Biology subjects

Carazo, J.-M.

Publications and source records attributed to Carazo, J.-M..

5 recordsLinked to original sources

bioRxiv2026

AlignPCA-2D: PCA-Reduced Euclidean Vector Alignment for 2D Classification in Cryo-EM

Cryogenic Electron Microscopy (cryo-EM) has transformed structural biology by enabling high-resolution reconstruction of macromolecular complexes from noisy projection images. However, the intrinsic heterogeneity and low signal-to-noise ratio of cryo-EM datasets make 2D classification a critical and computationally demanding step in the processing work-flow. Here, we introduce AlignPCA-2D, a PCA-space Euclidean vector alignment method for fast, interpretable 2D classification in cryo-EM. By projecting particle images and class representations into a compressed latent PCA space, AlignPCA-2D reduces data dimensionality while pre-serving meaningful structural variability. The image-to-class assignment is then performed using Euclidean distance, enabling efficient and accurate classification. We benchmark AlignPCA-2D against established cryo-EM software, such as RELION and cryoSPARC, and demonstrate that it achieves competitive alignment accuracy while substantially reducing computational cost. This approach provides a lightweight alternative for large-scale 2D classification tasks, and its modular design makes it compatible with existing cryo-EM processing pipelines. O_TBL View this table: org.highwire.dtl.DTLVardef@1e384org.highwire.dtl.DTLVardef@2474org.highwire.dtl.DTLVardef@15966c1org.highwire.dtl.DTLVardef@6934adorg.highwire.dtl.DTLVardef@1017b4e_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2.C_FLOATNO O_TABLECAPTIONParticle retention and overlap among 2D classification methods C_TABLECAPTION C_TBL

biophysics↗

bioRxiv2025

Insights from aquaporin structures into drug-resistant sleeping sickness

Trypanosoma brucei is the causal agent of African trypanosomiasis in humans and animals, the latter resulting in significant negative economic impacts in afflicted areas of the world. Resistance has arisen to the trypanocidal drugs pentamidine and melarsoprol through mutations in the aquaglyceroporin TbAQP2 that prevent their uptake. Here we use cryogenic electron microscopy to determine the structure of TbAQP2 from Trypanosoma brucei, bound to either the substrate glycerol or to the sleeping sickness drugs, pentamidine or melarsoprol. The drugs bind within the AQP2 channel at a site completely overlapping that of glycerol. Mutations leading to a drug-resistant phenotype were found in the channel lining. Molecular dynamics simulations showed the channel can be traversed by pentamidine, with a low energy binding site at the centre of the channel, flanked by regions of high energy association at the extracellular and intracellular ends. Drug-resistant TbAQP2 mutants are still predicted to bind pentamidine, but the much weaker binding in the centre of the channel observed in the MD simulations would be insufficient to compensate for the high energy processes of ingress and egress, hence impairing transport at pharmacologically relevant concentrations. The structures of drug-bound TbAQP2 represent a novel paradigm for drug-transporter interactions that could provide new mechanisms for targeting drugs into pathogens and human cells.

molecular biology↗

bioRxiv2022

A fijivirus major viroplasm protein shows RNA-stimulated ATPase activity by adopting pentameric and hexameric assemblies of dimers

The fijivirus Mal de Rio Cuarto virus (MRCV) causes a devastating maize disease. Its non-structural protein P9-1, which shows ATPase and RNA binding activities, is the major component of the intracellular viroplasm where virus replication takes place. Here, we established that the 24 C-terminal residues (C-arm) of P9-1 are required for the formation of viroplasm-like structures (VLS) in vivo and for the protein multimerization in vitro. Employing an integrative structural approach, we found that the C-arm is dispensable for P9-1 dimer assembly, but essential for the formation of doughnut-shaped pentamers and hexamers of dimers (decamers and dodecamers). Both assemblies, larger than those reported for other reoviruses, contain disordered loops oriented towards the inner pore of the structures, where RNA binding sites and conditional proteasome-mediated degradation signals (PEST) were predicted. In vitro assays demonstrated that ssRNA binding is favored towards P9-1 (do)decamers over the dimeric {Delta}C-arm version. In addition, although both P9-1 and P9-1{Delta}C-arm catalyze the hydrolysis of ATP with similar activity values, an RNA-stimulated ATPase activity was only observed in the full-length protein, indicating a C-arm-mediated interaction between the ATP catalytic site and the allosteric RNA binding sites in the (do)decameric assemblies. Computational studies revealed a stronger preference of phosphate moieties to the decamer in the pore and the C-arm regions, suggesting that the allosteric communication between the ATP and RNA binding sites is favored with this protein arrangement. Overall, our work reveals the structural versatility of a major viroplasm protein providing unprecedented insights into fijivirus viroplasm assembly and function and establishes the structural basis for the development of antiviral strategies against the Mal de Rio Cuarto crop disease.

biochemistry↗

bioRxiv2021

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: the case of the spike A222V mutation

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has now reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.

molecular biology↗

bioRxiv2016

Quantitative analysis of 3D alignment quality: itsimpact on soft-validation, particle pruning andhomogeneity analysis

Single Particle Analysis using cryo-electron microscopy is a structural biology technique to capture the three-dimensional conformation of biological macromolecules. The projection images used to construct the 3D density map are characterized by a very low signal-to-noise ratio to minimize radiation damage in the samples. As a consequence, the 3D alignment process is a challenging and error prone task and this job usually determines the success or failure of the macromolecule reconstruction. In this work, we present a soft-alignment validation approach, which can quantify the alignment precision and accuracy as well as the data homogeneity of the single particles when they are confronted with the resultant reconstructed 3DEM map. We have also applied this method to data homogeneity analysis and particle pruning, improving the data quality and as a consequence the final map resolution.

molecular biology↗