Ultra-Sensitive and Specific Detection of S. aureus Bacterial Cultures Using an Oligonucleotide Probe Integrated in a Lateral Flow-Based Device.

The identification of pathogens causing infectious diseases is still based on laborious and time-consuming techniques. Therefore, there is an urgent need for the development of novel methods and devices that can considerably reduce detection times, allowing the health professionals to administer the right treatment at the right time. Lateral flow-based systems provide fast, cheap and easy to use alternatives for diagnosis. Herein, we report on a lateral flow approach for specifically detecting S. aureus bacteria within 6 h.

Sirt3 increases CNPase enzymatic activity through deacetylation and facilitating substrate accessibility.

Myocardial 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) metabolizes a nucleoside 2',3'-cyclic phosphate to a nucleoside 2'-phosphate. Recently, the roles of CNPase in the pathophysiological processes of heart failure have emerged. The mitochondrial acylome subjected to SIRT3 regulation give us comprehensive understanding of acylation modifications to a vast array of protein targets, and the list of acetylated mitochondrial proteins is still growing. However, it remains elusive whether CNPase is subjected to the regulation of acetylation and deacetylation, and the effects of which on CNPase enzymatic activity are still unknown. In this study, the mitochondrial distribution of CNPase was identified by immunofluorescence and cytosol/mitochondria fractioning. The immunofluorescence staining pattern of CNPase and Sirt3 overlapped on the same focal plane. Moreover, Sirt3 associates directly with CNPase, and the CNPase enzymatic activity was subjected to Sirt3 activity. Then biochemical methods using acetic anhydride was employed to acetylate the CNPase proteins, the enzymatic activity of CNPase decreased. Furthermore, co-immunoprecipitation coupled mass spectrometry identifies K196, K379, K128 as the main acetylation sites. Molecular dynamic simulation shows that acetylation modification suppressed the CNPase enzymatic activity through decreasing the opening probability of the binding pocket and restricting substrate accessibility. Together with these findings, this study reveals a molecular mechanism underlying Sirt3 regulating CNPase enzymatic activity, and suggests that targeting CNPase's post-translational modifications represents a promising therapeutic strategy.

In silico identification of novel PrfA inhibitors to fight listeriosis: A virtual screening and molecular dynamics studies.

Listeria monocytogenes is considered to be one of the most dangerous foodborne pathogens as it can cause listeriosis, a life-threatening human disease. While the incidence of listeriosis is very low its fatality rate is exceptionally high. Because many multi-resistance Listeria monocytogenes strains that do not respond to conventional antibiotic therapy have been recently described, development of new antimicrobials to fight listeriosis is necessary. The positive regulatory factor A (PrfA) is a key homodimeric transcription factor that modulates the transcription of multiple virulence factors which are ultimately responsible of Listeria monocytogenes' pathogenicity. In the present manuscript we describe several new potential PrfA inhibitors that were identified after performing ligand-based virtual screening followed by molecular docking calculations against the wild-type PrfA structure. The three top-scored drug-likeness inhibitors bound to the wild-type PrfA structure were further assessed by Molecular Dynamics (MD) simulations. Besides, the three top-scored inhibitors were docked into a constitutive active apoPrfA mutant structure and the corresponding complexes were also simulated by MD. According to the obtained data, PUBChem 87534955 (P875) and PUBChem 58473762 (P584) may not only bind and inhibit wild-type PrfA but the aforementioned apoPrfA mutant as well. Therefore, P875 and P584 might represent good starting points for the development of a completely new set of antimicrobial agents to treat listeriosis.

The closed conformation of the LDL receptor is destabilized by the low Ca(++) concentration but favored by the high Mg(++) concentration in the endosome.

The LDL receptor (LDLR) internalizes LDL and VLDL particles. In the endosomes, it adopts a closed conformation important for recycling, by interaction of two modules of the ligand binding domain (LR4-5) and a ß-propeller motif. Here, we investigate by SPR the interactions between those two modules and the ß-propeller. Our results indicate that the two modules cooperate to bind the ß-propeller. The binding is favored by low pH and by high [Ca(++)]. Our data show that Mg(++), at high concentration in the endosome, favors the formation of the closed conformation by replacing the structuring effect of Ca(++) in LR5. We propose a sequential model of LDL release where formation of the close conformation follows LDL release.

