Biology subjects

SERRA, E.

Publications and source records attributed to SERRA, E..

3 recordsLinked to original sources

bioRxiv2026

Proteomic mapping of novel tubulin post-translational modifications in Trypanosoma cruzi cytoskeleton

Microtubules (MTs) play central roles in the organization and morphology of trypanosomatid parasites, forming highly specialized cytoskeletal structures such as the subpellicular corset, the flagellar axoneme, and the mitotic spindle. Functional specialization of MTs is regulated by the "tubulin code", which is defined by the combination of different - and {beta}-tubulin isotypes, a set of post-translational modifications (PTMs) and specific MT-binding proteins. Although multiple tubulin PTMs have been described in trypanosomatids using specific antibodies or mass spectrometry, to date no comprehensive mapping has been reported in Trypanosoma cruzi, the causative agent of Chagas Disease. In the present work, we performed a high-resolution proteomic analysis of PTMs present in - and {beta}-tubulin subunits of the T. cruzi Dm28c strain, using tubulin-enriched extracts obtained by in vitro polymerization. Multiple PTMs were identified, including acetylation, methylation, phosphorylation, and polyglutamylation, for which many modified amino acids had not been previously reported in trypanosomatids. Structural mapping of these modifications onto a predicted /{beta}-tubulin heterodimer showed that most modified residues are located in solvent-exposed regions of the protein. Together, these findings provide the first systematic map of tubulin PTMs in T. cruzi and support the existence of a complex tubulin code contributing to microtubule regulation in this parasite.

cell biology↗

bioRxiv2025

Context-Dependent Protein Structure Prediction Analysis and Stoichiometry Inference with MultimerMapper

Advances in artificial intelligence (AI) have transformed the field of protein structure, notably with the accuracy level reached by AlphaFold in the prediction of monomeric and multimeric protein structures. However, while cloud implementations have broadened access to these methods, there is still a lack of non-AI tools to systematically interpret and analyze the resulting data, especially under varying modeling contexts. Here, we present MultimerMapper, a pipeline and software suite designed to extract, integrate, analyze, and visualize the behavior of multimeric systems in ensembles of overlapping protein structure predictions. It utilizes statistics and graph theory, combined with novel approaches, to interpret how protein-protein interfaces and protein conformation behave across different modeling contexts. Starting from a list of input sequences, MultimerMapper guides users through the generation and interpretation of structure prediction ensembles. It produces interactive 2D and 3D visualizations, highlights higher-order subassemblies, infers probable stoichiometries, and identifies alternative interaction modes and conformational changes associated with the presence or absence of specific proteins. MultimerMapper is cross-platform, freely available, and easily integrates with existing workflows. It offers a new perspective on the dynamic nature of predicted protein complexes, supporting researchers in the exploration of functional mechanisms and assembly paths.

bioinformatics↗

bioRxiv2022

Deciphering divergent trypanosomatid nuclear complexes by analyzing interactomic datasets with AlphaFold2 and genetic approaches

Acetylation signaling pathways in trypanosomatids, a group of early branching organisms, are poorly understood due to highly divergent protein sequences. To overcome this challenge, we used interactomic datasets and AlphaFold2-multimer to predict direct interactions and validated them using yeast two and three-hybrid assays. We focused on MRG domain-containing proteins and their interactions, typically found in histone acetyltransferase/deacetylase complexes. The results identified a structurally conserved complex, TcTINTIN, which is orthologous to human and yeast TINTIN complexes; and another trimeric complex involving an MRG domain, only seen in trypanosomatids. The identification of a key component of TcTINTIN, TcMRGBP, would not have been possible through traditional homology-based methods. We also conducted molecular dynamics simulations, revealing a conformational change that potentially affects its affinity for TcBDF6. The study also revealed a novel way in which an MRG domain participates in simultaneous interactions with two MRG binding proteins binding two different surfaces, a phenomenon not previously reported. Overall, this study demonstrates the potential of using AlphaFold2-processed interactomic datasets to identify protein complexes in deeply branched eukaryotes, which can be challenging to study based on sequence similarity. The findings provide new insights into the acetylation signaling pathways in trypanosomatids, specifically highlighting the importance of MRG domain-containing proteins in forming complexes, which may have important implications for understanding the biology of these organisms and developing new therapeutics. On the other hand, our validation of AlphaFold2 models for the determination of multiprotein complexes illuminates the power of using such artificial intelligence-derived tools in the future development of biology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/516520v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@16e7750org.highwire.dtl.DTLVardef@15b3b76org.highwire.dtl.DTLVardef@9cf1e9org.highwire.dtl.DTLVardef@1ce0ee0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