Impact of chlorogenic acid on surface and phase properties of cholesterol-enriched phosphatidylcholine membranes.

This study analyses the insertion of Chlorogenic acid (CGA) in phosphatidylcholine (PC) membranes enriched with cholesterol (Chol). While cholesterol decreases the area per lipid and increases the dipole potential, CGA increases and decreases these values, respectively. When CGA is inserted into cholesterol-containing DMPC membranes, these effects cancel out, resulting in values that overlap with those of DMPC monolayers without Chol and CGA. The presence of CGA also compensates the increase of dipole potential produced by Chol which can be explain as a consequence of the orientation of CGA molecule at the interphase opposing the cholesterol dipole moieties and water dipoles. This compensatory effect is less effective when lipids lack carbonyl groups (CO). When monolayers are composed by unsaturated PCs the Chol compensation is found at higher concentrations of CGA due to the direct interaction between CGA and Chol. These results suggest that cholesterol modulates the interaction and distribution of CGA in the lipid membrane, which may have implications for its biological activity.

Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory.

Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood-brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale-yellow organic molecules (copigments). The present work carried out a theoretical study of the copigmentation process between cyanidin and resveratrol (CINRES). We used three levels of density functional theory: M06-2x/6-31g+(d,p) (d3bj); ωB97X-D/6-31+(d,p); APFD/6-31+(d,p), implemented in the Gaussian16W package. In a vacuum, the CINRES was found at a copigmentation distance of 3.54 Å between cyanidin and resveratrol. In water, a binding free energy ∆G was calculated, rendering -3.31, -1.68, and -6.91 kcal/mol, at M06-2x/6-31g+(d,p) (d3bj), ωB97X-D/6-31+(d,p), and APFD/6-31+(d,p) levels of theory, respectively. A time-dependent density functional theory (TD-DFT) was used to calculate the UV spectra of the complexes and then compared to its parent molecules, resulting in a lower energy gap at forming complexes. Excited states' properties were analyzed with the ωB97X-D functional. Finally, Shannon aromaticity indices were calculated and isosurfaces of non-covalent interactions were evaluated.

Repaglinide Induces ATF6 Processing and Neuroprotection in Transgenic SOD1G93A Mice.

The interaction of the activating transcription factor 6 (ATF6), a key effector of the unfolded protein response (UPR) in the endoplasmic reticulum, with the neuronal calcium sensor Downstream Regulatory Element Antagonist Modulator (DREAM) is a potential therapeutic target in neurodegeneration. Modulation of the ATF6-DREAM interaction with repaglinide (RP) induced neuroprotection in a model of Huntington's disease. Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder with no cure, characterized by the progressive loss of motoneurons resulting in muscle denervation, atrophy, paralysis, and death. The aim of this work was to investigate the potential therapeutic significance of DREAM as a target for intervention in ALS. We found that the expression of the DREAM protein was reduced in the spinal cord of SOD1G93A mice compared to wild-type littermates. RP treatment improved motor strength and reduced the expression of the ALS progression marker collagen type XIXα1 (Col19α1 mRNA) in the quadriceps muscle in SOD1G93A mice. Moreover, treated SOD1G93A mice showed reduced motoneuron loss and glial activation and increased ATF6 processing in the spinal cord. These results indicate that the modulation of the DREAM-ATF6 interaction ameliorates ALS symptoms in SOD1G93A mice.

Iron reducing sludge as a source of electroactive bacteria: assessing iron reduction in biofilm bacteria, planktonic cells and isolates from a microbial fuel cell.

