Tag Archives: enzymes

PhD Student Nayanika Das Begins Research Visit at the University of Groningen

Posted by 10 de October de 2025

We are delighted to share that our PhD student Nayanika Das has embarked on a research visit to the laboratory of Prof. Gerard Roelfes at the University of Groningen, The Netherlands. This visit marks an exciting step forward in her doctoral work on understanding and optimizing the function of enzymes, this time for proteins containing artificial amino acids.

During her stay, Nayanika will collaborate closely with the Roelfes group to investigate the incorporation of the noncanonical amino acid para-aminophenylalanine (pAF) into the nonenzymatic protein scaffold LmrR. Remarkably, this modification transforms LmrR into a proficient and stereoselective artificial enzyme (LmrR_pAF) — an elegant example of how chemical innovation can endow proteins with entirely new catalytic functions.

Nayanika’s research will combine experimental validation in the laboratory with computational modeling efforts. Specifically, she will contribute to the development of an Empirical Valence Bond (EVB) model aimed at uncovering the molecular details of the mechanism of action of pAF in the reactions catalyzed by LmrR_pAF. By integrating theoretical and experimental approaches, her work will help elucidate how artificial amino acids expand the functional landscape of proteins and open new avenues for biocatalysis and synthetic biology.

We wish Nayanika a productive and inspiring stay in Groningen and look forward to the exciting results that will emerge from this collaboration with the Roelfes Lab.

Nayanika Das Presents Advances in Enzyme Evolution at the SEB International Congress

Posted by 28 de June de 2025

PhD student Nayanika Das participated in the 18th International Congress of the Spanish Biophysical Society, held from June 24 to 27, 2025, at the Faculty of Chemistry of the Complutense University of Madrid. This event, organized by the Spanish Biophysical Society, brings together scientists from various disciplines and stages of their research careers to explore cutting-edge topics in the field of biophysics.

During the congress, Nayanika presented her results in poster format, entitled: “Exploring the Evolutionary Dynamics between GPX6 Orthologs and Comparing Their Catalytic Efficiency Using Empirical Valence Bond (EVB) Calculations.” Her work shows why the substitution of selenocysteine with cysteine in GPX6 significantly reduces catalytic efficiency, supporting the proposed mechanistic hypothesis, and it also extends the analysis to explore the energy landscape of cummulative mutations between Sec- and Cys- containing GPX6 proteins in nature. Thus, using a greedy algorithm, key mutations with lower activation barriers were identified that could stabilize the enzyme and offer an energetically favorable evolutionary path between homolog proteins.

Nayanika Das presents a poster at RQTC/SCQ on recent work in GPX6 evolution and activity

Posted by 1 de February de 2023

In a recent work coordinated by Sergi Castellano (UCL), and in collaboration with Elias Arnér research group (Karolinska), we have investigated the phylogeny of Glutathione Peroxydase 6 (GPX6) and evaluated the effect of Cys/Sec variants in the loss/gain of its peroxidase activity and glutathione binding. In this poster, Nayanika presents her PhD project (cosupervised by Prof. Vijay Baladhye, Savitribai Phule Pune University) on the evaluation of the enzymatic activity of the protein in relation to its evolutionary history, grounded by the recent paper, that also included our former member Martin Floor. The presentation took place during the 1st meeting on Theoretical and Computational Chemistry by the Catalan Chemistry Society. Exciting PhD project ahead!