Biology subjects

Marana, S. R.

Publications and source records attributed to Marana, S. R..

7 recordsLinked to original sources

bioRxiv2026

Semantic networks as a tool for analyzing conceptual organization in active teaching methodologies in Microbiology

Active teaching methodologies have been widely used to promote meaningful learning and student autonomy. In this context, quantitative approaches can help assess how students organize and integrate knowledge throughout the learning process. Among these approaches, semantic co-occurrence networks stand out, as they are capable of identifying relationships between words and revealing the conceptual structure of textual productions. The objective of this study was to investigate whether semantic network analyses can characterize differences in students conceptual organization in Microbiology during their participation in the active teaching methodology "Adopt a Bacterium." To this end, a case study was conducted in the Bacteriology course at the Institute of Biomedical Sciences of the University of Sao Paulo, analyzing the textual productions of two groups of students in the years 2024 and 2025 during their study of the bacterial genus Bacillus. The texts were evaluated using semantic co-occurrence networks, taking into account metrics of structure and conceptual integration. The results showed that both groups covered the microbiological content outlined in the course, though with different thematic focuses and approaches to integrating the concepts. Although both years featured modular structures (a statistical mode of 9 subgraphs), in 2025 the network exhibited greater discursive robustness (2 to 4 times more words with high Betweenness centrality) than in 2024. It is concluded that semantic network analysis allows for the characterization of differences in conceptual organization among students using active learning methodologies, serving as a complementary tool for assessing meaningful learning in Microbiology.

scientific communication and education↗

bioRxiv2025

A general model for analysis of linear and hyperbolic enzyme inhibition mechanisms

The mechanisms of reversible inhibitors with a single binding site on enzymes are usually divided into basic groups: linear and hyperbolic, also called partial. Each of them subdivided into types: competitive, non-competitive and mixed. These six mechanisms are often considered separate identities. Here, prompted by the characterization of the inhibition of the wild-type and mutant {beta}-glucosidase Sf{beta}gly by Imidazole and Tris (2-amino-2-(hydroxymethyl)-1,3-propanediol) we developed a unifying enzyme kinetic model that integrates these six basic inhibition mechanism onto a single one. From this model we deduced a general enzyme kinetic equation that through modulation of simple parameters, i.e. the relative inhibitor affinity for two binding sites and the reactivity of the enzyme-substrate-inhibitor complex, is converted into the particular kinetic equation of each of those six inhibition mechanism. In short, we conclude that six fundamental inhibition mechanisms, linear and hyperbolic, are not isolate compartments, but actually facets of the same general model here presented.

biochemistry↗

bioRxiv2025

Impact of changes in buffer ionic concentration and mutations on a GH1 β-Glucosidase homodimer

Oligomerization is a key feature of protein function, with approximately 30% of proteins exhibiting this trait. The homodimeric form of proteins, such as the GH1 {beta}-Glucosidase from Spodoptera frugiperda (Sf{beta}gly), plays a significant role in enzyme activity. In this study, we investigate the homodimerization of Sf{beta}gly, which forms a cyclic C2 dimer with a well-defined interface. Using size exclusion chromatography and SEC-MALS, we characterized the homodimerization behavior of Sf{beta}gly at equilibrium conditions in different ionic concentrations of phosphate buffer. The dissociation constants (KD) increase with decreasing ionic concentration, suggesting that the hydrophobic effect is central to homodimer formation. Site-directed mutagenesis of key residues at the dimer interface further elucidated the contributions of specific amino acid residues to dimer stability. Mutations affecting both, apolar and hydrogen bond-forming residues, significantly increased the KD. However, mutations of hydrogen bond-forming residues caused a smaller KD change than apolar residue mutations, suggesting that while the latter is the driving factor in the dimerization, the former may play a crucial role in guiding the monomers relative orientation. These findings enhance our understanding of protein oligomerization in GH1 {beta}-Glucosidases and its implications for protein design and function.