In this study, bacteria from a microbial fuel cell (MFC) and isolates were evaluated on their Fe3+ reduction capability at different concentrations of iron using acetate as the sole source of carbon. The results demonstrated that the planktonic cells can reach an iron reduction up to 60% at 27 mmol Fe3+. Azospira oryzae (µ 0.89 ± 0.27 d-1) and Cupriavidus metallidurans CH34 (µ 2.34 ± 0.81 d-1) presented 55 and 62% of Fe3+ reduction, respectively, at 16 mmol l-1. Enterobacter bugandensis (µ 0.4 ± 0.01 d-1) 40% Fe3+ at 27 mmol l-1, Citrobacter freundii ATCC 8090 (µ 0.23 ± 0.05 d-1) and Citrobacter murliniae CDC2970-59 (µ 0.34 ± 0.02 d-1) reduced Fe3+ in ~ 50%, at 55 mmol l-1. This is the first report on these bacteria on a percentage of iron reduction. These results may be useful for anode design to contribute to a higher energy generation in MFCs.

Modelling the Human Blood-Brain Barrier in Huntington Disease.

While blood-brain barrier (BBB) dysfunction has been described in neurological disorders, including Huntington's disease (HD), it is not known if endothelial cells themselves are functionally compromised when promoting BBB dysfunction. Furthermore, the underlying mechanisms of BBB dysfunction remain elusive given the limitations with mouse models and post mortem tissue to identify primary deficits. We established models of BBB and undertook a transcriptome and functional analysis of human induced pluripotent stem cell (iPSC)-derived brain-like microvascular endothelial cells (iBMEC) from HD patients or unaffected controls. We demonstrated that HD-iBMECs have abnormalities in barrier properties, as well as in specific BBB functions such as receptor-mediated transcytosis.

Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models.

The COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs). The mixture of homologues called ivermectin (avermectin-B1a + avermectin-B1b) has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the effect of each homologue on the flexibility and stiffness of proteins associated with COVID-19, described as ivermectin targets. We observed that each homologue was stably bound to the proteins studied and was able to induce detectable changes with Elastic Network Models (ENM). The perturbations induced by each homologue were characteristic of each compound and, in turn, were represented by a disruption of native intramolecular networks (interactions between residues). The homologues were able to slightly modify the conformation and stability of the connection points between the Cα atoms of the residues that make up the structural network of proteins (nodes), compared to free proteins. Each homologue was able to modified differently the distribution of quasi-rigid regions of the proteins, which could theoretically alter their biological activities. These results could provide a biophysical-computational view of the potential MTD mechanism that has been reported for ivermectin.

Application of an in Vitro Blood-Brain Barrier Model in the Selection of Experimental Drug Candidates for the Treatment of Huntington's Disease.

Huntington's disease (HD) is a neurodegenerative disease caused by polyglutamine expansion in the huntingtin protein. For drug candidates targeting HD, the ability to cross the blood-brain barrier (BBB) and reach the site of action in the central nervous system (CNS) is crucial for achieving pharmacological activity. To assess the permeability of selected compounds across the BBB, we utilized a two-dimensional model composed of primary porcine brain endothelial cells and rat astrocytes. Our objective was to use this in vitro model to rank and prioritize compounds for in vivo pharmacokinetic and brain penetration studies. The model was first characterized using a set of validation markers chosen based on their functional importance at the BBB. It was shown to fulfill the major BBB characteristics, including functional tight junctions, high transendothelial electrical resistance, expression, and activity of influx and efflux transporters. The in vitro permeability of 54 structurally diverse known compounds was determined and shown to have a good correlation with the in situ brain perfusion data in rodents. We used this model to investigate the BBB permeability of a series of new HD compounds from different chemical classes, and we found a good correlation with in vivo brain permeation, demonstrating the usefulness of the in vitro model for optimizing CNS drug properties and for guiding the selection of lead compounds in a drug discovery setting.

Safety and Efficacy of the Intravenous Infusion of Umbilical Cord Mesenchymal Stem Cells in Patients With Heart Failure: A Phase 1/2 Randomized Controlled Trial (RIMECARD Trial [Randomized Clinical Trial of Intravenous Infusion Umbilical Cord Mesenchymal Stem Cells on Cardiopathy]).

