Biology subjects

Correa-Basurto, J.

Publications and source records attributed to Correa-Basurto, J..

5 recordsLinked to original sources

bioRxiv2026

Stenotrophomonas oleivorans sp. nov. A polycyclic aromatic hydrocarbon-degrading strain isolated from crude oil contaminated soil

ASS1 was isolated as a motile Stenotrophomonas strain from crude oil-contaminated soils in Tabasco, Mexico. We characterized this strain using physiological and biochemical traits. ASS1 grew at temperature 25-37 (optimally at 37 {degrees} C) and at pH 6 to 8 (optimally at pH 7 to 8). The assembled genome has a total length of 4.56MB with a G + C content of 66.6%. The 16S rRNA gene sequence analysis confirmed that this strain belongs to the genus Stenotrophomonas. Based on the 16S rRNA analysis, Stenotrophomonas geniculata ATCC 19374 is the closest species, and it shares 99.86% similarity with ASS1. Similarly, a phylogenomic tree based on core genome sequence revealed that the closest species to ASS1 is Stenotrophomonas geniculata ATCC 19374. The major fatty acids in ASS1 are C16:0, antesio C15:0, iso C12:0, iso C15:0, iso C17:0 and C18:0. The genome of ASS1 consists of 4,373,402 bp. The Average Nucleotide Identity (ANI) values for ASS1 which it shared with its closest phylogenetic neighbors, are Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] 92.66 %, Stenotrophomonas maltophilia 13637[T] 92.15%, Stenotrophomonas maltophilia K279a 92.13% Stenotrophomonas maltophilia R551-3 92.15% Stenotrophomonas maltophilia MTCC 434 [T] 92.08% and Pseudomonas hibisicicola ATCC [T] 91.66%. ASS1 possesses genes that are essential for the degradation of Polycyclic Aromatic hydrocarbon. Genes such as 1, 2 dihydroxyl 1, 2 dihydronaphthalene dehydrogenase; MG068 17425, homologous to 2 hydroxyl chromene 2 carboxylate isomerases; MG 18055, homologous to salicylaldehyde dehydrogenase and MG068 20095, homologous to naphthalene 1, 2 dioxygenases were identified in ASS1. The dDDH value between ASS1 and its closest neighbor Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] is 50%, which is the highest for all the typed species and as such we proposed that ASS1 is a novel species with the name Stenotrophomonas oleivorans sp. nov. sp. nov. and ASS1T as the typed strain

microbiology↗

bioRxiv2025

Antidepressants interact with an LPA3 receptor binding site: functional and docking studies

The action of the antidepressants imipramine, amitriptyline, and paroxetine on LPA3 receptors was studied in cellulo, using receptor-transfected HEK 293 Flp-In TREx cells, and in silico, through docking simulations. These drugs showed a low affinity for LPA3 receptors with lesser efficacy than LPA (paroxetine {approx} 60% and imipramine and amitriptyline {approx} 30%). When LPA-treated cells (with the agonist present) were challenged with the antidepressants, paroxetine triggered a robust increase in intracellular calcium, whereas imipramine and amitriptyline decreased the calcium concentration below baseline values. For ERK 1/2 phosphorylation, imipramine induced a rapid and potent increase, whereas amitriptyline and paroxetine reduced ERK 1/2 phosphorylation below baseline. Similarly, imipramine produced rapid and robust ERK phosphorylation in LPA-stimulated cells, but amitriptyline decreased ERK 1/2 phosphorylation. Activation with the antidepressants leads to LPA3 internalization; dramatic morphological changes accompany these actions. Docking simulations showed these drugs interact with an LPA3 receptor pocket, denominated Upper Cavity. Although the agonist binding cavity was the same, the amino acids interacting with the various ligands were distinct due to their different chemical structure. The manuscript advances knowledge on the mechanisms of antidepressant effects on LPA3 receptors, which might have potential therapeutic implications.

pharmacology and toxicology↗

bioRxiv2024

LPA3 receptors have orthosteric and allosteric binding sites evidenced under docking studies.