biochemistry↗

bioRxiv2024

Tris inhibits a GH1 β-glucosidase by a linear mixed inhibition mechanism

Here we demonstrate that Tris (2-amino-2-(hydroxymethyl)-1,3-propanediol), largely used as buffering agent, is a linear mixed inhibitor (Ki = 12 {+/-} 2 mM and = 3 {+/-} 1) of the GH1 {beta}-glucosidase from the insect Spodoptera frugiperda (Sf{beta}gly). Such inhibition mechanism implies in the formation of a non-productive ESI complex involving Sf{beta}gly, substrate and Tris. In addition, Tris binding reduces by 3 fold the enzyme affinity for the substrate. Hence, at concentrations higher than the Ki, Tris can completely abolish Sf{beta}gly activity, whereas even at lower concentrations the presence of Tris causes underestimation of {beta}-glucosidase kinetic parameters (Km and kcat). In agreement to the inhibition mechanism, computational docking showed that Tris could bind to a pocket placed at the lateral of the active site opening in the Sf{beta}gly-substrate complex, hence leading to the formation of a ESI complex. Computational docking also showed that Tris may find binding spots in the interior of the active site of the Sf{beta}gly and several GH1 {beta}-glucosidases. Moreover, the variety of their active site shapes results in a multiplicity of binding profiles, foreseeing different inhibition mechanism. Thus, Tris inhibition is probably common among GH1 {beta}-glucosidases. This remark should be taken into account in their study, highlighting the importance of the appropriate buffer for accurate enzyme characterization.

biochemistry↗

bioRxiv2020

Molecular and functional basis of a novel Amazonian Dark Earth Esterase 1 (Ade1) with hysteresis behavior and quorum-quenching activity

Amazon Dark Earth (ADE) soil is rich in organic compounds and its fertility has been associated with a high diversity of microorganisms. Herein, we investigate the biochemical and functional features of a novel esterase, Ade1, obtained from a metagenomic library of Amazonian Dark Earth soils of the Amazonian Rainforest, in Brazil. The esterases cleave ester bonds to form a carboxylic and an alcohol group. Esterases and lipases are enzymes found in almost all living organisms, demonstrating their biological relevance. We reported that Ade1 belongs to an /{beta}-hydrolase superfamily. We suggest that Ade1 is a moonlighting enzyme with hysteresis behavior and quorum-quenching activity, which may play a key role in the metabolism of a Gram-negative proteobacteria. In addition, molecular dynamics simulations reveal that the hysteresis behavior is directly associated with structural properties of the cap domain. Our findings reveal details of the molecular basis, catalytic and structural mechanisms of a novel /{beta}-hydrolase, which may be applied to other esterases of biotechnological, food, and/or pharmaceutical interest. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biochemistry↗

bioRxiv2020

Molecular dynamics reveals complex compensatory effects of ionic strength on the SARS-CoV-2 Spike/hACE-2 interaction

The SARS-CoV-2 pandemic has already killed more than 800,000 people worldwide. To gain entry, the virus uses its spike protein to bind to host hACE-2 receptors on the host cell surface and mediate fusion between viral and cell membranes. As initial steps leading to virus entry involves significant changes in protein conformation as well as in the electrostatic environment in the vicinity of the spike-hACE-2 complex, we explored the sensitivity of the interaction to changes in ionic strength through computational simulations and surface plasmon resonance. We identified two regions in the receptor-binding domain (RBD), E1 and E2, which interact differently with hACE-2. At high salt concentration, E2-mediated interactions are weakened but are compensated by strengthening E1-mediated hydrophobic interactions. These results provide a detailed molecular understanding of spike RBD/hACE-2 complex formation and stability under a wide range of ionic strengths. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/267351v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1a7dc02org.highwire.dtl.DTLVardef@15d3c78org.highwire.dtl.DTLVardef@2d09c1org.highwire.dtl.DTLVardef@db78a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

Combining free energy simulations and NMR chemical-shift perturbation to identify transient cation-π contacts in proteins

Flexible protein regions containing cationic and aromatic side-chains exposed to solvent may form transient cation-{pi} interactions with structural and functional roles. To evaluate their stability and identify important intramolecular cation-{pi} contacts, a combination of free energy profiles estimated from umbrella sampling with molecular dynamics simulations and chemical shift perturbations (CSP) obtained from NMR experiments is applied here to the complete catalytic domain of human phosphatase Cdc25B. This protein is a good model system for transient cation-{pi} interactions as it contains only one Trp residue (W550) in the disordered C-terminal segment and a total of 17 Arg residues, many exposed to solvent. Eight putative Arg-Trp pairs were simulated here. Only R482 and R544 show bound profiles corresponding to important transient cation-{pi} interactions, while the others have dissociative or almost flat profiles. These results are corroborated by CSP analysis of three Cdc25B point mutants (W550A, R482A and R544A) disrupting cation-{pi} contacts. The proposed validation of statistically representative molecular simulations by NMR spectroscopy could be applied to identify transient contacts of proteins in general but carefully, as NMR chemical shifts are sensitive to changes in both molecular contacts and conformational distributions.

biophysics↗