RATIONALE: Umbilical cord-derived mesenchymal stem cells (UC-MSC) are easily accessible and expanded in vitro, possess distinct properties, and improve myocardial remodeling and function in experimental models of cardiovascular disease. Although bone marrow-derived mesenchymal stem cells have been previously assessed for their therapeutic potential in individuals with heart failure and reduced ejection fraction, no clinical trial has evaluated intravenous infusion of UC-MSCs in these patients. OBJECTIVE: Evaluate the safety and efficacy of the intravenous infusion of UC-MSC in patients with chronic stable heart failure and reduced ejection fraction. METHODS AND RESULTS: Patients with heart failure and reduced ejection fraction under optimal medical treatment were randomized to intravenous infusion of allogenic UC-MSCs (Cellistem, Cells for Cells S.A., Santiago, Chile; 1×106 cells/kg) or placebo (n=15 per group). UC-MSCs in vitro, compared with bone marrow-derived mesenchymal stem cells, displayed a 55-fold increase in the expression of hepatocyte growth factor, known to be involved in myogenesis, cell migration, and immunoregulation. UC-MSC-treated patients presented no adverse events related to the cell infusion, and none of the patients tested at 0, 15, and 90 days presented alloantibodies to the UC-MSCs (n=7). Only the UC-MSC-treated group exhibited significant improvements in left ventricular ejection fraction at 3, 6, and 12 months of follow-up assessed both through transthoracic echocardiography (P=0.0167 versus baseline) and cardiac MRI (P=0.025 versus baseline). Echocardiographic left ventricular ejection fraction change from baseline to month 12 differed significantly between groups (+7.07±6.22% versus +1.85±5.60%; P=0.028). In addition, at all follow-up time points, UC-MSC-treated patients displayed improvements of New York Heart Association functional class (P=0.0167 versus baseline) and Minnesota Living with Heart Failure Questionnaire (P<0.05 versus baseline). At study completion, groups did not differ in mortality, heart failure admissions, arrhythmias, or incident malignancy. CONCLUSIONS: Intravenous infusion of UC-MSC was safe in this group of patients with stable heart failure and reduced ejection fraction under optimal medical treatment. Improvements in left ventricular function, functional status, and quality of life were observed in patients treated with UC-MSCs. CLINICAL TRIAL REGISTRATION: URL: https://www.clinicaltrials.gov/ct2/show/NCT01739777. Unique identifier: NCT01739777.

Transcriptional repressor DREAM regulates trigeminal noxious perception.

Expression of the downstream regulatory element antagonist modulator (DREAM) protein in dorsal root ganglia and spinal cord is related to endogenous control mechanisms of acute and chronic pain. In primary sensory trigeminal neurons, high levels of endogenous DREAM protein are preferentially localized in the nucleus, suggesting a major transcriptional role. Here, we show that transgenic mice expressing a dominant active mutant of DREAM in trigeminal neurons show increased responses following orofacial sensory stimulation, which correlates with a decreased expression of prodynorphin and brain-derived neurotrophic factor in trigeminal ganglia. Genome-wide analysis of trigeminal neurons in daDREAM transgenic mice identified cathepsin L and the monoglyceride lipase as two new DREAM transcriptional targets related to pain. Our results suggest a role for DREAM in the regulation of trigeminal nociception. This article is part of the special article series "Pain".

Kcnip1 a Ca²âº-dependent transcriptional repressor regulates the size of the neural plate in Xenopus.