Comparative studies using (lysophosphatidic acid) LPA and the synthetic agonist, oleoyl-methoxy glycerophosphothionate, OMPT, in cells expressing the LPA3 receptor revealed differences in the action of these agents. The possibility that more than one recognition cavity might exist for these ligands in the LPA3 receptor was considered. We performed agonist docking studies exploring the whole protein to obtain tridimensional details of the ligand-receptor interaction. Functional in-cellulo experiments using mutants were also executed. Our work includes blind docking using the unrefined and refined proteins subjected to hot spot predictions. Distinct ligand protonation (charge-1 and-2) states were evaluated. One LPA recognition cavity is located near the lower surface of the receptor close to the cytoplasm (Lower Cavity). OMPT displayed an affinity for an additional identification cavity detected in the transmembrane and extracellular regions (Upper Cavity). Docking targeted to Trp102 favored binding of both ligands in the transmembrane domain near the extracellular areas (Upper Cavity), but the associating amino acids were not identical due to close sub-cavities. In the in-cellulo studies, LPA action was much less affected by the distinct mutations than that of OMPT (which was almost abolished). Docking and functional data suggest distinct agonist binding cavities in the LPA3 receptor

biochemistry↗

bioRxiv2022

Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide

New therapies that allow natural healing processes are required. Such as the endogenous peptide called Angiotensin-(1-7), a safe and eff e drug, which is able to re-balance the Renin-Angiotensin system affected during several pathologies, including the new COVID-19; cardiovascular, renal, and pulmonary disease; diabetes; neuropathic pain; Alzheimer and cancer. However, one of the limiting factors for its application is its unfavorable pharmacokinetic profile. In this work, we propose the coupling of Angiotensin-(1-7) to PAMAM dendrimers in order to evaluate the capacity of the nanocarrier to improve isolated peptide features and to gain insight into the structural as well as the energetic basis of its molecular binding. The In Silico tests were performed in acidic and neutral pH conditions as well as amino-terminated and hydroxyl-terminated PAMAM dendrimers. High-rigor computational approaches, such as molecular dynamics and metadynamics simulations were used. We found that, at neutral pH, PAMAM dendrimers with both terminal types are able to interact stably with 3 Angioteinsin-(1-7) peptides through ASP1, TYR4 and PRO7 key aminoacids, however, there are some differences in the binding sites of the peptides. In general, they bind on the surface in the case of the hydroxyl-terminated compact dendrimer and in the internal zone in the case of the amino-terminated open dendrimer. At acidic pH, PAMAM dendrimers with both terminal groups are still able to interact with peptides either internalized or in its periphery, however, the number of contacts, the percentage of coverage and the number of HBs are lesser than at neutral pH, suggesting a state for peptide release. In summary, amino-terminated PAMAM dendrimer showed slightly better features to bind, load and protect Angiotensin-(1-7) peptides.

biophysics↗

bioRxiv2019

Multidimensional analysis of extended molecular dynamics simulations shows the complexity of signal transduction by the histamine H3 membrane receptor

In this work, we study the mechanisms of classical activation and inactivation of signal transduction by the histamine H3 receptor, a 7-helix transmembrane bundle G-Protein Coupled Receptor through long-time-scale molecular dynamics simulations of the receptor embedded in a hydrated double layer of dipalmitoyl phosphatidyl choline, a zwitterionic poly-saturated ordered lipid. Three systems were prepared: the apo receptor, representing the constitutively active receptor; and two holo-receptors -the receptor coupled to the antagonist/inverse agonist ciproxifan and representing the inactive state of the receptor, and the receptor coupled to the endogenous agonist histamine and representing the active state of the receptor. An extensive analysis of the simulation shows that the three states of H3R present significant structural and dynamical differences, as well as a complex behavior given that the measured properties interact in multiple and inter-dependent ways. In addition, the simulations describe an unexpected escape of histamine from the orthosteric binding site, in agreement with the experimental modest affinities and rapid off-rates of agonists.

bioinformatics↗