Biology subjects

Rodrigues, J. A.

Publications and source records attributed to Rodrigues, J. A..

3 recordsLinked to original sources

bioRxiv2023

Allosteric site variants affect GTP hydrolysis on RAS

AbstractRAS GTPases are proto-oncoproteins that regulate cell growth, proliferation, and differentiation in response to extracellular signals. The signaling functions of RAS, and other small GTPases, are dependent on their ability to cycle between GDP-bound and GTP-bound states. Structural analyses suggest that GTP hydrolysis catalyzed by HRAS can be regulated by an allosteric site located between helices 3, 4 and loop 7. Here we explore the relationship between intrinsic GTP hydrolysis on HRAS and the position of helix 3 and loop 7 through manipulation of the allosteric site, showing that the two sites are functionally connected. We generated several hydrophobic mutations in the allosteric site of HRAS to promote shifts in helix 3 relative to helix 4. By combining crystallography and enzymology to study these mutants, we show that closure of the allosteric site correlates with increased hydrolysis of GTP on HRAS in solution. Interestingly, binding to the RAS binding domain of RAF kinase (RAF-RBD) inhibits GTP hydrolysis in the mutants. This behavior may be representative of a cluster of poorly understood mutations that occur in human tumors, which potentially cooperate with RAF complex formation to stabilize the GTP-bound state of RAS.

biochemistry↗

bioRxiv2020

Double-layer flexible neuronal probe with closely spaced electrodes for high-density in vivo brain recordings

Flexible probes for brain activity recordings are an attractive emerging approach that reduces mechanical mismatch between probe and neuronal tissue, thus minimizing the risk of brain damage or glial scaring. Although promising, flexible probes still present some technical challenges namely: i) how to overcome probe buckling during brain insertion given its intrinsically low mechanical rigidity; ii) how to fabricate closely spaced electrode configurations for high density recordings by standard lithography techniques in the flexible substrate. Here, we present a new flexible probe based solely on standard and low-cost lithography processes, which has closely spaced 10 m diameter gold electrode sites on a polyimide substrate with inter-site distances of only 5 m. By using a double-layer design and fabrication approach we were able to accommodate closely spaced electrode sites at two different depths from probe surface while also providing additional stiffening, just sufficient to prevent probe buckling during brain insertion. Detailed probe characterization through metrology of structural and electrical properties and chemical composition analysis, as well as functional assessment through in vivo high-density recordings of neuronal activity in the mouse cortex, confirmed the viability of this new fabrication approach and that this probe can be used for obtaining high quality brain recordings with excellent signal-to-noise ratio (SNR).

bioengineering↗

bioRxiv2020

N6-methyladenosine in poly(A) tails stabilize VSG transcripts

RNA modifications are important regulators of gene expression. In Trypanosoma brucei, transcription is polycistronic and thus most regulation happens post-transcriptionally. N6-methyladenosine (m6A) has been detected in this parasite, but its function remains unknown. Here we show that [~]50% of the m6A is located in the poly(A) tail of the monoallelically expressed Variant Surface Glycoprotein (VSG) transcript. m6A residues are removed from the VSG poly(A) tail prior to deadenylation and mRNA degradation. Using genetic tools, we identified a 16-mer motif in the 3UTR of VSG that acts as a cis-acting motif required for inclusion of m6A in the poly(A) tail. Removal of this motif from the VSG 3 UTR results in poly(A) tails lacking m6A, rapid deadenylation and mRNA degradation. To our knowledge this is the first identification of an RNA modification in the poly(A) tail of any eukaryote, uncovering a novel post-transcriptional mechanism of gene regulation.

molecular biology↗