In amphibian embryos, our previous work has demonstrated that calcium transients occurring in the dorsal ectoderm at the onset of gastrulation are necessary and sufficient to engage the ectodermal cells into a neural fate by inducing neural specific genes. Some of these genes are direct targets of calcium. Here we search for a direct transcriptional mechanism by which calcium signals are acting. The only known mechanism responsible for a direct action of calcium on gene transcription involves an EF-hand Ca²âº binding protein which belongs to a group of four proteins (Kcnip1 to 4). Kcnip protein can act in a Ca²âº-dependent manner as a transcriptional repressor by binding to a specific DNA sequence, the Downstream Regulatory Element (DRE) site. In Xenopus, among the four kcnips, we show that only kcnip1 is timely and spatially present in the presumptive neural territories and is able to bind DRE sites in a Ca²âº-dependent manner. The loss of function of kcnip1 results in the expansion of the neural plate through an increased proliferation of neural progenitors. Later on, this leads to an impairment in the development of anterior neural structures. We propose that, in the embryo, at the onset of neurogenesis Kcnip1 is the Ca²âº-dependent transcriptional repressor that controls the size of the neural plate. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.

Toll-like receptor 3 pre-conditioning increases the therapeutic efficacy of umbilical cord mesenchymal stromal cells in a dextran sulfate sodium-induced colitis model.

BACKGROUND AIMS: Immunomodulatory properties of human umbilical cord-derived mesenchymal stromal cells (UCMSCs) can be differentially modulated by toll-like receptors (TLR) agonists. Here, the therapeutic efficacy of short TLR3 and TLR4 pre-conditioning of UCMSCs was evaluated in a dextran sulfate sodium (DSS)-induced colitis in mice. The novelty of this study is that although modulation of human MSCs activity by TLRs is not a new concept, this is the first time that short TLR pre-conditioning has been carried out in a murine inflammatory model of acute colitis. METHODS: C57BL/6 mice were exposed to 2.5% dextran sulfate sodium (DSS) in drinking water ad libitum for 7 days. At days 1 and 3, mice were injected intraperitoneally with 1 × 10(6) UCMSCs untreated or TLR3 and TLR4 pre-conditioned UCMSCs. UCMSCs were pre-conditioned with poly(I:C) for TLR3 and LPS for TLR4 for 1 h at 37°C and 5% CO2. We evaluated clinical signs of disease and body weights daily. At the end of the experiment, colon length and histological changes were assessed. RESULTS: poly(I:C) pre-conditioned UCMSCs significantly ameliorated the clinical and histopathological severity of DSS-induced colitis compared with UCMSCs or LPS pre-conditioned UCMSCs. In contrast, infusion of LPS pre-conditioned UCMSCs significantly increased clinical signs of disease, colon shortening and histological disease index in DSS-induced colitis. CONCLUSIONS: These results show that short in vitro TLR3 pre-conditioning with poly(I:C) enhances the therapeutic efficacy of UCMSCs, which is a major breakthrough for developing improved treatments to patients with inflammatory bowel disease.

Soluble carbohydrate content variation in Sanionia uncinata and Polytrichastrum alpinum, two Antarctic mosses with contrasting desiccation capacities.

BACKGROUND: Cryptogamic vegetation dominates the ice-free areas along the Antarctic Peninsula. The two mosses Sanionia uncinata and Polytrichastrum alpinum inhabit soils with contrasting water availability. Sanionia uncinata grows in soil with continuous water supply, while P. alpinum grows in sandy, non-flooded soils. Desiccation and rehydration experiments were carried out to test for differences in the rate of water loss and uptake, with non-structural carbohydrates analysed to test their role in these processes. RESULTS: Individual plants of S. uncinata lost water 60 % faster than P. alpinum; however, clumps of S. uncinata took longer to dry than those of P. alpinum (11 vs. 5 h, respectively). In contrast, rehydration took less than 10 min for both mosses. Total non-structural carbohydrate content was higher in P. alpinum than in S. uncinata, but sugar levels changed more in P. alpinum during desiccation and rehydration (60-50 %) when compared to S. uncinata. We report the presence of galactinol (a precursor of the raffinose family) for the first time in P. alpinum. Galactinol was present at higher amounts than all other non-structural sugars. CONCLUSIONS: Individual plants of S. uncinata were not able to retain water for long periods but by growing and forming carpets, this species can retain water the longest. In contrast individual P. alpinum plants required more time to lose water than S. uncinata, but as moss cushions they suffered desiccation faster than the later. On the other hand, both species rehydrated very quickly. We found that when both mosses lost 50 % of their water, carbohydrates content remained stable and the plants did not accumulate non-structural carbohydrates during the desiccation prosses as usually occurs in vascular plants. The raffinose family oligosaccarides decreased during desiccation, and increased during rehydration, suggesting they function as osmoprotectors.