Intradomain Confinement of Disulfides in the Folding of Two Consecutive Modules of the LDL Receptor.

The LDL receptor internalizes circulating LDL and VLDL particles for degradation. Its extracellular binding domain contains ten (seven LA and three EGF) cysteine-rich modules, each bearing three disulfide bonds. Despite the enormous number of disulfide combinations possible, LDLR oxidative folding leads to a single native species with 30 unique intradomain disulfides. Previous folding studies of the LDLR have shown that non native disulfides are initially formed that lead to compact species. Accordingly, the folding of the LDLR has been described as a "coordinated nonvectorial" reaction, and it has been proposed that early compaction funnels the reaction toward the native structure. Here we analyze the oxidative folding of LA4 and LA5, the modules critical for ApoE binding, isolated and in the LA45 tandem. Compared to LA5, LA4 folding is slow and inefficient, resembling that of LA5 disease-linked mutants. Without Ca++, it leads to a mixture of many two-disulfide scrambled species and, with Ca++, to the native form plus two three-disulfide intermediates. The folding of the LA45 tandem seems to recapitulate that of the individual repeats. Importantly, although the folding of the LA45 tandem takes place through formation of scrambled isomers, no interdomain disulfides are detected, i.e. the two adjacent modules fold independently without the assistance of interdomain covalent interactions. Reduction of incredibly large disulfide combinatorial spaces, such as that in the LDLR, by intradomain confinement of disulfide bond formation might be also essential for the efficient folding of other homologous disulfide-rich receptors.

Low-density lipoprotein receptor is a calcium/magnesium sensor - role of LR4 and LR5 ion interaction kinetics in low-density lipoprotein release in the endosome.

The low-density lipoprotein receptor (LDLR) captures circulating lipoproteins and delivers them in the endosome for degradation. Its function is essential for cholesterol homeostasis, and mutations in the LDLR are the major cause of familiar hypercholesterolemia. The release of LDL is usually attributed to endosome acidification. As the pH drops, the affinity of the LDLR/LDL complex is reduced, whereas the strength of a self-complex formed between two domains of the receptor (i.e. the LDL binding domain and the ß-propeller domain) increases. However, an alternative model states that, as a consequence of a drop in both pH and Ca(2+) concentration, the LDLR binding domain is destabilized in the endosome, which weakens the LDLR/LDL complex, thus liberating the LDL particles. In the present study, we test a key underlying assumption of the second model, namely that the lipoprotein binding repeats of the receptor (specifically repeats 4 and 5, LR4 and LR5) rapidly sense endosomal changes in Ca(2+) concentration. Our kinetic and thermodynamic analysis of Ca(2+) and Mg(2+) binding to LR4 and LR5, as well as to the tandem of the two (LR4-5), shows that both repeats spontaneously release Ca(2+) in a time scale much shorter than endosomal delivery of LDL, thus acting as Ca(2+) sensors that become unfolded under endosomal conditions. Our analysis additionally explains the lower Ca(2+) affinity of repeat LR4, compared to LR5, as arising from a very slow Ca(2+) binding reaction in the former, most likely related to the lower conformational stability of apolipoprotein LR4, compared to apolipoprotein LR5, as determined from thermal unfolding experiments and molecular dynamics simulations.

LDL receptor/lipoprotein recognition: endosomal weakening of ApoB and ApoE binding to the convex face of the LR5 repeat.

The molecular mechanism of lipoprotein binding by the low-density lipoprotein (LDL) receptor (LDLR) is poorly understood, one reason being that structures of lipoprotein-receptor complexes are not available. LDLR uses calcium-binding repeats (LRs) to interact with apolipoprotein B and apolipoprotein E (ApoB and ApoE). We have used NMR and SPR to characterize the complexes formed by LR5 and three peptides encompassing the putative binding regions of ApoB (site A and site B) and ApoE. The three peptides bind at the hydrophilic convex face of LR5, forming complexes that are weakened at low [Ca(2+) ] and low pH. Thus, endosomal conditions favour dissociation of LDLR/lipoprotein complexes regardless of whether active displacement of bound lipoproteins by the ß-propeller in LDLR takes place. The multiple ApoE copies in ß very low density lipoproteins (ß-VLDLs), and the presence of two competent binding sites (A and B) in LDLs, suggest that LDLR chelates lipoproteins and enhances complex affinity by using more than one LR.

