme inhibitors or beneficial alterations for biotechnological use, for example, for improving plants of agronomic interest.

Research Lines

Study of the structure-function relationship in molecular chaperones

The cellular proteome results from the balance of protein synthesis and degradation. The cell's fate depends on its ability to maintain protein homeostasis (proteostasis). Disruption of the appropriate proteome for a given situation can significantly damage the cell and even its death.

Many mechanisms respond to proteome variations by regulated systems. These mechanisms are known as "protein quality control," consisting of a network of molecular chaperones, proteases, and accessory proteins that eliminate damaged proteins, solubilize potentially toxic aggregates or assist in protein folding.

In certain situations, the protein quality control can get overloaded. For this reason, the cytosol and organelles trigger genetic programs resulting in the overexpression of gene coding for the protein quality control members. This process is known as unfolded protein response (UPR).

We study the conditions that set the UPR in motion and the communication of the stress to the nucleus. We are also interested in knowing the defense mechanisms that are activated in the cell to ensure its survival. We use techniques such as proteomics, western blots, plant transformation, and nuclear magnetic resonance. Directors: Dr. Germán Rosano / Dr. Eduardo Ceccarelli.

Study of the structure-function relationship in flavoenzymes

Ferredoxin-NADP+ reductases (FNR) constitute a family of monomeric proteins that contain non-covalently bound FAD as a prosthetic group. These widely distributed flavoenzymes are involved in the electron transfer of biologically important processes. FNRs catalyze the reversible electron transfer between NADP(H) and one-electron carriers such as ferredoxin or flavodoxin. They are classified as plant and mitochondrial-type. Plant-type FNRs are grouped into plastidic and bacterial classes. Bacterial FNRs participate in metabolic pathways, especially appropriate for developing antimicrobial agents because they are not present in humans. Thus, they can be used to design inhibitors in the fight against diseases caused by different pathogens.

Our studies aim to understand the catalytic mechanism of FNRs from plants and bacteria, and those relevant metabolic processes in which they participate, with particular emphasis on the structural characteristics that define their catalytic efficiency. We focus on the structural and functional analysis of FNRs and the identification and characterization of their natural substrates.

Our experimental approach includes analysis of recombinant wild-type and protein-engineered enzymes. We study enzymes by kinetic analysis, biophysical and structural methods, and modeling of protein structures and their substrates. Directors: Dr. Daniela Catalano Dupuy / Dr. Eduardo Ceccarelli.

Selected Publications

  • Structural features of the plant N-recognin ClpS1 and sequence determinants in its targets that govern substrate selection. FEBS Lett.;595(11):1525-1541. Journal Cover.  Aguilar Lucero D, Cantoia A, Sánchez-López C, Binolfi A, Mogk A, Ceccarelli EA, Rosano GL. (2021) doi: 10.1002/1873-3468.14081
  • A new catalytic mechanism of bacterial ferredoxin‐NADP+ reductases due to a particular NADP+ binding mode. Protein Science. 30(10):2106-2120. Monchietti, P.; López-Rivero, A.; Ceccarelli, E. A. and Catalano-Dupuy, D. L. (2021) doi: 10.1002/pro.4166.
  • Biochemical characterization of ClpB3, a chloroplastic disaggregase from Arabidopsis thaliana. Plant Mol Biol 104, 451–465. Parcerisa IL, Rosano GL, Ceccarelli EA. 2020 Aug 16. doi: 10.1007/s11103-020-01050-7.
  • A bacterial [4Fe-4S] ferredoxin as redox partner of the plastidic-type ferredoxin-NADP+ reductase from Leptospira interrogansBiochimica et Biophysica Acta (BBA)-General Subjects. 1863(4): 651-660. López-Rivero, A.; Rossi, A., Ceccarelli, E. A. and Catalano-Dupuy, D. L. (2019) doi: 10.1016/j.bbagen.2019.01.004.
  • New tools for recombinant protein production in Escherichia coli: a 5-year update. Protein Sci 28(8):1412-1422. Journal Cover. Rosano G.L., Morales E.S., Ceccarelli E.A. doi: 10.1002/pro.3668
  • ClpS1 From Arabidopsis thaliana Chloroplasts Recognizes Canonical N-Degrons Of The Bacterial N-End Rule. Plant and Cell Physiology 1;59(3):624-636. Editor’s Choice Paper of the Month/ Journal Cover. Colombo C.V., Rosano G.L., Mogk A., and Ceccarelli E.A. (2018).
  • Structural and mutational analysis of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism. PLoS ONE 12(8): e0182535. Soldano, A., Klinke, S., Otero, L. H., Rivera, M., Catalano-Dupuy, D. L. and Ceccarelli, E. A. (2017) doi:10.1371/journal.pone.0182535).
  • Heme-Iron Utilization by Leptospira interrogans Requires a Heme Oxygenase and a Plastidic-Type Ferredoxin-NADP+ Reductase. Biochimica et Biophysica Acta (BBA)-General Subjects 1840(11): 3208–3217. Soldano, A., Yao, H., Rivera, M., Ceccarelli, E. A. and Catalano-Dupuy, D. L. (2014). doi: 10.1016/j.bbagen.2014.07.021
  • Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 172 (5). Journal cover. Rosano G.L., Ceccarelli E.A. (2014) 10.3389/fmicb.2014.00172
  • Redox Proteins as Targets for Drugs Development against Pathogens. Current Pharmaceutical Design. 19(14): 2594-605. Catalano-Dupuy, D. L., López-Rivero, A., Soldano, A. and Ceccarelli, E. A. (2013). doi: 10.2174/1381612811319140009.

For a complete list, check my Google Scholar/ORCID/RESEARCH GATE/Scopus profile

Twitter: @LabCeccarelli