[Clinical outcome after discontinuation of infliximab in patients with ulcerative colitis in deep remission]. / Evolución clínica tras la suspensión de infliximab en pacientes con colitis ulcerosa en remisión profunda.

INTRODUCTION: Infliximab (IFX) is effective in treating ulcerative colitis (UC) and in achieving mucosal healing (MH). Little is known about the role of mucosal healing (MH) in the subsequent evolution of the disease and the consequences of discontinuing treatment. AIMS: To evaluate the characteristics and evolution of patients with UC treated with IFX who discontinued treatment after disease remission. METHODS: Observational, prospective study of patients with moderate to severe UC, corticosteroid-resistant/corticosteroid-dependent, naïve to anti-TNF. IFX administration regimen: 5 mg/kg at 0-2-6 weeks and every 8 weeks thereafter until week 54. In patients achieving MH, IFX was discontinued and the patients were followed-up for at least 20 months. Clinical remission (CR): mayo score <2; Clinical response: decrease in mayo score of 3 points; MH: mayo score 0-1; Deep remission: patient with CR and MH. RESULTS: Of the 21 patients enrolled, 19 completed the study (colectomy, n = 1; non-responder, n = 1). Mean age: 47.8 years. UC: severe (n = 13) and moderate (n = 6); most patients (n = 11) were steroid-resistant; 57.8% received combined treatment with immunosuppressants, and 31.5% intensified treatment. Week 54: 16 patients (84.2%) showed clinical response, 13 (68.4%) showed CR, and 12 (63.2%) deep remission. Of these, 6 (25%) presented a new episode of UC, and in 3 (25%) IFX was restarted within 12 weeks of discontinuation, with all patients responding. Of the total sample, 91.7% remained IFX-free at week 8, and 75% at week 12, with no remission during follow-up. None of the patients required hospitalization or surgery. CONCLUSIONS: Half of patients with deep remission of UC with IFX therapy presented a new episode after treatment discontinuation, and in 25% IFX therapy was restarted.

Nitzschiatranstagensis Morales, Novais, Wetzel, Morais & Ector (Bacillariophyceae) - the second record in the Mediterranean Region.

Background: The Mediterranean Region holds significant ecological importance, characterised by its unique climate, biodiversity and the crucial role it plays in global ecosystems. Mediterranean streams are naturally highly-stressed environments mainly due to fluctuations in water quantity. River flow generally varies from perennial to ephemeral and temporary rivers constitute significant water resources. Streams that flow through Balearic Islands are subjected to these conditions. The majority of these streams sustain water flow for 4-5 months annually, with exceptions noted for streams associated with springs, which typically maintain water throughout most of the year.Benthic diatoms are widely recognised as reliable bioindicators of water quality, used in many aquatic ecosystems. Analysing diatom communities and their biodiversity serves as a valuable tool to ensure the ecological and sustainable utilisation of water resources as well as the accurate development of guidelines for their conservation.The field of diatom taxonomy and distribution plays a crucial role in advancing our understanding of aquatic ecosystems and their biodiversity. Species of the genus Nitzschia are extensively found throughout the Mediterranean Region, including the Balearic Islands. However, they have rarely been investigated in temporary streams. New information: This study presents the first record of Nitzschiatranstagensis Morales, Novais, Wetzel, Morais & Ector, outside the type locality and being the second record in Europe. In this study, the authors found this taxon in one temporary stream of Majorca Island, Torrent des Castellot in November 2005 (Balearic Islands). Nitzschiatranstagensis occurred at 2.6% abundance in this stream with oligotrophic waters (0.052 mg∙l-1 of nitrate), slightly alkaline pH values (7.8) and water conductivity levels of 626.5 µS cm-1. This species was recorded in the biofilm of the stones together with other taxa such as Achnanthidiumminutissimum (Kützing) Czarnecki (39.2%), Gomphonemarosenstockianum Lange-Bertalot & Reichardt (28.9%) and Halamphoraoligotraphenta (Lange-Bertalot) Levkov (20.4%). The Nitzschiatranstagensis frustules found in the examined material have similar dimensions and a higher fibulae count (8-11 in 10 µm vs. 6-10 in 10 µm) compared to the type material of Nitzschiatranstagensis. The habitat characteristics in which this species was found are described, together with LM micrographs of this taxon.