Molecular characterization of 16 hemophilia B families in Aragon, Spain.

Molecular characterization of hemophilia B at gene level has become an indispensable tool for a proper genetic counseling in carriers and for a closer surveillance of inhibitor development in several severe forms. Our study was aimed at characterizing the molecular defects in the factor IX (FIX) gene in hemophilia B families in Aragon, a center-east region of Spain. Direct sequencing of all regions of likely functional significance of the FIX gene was performed in the screened 18 hemophilia B families. Quantitative techniques, such as multiplex ligation-dependent prove amplification reaction, were carried out only in patients in whom no mutation was found. We have identified the molecular events responsible for hemophilia B in 16 unrelated families (eight with mild hemophilia B and eight with severe hemophilia B). Out of all families studied, we have found 14 missense mutations and two nonsense mutations; still we were unsuccessful in determining the genetic defects in two severe and unrelated families. Of the 16 characterized mutations, 14 of them lie in the protease domain in which one mutation, A233T, was surprisingly found in three unrelated families. We also report and discuss the pathogenicity of F314L, a novel mutation found in the protease domain. Our molecular data reflect a notable heterogeneity of the mutational spectrum mainly in the protease domain of FIX. This is the first mutation report on the disease in Aragon, Spain.

Changes in cardiovascular biomarkers in HIV-infected patients switching from ritonavir-boosted protease inhibitors to raltegravir.

BACKGROUND: : Switching from boosted protease inhibitors (PI/r) to raltegravir (RAL) results in a better plasma lipid profile than continuing PI/r. Whether this strategy affects plasma biomarkers associated with atherosclerosis is unknown. METHODS: : We assessed 48-week changes in fasting lipids and several biomarkers including serum high-sensitivity C-reactive protein (hsCRP), monocyte chemoattractant protein 1 (MCP-1), osteoprotegerin, interleukin (IL) 6, IL-10, tumor necrosis factor alpha (TNF-α), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), E-selectin and P-selectin, adiponectin, insulin, and D-dimer in otherwise healthy, virologically suppressed HIV-infected patients treated with PI/r who randomly switched from PI/r to RAL or continued with PI/r in the SPIRAL trial. Biomarkers and lipids at baseline and 48-week changes between both study arms were compared. Correlations between changes in biomarkers and changes in lipids were also evaluated. RESULTS: : Of 273 patients initiating study drugs in the SPIRAL trial, 233 (119 RAL, 114 PI/r) remained on allocated therapy for 48 weeks and had sera available for the purpose of this substudy. Triglycerides (-28%, P < 0.0001), total (-14%, P < 0.0001), low-density lipoprotein (-9%, P = 0.0069), and high-density lipoprotein (-10%, P = 0.0017) cholesterol decreased in RAL relative to the PI/r group. Among biomarkers, hsCRP (-40%, P < 0.0001), MCP-1 (-20%, P = 0.0003), osteoprotegerin (-13%, P = 0.0024), IL-6 (-46%,P < 0.0001), TNF-α (-27%, P = 0.0011), insulin (-26%, P < 0.0001), and D-dimer (-8%, P = 0.0187) decreased in RAL relative to PI/r group, whereas IL-10 (+1%, P = 0.7773), ICAM-1 (-6%, P = 0.1255), VCAM-1(0%, P = 0.8671), E-selectin (-9%, P = 0.2174), P-selectin (-6%, P = 0.3865), and adiponectin (+8%, P = 0.2028) remained unchanged. Biomarkers and lipids changes at 48 weeks were weakly correlated. CONCLUSION: : Switching from PI/r to RAL induced significant changes in several cardiovascular biomarkers that were not completely explained by lipid changes.

Thermodynamics of protein-cation interaction: Ca(+2) and Mg(+2) binding to the fifth binding module of the LDL receptor.

