Biology subjects

Pajkos, M.

Publications and source records attributed to Pajkos, M..

5 recordsLinked to original sources

bioRxiv2026

Generative design of intrinsically disordered proteins based on conditioned protein language models: Data is the limit

Intrinsically disordered proteins and regions (IDRs) are central to a multitude of biological processes. Despite extensive studies of their structural and physicochemical properties, the rational design of IDRs with defined conformational behavior remains challenging due to their ensemble nature. Here we present a generative framework for designing disordered protein sequences conditioned on target conformational ensemble descriptors using protein language models (pLMs). We formulate IDR design as the task of generating amino acid sequences predicted to realize specified biophysical properties and implement a Transformer encoder-decoder architecture that maps numerical descriptors to protein sequences. By training models on datasets spanning two orders of magnitude in size, we show that accurate control of conformational and physicochemical properties is achieved only at large data scale. These results demonstrate the feasibility of conditioning generative models on ensemble-level descriptors for IDR design. More broadly, these results support a data-centric paradigm for protein engineering, in which data availability emerges as a key limiting factor for the accurate design of IDRs.

bioinformatics↗

bioRxiv2026

Conformational ensembles of flexible multidomain proteins: How close are we to accurate and reliable predictions?

Multidomain proteins connected by flexible linkers populate conformational ensembles that are challenging to characterize using conventional structural biology methods. In domain-linker-domain (DLD) proteins, linker-mediated inter-domain relative positions and orientations are functionally relevant, yet their dynamical behavior in solution normally remain poorly described. Small-angle X-ray scattering (SAXS) provides ensemble-averaged structural information for such systems; however, coupling with computational modeling is required to accurately describe the dynamic behavior of this family of proteins in solution. Here, we present a systematic evaluation of five ensemble-generation strategies applied to a set of eighteen proteins sharing the same two globular domains, connected by naturally occurring linkers of varying length and composition. Modeling methods based on different underlying principles are compared by assessing their agreement to experimental SAXS data, showing a large disparity and systematic structural biases among them. Furthermore, for each approach, we examine the effect of refinement against SAXS restraints and assess its capacity to describe the experimental data, as well as the induced biases in global dimensions and inter-domain distance distributions. This analysis underlines the importance of the initial conformational pool for deriving experimentally compatible ensembles. Overall, this work provides a high-quality benchmark for SAXS-driven ensemble modeling of flexible, multidomain proteins and establishes a framework for the critical interpretation of solution scattering data in systems with pronounced conformational heterogeneity.

biophysics↗

bioRxiv2023

Entering new circles: Expansion of the LC8/DYNLL1 interactome in the ciliary-centrosomal network through system-driven motif evolution

LC8 is a eukaryotic hub protein that presents a highly conserved interface recognized by short linear motifs (SLiMs) in partner proteins. LC8 was originally associated with the dynein motor complex and was also suggested to promote dimerization of partner proteins. However, the growing list of validated partners with diverse functions suggests that LC8 plays a more general cellular role which is still not fully understood. In this work, we combined computational and experimental approaches in order to gain insights into the LC8 interaction network at the system level. Our machine-learning based pipeline together with functional enrichment analysis revealed that LC8 plays a central role in the ciliary-centrosomal system with several partners involved in various types of ciliopathies. By integrating proteomic data and functional annotations, we identified a high confidence, ciliary-centrosomal specific LC8 partner list of 57 proteins, 15 of which are central to centriole life-cycle organization. Validated binding motifs and the detailed characterization of the interaction with protein OFD1 emphasized the important role of LC8, which was confirmed by confocal microscopy. OFD1, which is a central player in this system, also stood out as an early and highly conserved LC8 partner. However, additional partners showed a more recent evolutionary origin featuring novel proteins as well as novel motifs. Altogether, our results highlight that LC8 plays a major role in the ciliary-centrosomal system and its interaction network underwent a major expansion. This system driven motif evolution contributed to the increased complexity of the organization and regulation of the ciliary-centrosomal system.

molecular biology↗

bioRxiv2022

Pipeline for transferring annotations between proteins beyond globular domains

BackgroundDisProt is the primary repository of Intrinsically Disordered Proteins. This database is manually curated and the annotations there have strong experimental support. Currently DisProt contains a relatively small number of proteins highlighting the importance of transferring verified disorder and other annotations, in such a way as to increase the number of proteins that could benefit from this valuable information. While the principles and practicalities of homology transfer are well-established for globular proteins, these are largely lacking for disordered proteins. MethodsWe used DisProt to evaluate the transferability of the annotation terms to orthologous proteins. For each protein, we looked for their orthologs, with the assumption that they will have a similar function. Then, for each protein and their orthologs we made multiple sequence alignments (MSAs). Global and regional quality of the MSAs was evaluated with the NorMD score. ResultsWe have designed a pipeline to obtain good quality MSAs and to transfer annotations from any protein to their orthologs. Applying the pipeline to DisProt proteins, from the 1931 entries with 5,623 annotations we can reach 97,555 orthologs and transfer a total of 301,190 terms by homology. We also provide a web server for consulting the results of DisProt proteins and execute the pipeline for any other protein. The server Homology Transfer IDP (HoTIDP) is accessible at http://hotidp.leloir.org.ar.

bioinformatics↗

bioRxiv2020

Ancient evolutionary origin of intrinsically disordered cancer risk regions

Cancer is a heterogeneous genetic disease that alters the proper functioning of proteins involved in key regulatory processes such as cell cycle, DNA repair, survival or apoptosis. Mutations often accumulate in hot-spots regions, highlighting critical functional modules within these proteins that need to be altered, amplified or abolished for tumor formation. Recent evidence suggests that these mutational hotspots can not only correspond to globular domains but also to intrinsically disordered regions (IDRs), which play a significant role in a subset of cancer types. IDRs have distinct functional properties that originate from their inherent flexibility. Generally, they correspond to more recent evolutionary inventions and show larger sequence variations across species. In this work we analyzed the evolutionary origin of disordered regions that are specifically targeted in cancer. Surprisingly, the majority of these disordered cancer risk regions showed remarkable conservation with ancient evolutionary origin, stemming from the earliest multicellular animals or even beyond. Nevertheless, we encountered several examples, where the mutated region emerged at a later stage compared to the origin of the gene family. We also showed the cancer risk regions become quickly fixated after their emergence, but evolution continues to tinker with their genes with novel regulatory elements introduced even at the level of humans. Our concise analysis provides a much clearer picture of the emergence of key regulatory elements in proteins and highlights the importance of taking into account the modular organisation of proteins for the analyses of evolutionary origin.

bioinformatics↗