Biophysical Analysis of Potential Inhibitors of SARS-CoV-2 Cell Recognition and Their Effect on Viral Dynamics in Different Cell Types: A Computational Prediction from In Vitro Experimental Data.

Recent reports have suggested that the susceptibility of cells to SARS-CoV-2 infection can be influenced by various proteins that potentially act as receptors for the virus. To investigate this further, we conducted simulations of viral dynamics using different cellular systems (Vero E6, HeLa, HEK293, and CaLu3) in the presence and absence of drugs (anthelmintic, ARBs, anticoagulant, serine protease inhibitor, antimalarials, and NSAID) that have been shown to impact cellular recognition by the spike protein based on experimental data. Our simulations revealed that the susceptibility of the simulated cell systems to SARS-CoV-2 infection was similar across all tested systems. Notably, CaLu3 cells exhibited the highest susceptibility to SARS-CoV-2 infection, potentially due to the presence of receptors other than ACE2, which may account for a significant portion of the observed susceptibility. Throughout the study, all tested compounds showed thermodynamically favorable and stable binding to the spike protein. Among the tested compounds, the anticoagulant nafamostat demonstrated the most favorable characteristics in terms of thermodynamics, kinetics, theoretical antiviral activity, and potential safety (toxicity) in relation to SARS-CoV-2 spike protein-mediated infections in the tested cell lines. This study provides mathematical and bioinformatic models that can aid in the identification of optimal cell lines for compound evaluation and detection, particularly in studies focused on repurposed drugs and their mechanisms of action. It is important to note that these observations should be experimentally validated, and this research is expected to inspire future quantitative experiments.

Ectopic expression of VAV1 reveals an unexpected role in pancreatic cancer tumorigenesis.

Herein, we show that the hematopoietic-specific GEF VAV1 is ectopically expressed in primary pancreatic adenocarcinomas due to demethylation of the gene promoter. Interestingly, VAV1-positive tumors had a worse survival rate compared to VAV1-negative tumors. Surprisingly, even in the presence of oncogenic KRAS, VAV1 RNAi abrogates neoplastic cellular proliferation in vitro and in vivo, thus identifying Vav1 as a growth-stimulatory protein in this disease. Vav1 acts synergistically with the EGF receptor to stimulate pancreatic tumor cell proliferation. Mechanistically, the effects of Vav1 require its GEF activity and the activation of Rac1, PAK1, and NF-kappaB and involve cyclin D1 upregulation. Thus, the discovery of prooncogenic pathways regulated by Vav1 makes it an attractive target for therapeutic intervention.

Comparative Analysis of CRISPR-Cas Systems in Pseudomonas Genomes.