The ligand binding domain of the LDL receptor (LDLR) contains seven structurally homologous repeats. The fifth repeat (LR5) is considered to be the main module responsible for the binding of lipoproteins LDL and beta-VLDL. LR5, like the other homologous repeats, is around 40-residue long and contains three disulfide bonds and a conserved cluster of negatively charged residues surrounding a hexacoordinated calcium ion. The calcium coordinating cage is formed by the backbone oxygens of W193 and D198, and side-chain atoms of D196, D200, D206, and E207. The functionality of LDLR is closely associated with the presence of calcium. Magnesium ions are to some extent similar to calcium ions. However, they appear to be involved in different physiological events and their concentrations in extracellular and intracellular compartments are regulated by different mechanisms. Whether magnesium ions can play a role in the complex cycle of LDLR internalization and recycling is not known. We report here a detailed study of the interaction between LR5 and these two cations combining ITC, emission fluorescence, high resolution NMR, and MD simulations, at extracellular and endosomal pHs. Our results indicate that the conformational stability and internal dynamics of LR5 are strongly modulated by the specific bound cation. It appears that the difference in binding affinity for these cations is somewhat compensated by their different concentrations in late LDL-associated endosomes. While the mildly acidic and calcium-depleted environment in late endosomes has been proposed to contribute significantly to LDL release, the presence of magnesium might assist in efficient LDLR recycling. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Mechanism of low density lipoprotein (LDL) release in the endosome: implications of the stability and Ca2+ affinity of the fifth binding module of the LDL receptor.

Uptake of low density lipoproteins (LDL) by their receptor, LDLR, is the primary mechanism by which cells incorporate cholesterol from plasma. Mutations in LDLR lead to familial hypercholesterolemia, a common disease affecting 1 in 500 of the human population. LDLR is a modular protein that uses several small repeats to bind LDL. The repeats contain around 40 residues, including three disulfide bonds and a calcium ion. Repeat 5 (LR5) is critical for LDL and beta-migrating very low density lipoprotein binding. Based on the crystal structure of LDLR at endosomal pH (but close to extracellular calcium concentration), LR5 has been proposed to bind to the epidermal growth factor (EGF) precursor domain of LDLR in the endosome, thus releasing the LDL particles previously bound in extracellular conditions. We report here the conformational stability of LR5 as a function of temperature and calcium concentration under both extracellular and endosomal pH conditions. The repeat was very stable when it bore a bound calcium ion but was severely destabilized in the absence of calcium and even further destabilized at acidic versus neutral pH. The temperature and calcium concentration dependence of LR5 stability clearly indicate that under endosomal conditions the unfolded conformation of the repeat is largely dominant. We thus propose a new mechanism for LDL release in the endosome in which calcium depletion and decreased stability at acidic pH drives LR5 unfolding, which triggers LDL release from the receptor. Subsequent binding of LR5 to the EGF precursor domain, if it takes place at low calcium concentrations, would contribute to a further shifting of the equilibrium toward dissociation.

Scrambled isomers as key intermediates in the oxidative folding of ligand binding module 5 of the low density lipoprotein receptor.

The ligand binding module five (LA5) of the low density lipoprotein receptor is a small, single-domain protein of 40 residues and three disulfide bonds with a calcium binding motif that is essential for its structure and function. Several mutations in LA5 have been reported to cause familial hypercholesterolemia by impairing a proper folding of the module. The current study reports the oxidative folding and reductive unfolding pathways of wild type and mutant LA5 modules through kinetic and structural analysis of the trapped intermediates. Wild type LA5 folding involves an initial phase of nonspecific packing where the sequential oxidation of its cysteines gives rise to complex equilibrated populations of intermediates. In the presence of calcium, the attainment of a coordination-competent conformation becomes the rate-limiting step of folding while binding of the ion funnels both thermodynamically and kinetically the folding reaction toward the native state. In the absence of calcium, a scrambled isomer (termed Xa) constitutes the global free energy minimum of the folding process. Xa and the native form are stable, inter-convertible species whose relative populations at equilibrium appear displaced in disease-linked mutants toward the scrambled form. Because stable scrambled isomers such as Xa avoid the exposition of reactive cysteines in misfolded modules, they might constitute a strategy to prevent wrong interactions with other domains during folding of the receptor. Comparison of the folding pathways of wild type and mutant LA5 provides the molecular basis to understand how LA modules fold into a functional conformation or upon mutation misfold and lead to disease.