Biology subjects

Santa, A.

Publications and source records attributed to Santa, A..

3 recordsLinked to original sources

bioRxiv2025

Redistribution of sidechain-sidechain interactions govern ligand-specific binding affinity changes in missense Shank1 PDZ mutants

Shank proteins represent a family of abundant scaffolds in the postsynaptic density. Their dysfunctions had been identified as possible causes behind autism spectrum disorders and various types of cancer. The remarkably promiscuous PDZ domain of the Shank family is highly conserved through isoforms, and contains a unique dynamic segment, the {beta}2-{beta}3 loop, located close to the binding site. We used the Shank1 PDZ as a model system to analyze the perturbing effects of five disease-associated missense mutations on the binding of different partner peptides. Using experimental methods and molecular dynamics simulations, we characterized the interactions in detail, focusing on their dynamic aspect. While the investigated variants in general weaken most interactions, the R736Q variant, unique in having increased thermal stability, also binds the GKAP peptide with higher affinity than the wild type. Overall, our results show that the perturbing effect of mutations is highly partner-specific and depends on the dynamic rearrangements of both uniformly occurring and ligand-specific residue-residue interactions.

molecular biology↗

bioRxiv2023

Patterned Metal Grids for Flexible and Transparent Neural Microelectrode Arrays

Flexible and transparent microelectrodes can provide large-scale neural recordings with temporal and spatial resolution when used alongside functional calcium imaging. Patterned metal grids defined by direct laser writing (DWL) are a promising approach for these electrodes, as they resort to standard microfabrication processes and materials, allowing the possibility of mass production. For these reasons, a study exploring transparent grid-based electrodes using DWL for measuring electrocorticography signal was performed. Patterned metal grids with 1 m of linewidth and 22 m of spacing between lines showed a sheet resistance of 6 {Omega}/sq and a transmittance of 81% at 550 nm. The grids were transferred to a 5 m Parylene-C membrane using an optimized procedure that involves an oxygen plasma pre-treatment. This procedure ensures mechanical robustness and stability of the grids. Finally, a flexible and transparent prototype was fabricated with a microelectrode array composed by 16 electrodes with 500 m of diameter. These microelectrodes shown an impedance of 10 k{Omega} at 1 kHz in saline solution and they are highly conformal facilitating in vivo implantation and the recording of neural activity in the mouse cerebellum surface. To conclude, patterned metal grids based-electrodes exhibit a promising performance compared to transparent conductive oxides or graphene. Moreover, the introduction of DLW enables easy and fast manipulation of grid shape and dimensions without the need of physical masks, while keeping large scale compatibility, which is important for tools used in neuroscience community.

neuroscience↗

bioRxiv2021

Charged sequence motifs increase affinity towards liquid-liquid phase separation

Protein phase separation is a major governing factor in multiple cellular processes, such as those concerning RNA metabolism and RNA-binding proteins. Despite many key observations, the exact structural characteristics of proteins involved in the process are still not fully deciphered. In this work we show that proteins harbouring sequence regions with specific charged residue patterns are significantly associated with liquid-liquid phase separation. In particular, regions with repetitive arrays of alternating charges show the strongest association, whereas segments with generally high charge density and single -helices also show detectable but weaker connections.

bioinformatics↗