Pseudomonas is a bacterial genus with some saprophytic species from land and others associated with opportunistic infections in humans and animals. Factors such as pathogenicity or metabolic aspects have been related to CRISPR-Cas, and in silico studies into it have focused more on the clinical and non-environmental setting. This work aimed to perform an in silico analysis of the CRISPR-Cas systems present in Pseudomonas genomes. It analyzed 275 complete genomic sequences of Pseudomonas taken from the NCBI database. CRISPR loci were obtained from CRISPRdb. The genes associated with CRISPR (cas) and CAS proteins, and the origin and diversity of spacer sequences, were identified and compared by BLAST. The presence of self-targeting sequences, PAMs, and the conservation of DRs were visualized using WebLogo 3.6. The CRISPR-like RNA secondary structure prediction was analyzed using RNAFold and MFold. CRISPR structures were identified in 19.6% of Pseudomonas species. In all, 113 typical CRISPR arrays with 18 putative cas were found, as were 2050 spacers, of which 52% showed homology to bacteriophages, 26% to chromosomes, and 22% to plasmids. No potential self-targeting was detected within the CRISPR array. All the found DRs can form thermodynamically stable secondary RNA structures. The comparison of the CRISPR/Cas system can help understand the environmental adaptability of each evolutionary lineage of clinically and environmentally relevant species, providing data support for bacterial typing, traceability, analysis, and exploration of unconventional CRISPR.

Stochastic Nature and Intramolecular Coupling in Optical Response Profiles: Critical Analysis through Semiclassical Models.

We have studied the nonlinear absorptive and dispersive responses considering a molecular system consisting of two-levels, where aspects of the vibrational internal structure and intramolecular coupling are inserted, in addition to the considerations of interaction with the thermal reservoir. The Born-Oppenheimer electronic energy curve for this molecular model consists of two-intercrossing harmonic oscillator potentials with minima displaced in energy and nuclear coordinate. The results obtained show how these optical responses are sensitive to explicit considerations of both intramolecular coupling and the presence of the solvent through their stochastic interaction. Our study shows that the permanent dipoles of the system and the transition dipoles induced by electromagnetic field effects represent critical quantities for the analysis. The solvent action in our model is treated through the natural Bohr frequency shift to a time-dependent function, with explicit manifestations in its comparison as if the upper state were broadened. Significant variations in the nonlinear optical properties for cases of perturbative and saturative treatments, relaxation times, and optical propagation, mainly due to changes in the probe and pump intensities, are studied. Our studies relating the intramolecular effects with those generated by the presence of the solvent and its stochastic interaction with the solute of study, have allowed not only to analyze the influence of these in the profile of the optical responses, but they could also provide some insights into the analysis and characterization of molecular systems through nonlinear optical properties.

Intrinsic Dynamics of the ClpXP Proteolytic Machine Using Elastic Network Models.

ClpXP complex is an ATP-dependent mitochondrial matrix protease that binds, unfolds, translocates, and subsequently degrades specific protein substrates. Its mechanisms of operation are still being debated, and several have been proposed, including the sequential translocation of two residues (SC/2R), six residues (SC/6R), and even long-pass probabilistic models. Therefore, it has been suggested to employ biophysical-computational approaches that can determine the kinetics and thermodynamics of the translocation. In this sense, and based on the apparent inconsistency between structural and functional studies, we propose to apply biophysical approaches based on elastic network models (ENM) to study the intrinsic dynamics of the theoretically most probable hydrolysis mechanism. The proposed models ENM suggest that the ClpP region is decisive for the stabilization of the ClpXP complex, contributing to the flexibility of the residues adjacent to the pore, favoring the increase in pore size and, therefore, with the energy of interaction of its residues with a larger portion of the substrate. It is predicted that the complex may undergo a stable configurational change once assembled and that the deformability of the system once assembled is oriented, to increase the rigidity of the domains of each region (ClpP and ClpX) and to gain flexibility of the pore. Our predictions could suggest under the conditions of this study the mechanism of the interaction of the system, of which the substrate passes through the unfolding of the pore in parallel with a folding of the bottleneck. The variations in the distance calculated by molecular dynamics could allow the passage of a substrate with a size equivalent to ∼3 residues. The theoretical behavior of the pore and the stability and energy of binding to the substrate based on ENM models suggest that in this system, there are thermodynamic, structural, and configurational conditions that allow a possible translocation mechanism that is not strictly sequential.