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The mutations G170R and I244T are the most common disease cause in primary hyperoxaluria type I (PH1). These mutations cause the misfolding of the AGT protein in the minor allele AGT-LM that contains the P11L polymorphism, which may affect the folding of the N-terminal segment (NTT-AGT). The NTT-AGT is phosphorylated at T9, although the role of this event in PH1 is unknown. In this work, phosphorylation of T9 was mimicked by introducing the T9E mutation in the NTT-AGT peptide and the full-length protein. The NTT-AGT conformational landscape was studied by circular dichroism, NMR, and statistical mechanical methods. Functional and stability effects on the full-length AGT protein were characterized by spectroscopic methods. The T9E and P11L mutations together reshaped the conformational landscape of the isolated NTT-AGT peptide by stabilizing ordered conformations. In the context of the full-length AGT protein, the T9E mutation had no effect on the overall AGT function or conformation, but enhanced aggregation of the minor allele (LM) protein and synergized with the mutations G170R and I244T. Our findings indicate that phosphorylation of T9 may affect the conformation of the NTT-AGT and synergize with PH1-causing mutations to promote aggregation in a genotype-specific manner. Phosphorylation should be considered a novel regulatory mechanism in PH1 pathogenesis. [ABSTRACT FROM AUTHOR]

Proteomic, cellular and biochemical analysis of the stress protein NUPR1 reveals that it binds to PARP1 into the nucleus and inhibits PARP1 activity in vitro. Mutations on residues Ala33 or Thr68 of NUPR1 or treatment with its inhibitor ZZW-115 inhibits this effect. PARylation induced by 5-fluorouracil (5-FU) treatment is strongly enhanced by ZZW-115 and associated with a decrease of NAD+/NADH ratio and rescued by the PARP inhibitor olaparib. Cell death induced by ZZW-115 treatment of pancreas cancer-derived cells is rescued by olaparib and improved with PARG inhibitor PDD00017273. The mitochondrial catastrophe induced by ZZW-115 treatment or by genetic inactivation of NUPR1 is associated to a hyperPARylation of the mitochondria, disorganization of the mitochondrial network, mitochondrial membrane potential decrease, and with increase of superoxide production, intracellular level of reactive oxygen species (ROS) and cytosolic levels of Ca2+. These features are rescued by olaparib or NAD+ precursor nicotinamide mononucleotide in a dose-dependent manner and partially by antioxidants treatments. In conclusion, inactivation of NUPR1 induces a hyperPARylation, which in turn, induces a mitochondrial catastrophe and consequently a cell death through a non-canonical Parthanatos, since apoptosis inducing-factor (AIF) is not translocated out of the mitochondria. NUPR1 binds to PARP1 and inhibits PARP1 activity in pancreatic cancer cells, with the NUPR1 inhibitor ZZW-115 abolishing the protective effect of NUPR1, inducing strong hyperPARylation and cell death by mitochondrial dysfunction. [ABSTRACT FROM AUTHOR]

Choline‐O‐sulfatase (COSe; EC 3.1.6.6) is a member of the alkaline phosphatase (AP) superfamily, and its natural function is to hydrolyze choline‐O‐sulfate into choline and sulfate. Despite its natural function, the major interest in this enzyme resides in the landmark catalytic/substrate promiscuity of sulfatases, which has led to attention in the biotechnological field due to their potential in protein engineering. In this work, an in‐depth structural analysis of wild‐type Sinorhizobium (Ensifer) meliloti COSe (SmeCOSe) and its C54S active‐site mutant is reported. The binding mode of this AP superfamily member to both products of the reaction (sulfate and choline) and to a substrate‐like compound are shown for the first time. The structures further confirm the importance of the C‐terminal extension of the enzyme in becoming part of the active site and participating in enzyme activity through dynamic intra‐subunit and inter‐subunit hydrogen bonds (Asn146A–Asp500B–Asn498B). These residues act as the 'gatekeeper' responsible for the open/closed conformations of the enzyme, in addition to assisting in ligand binding through the rearrangement of Leu499 (with a movement of approximately 5 Å). Trp129 and His145 clamp the quaternary ammonium moiety of choline and also connect the catalytic cleft to the C‐terminus of an adjacent protomer. The structural information reported here contrasts with the proposed role of conformational dynamics in promoting the enzymatic catalytic proficiency of an enzyme. [ABSTRACT FROM AUTHOR]

The phosphomimetic mutation S82D in the cancer‐associated, FAD‐dependent human NADP(H):quinone oxidoreductase 1 (hNQO1) causes a decrease in flavin‐adenine dinucleotide‐binding affinity and intracellular stability. We test in this work whether the evolutionarily recent neutral mutation R80H in the vicinity of S82 may alter the strong functional effects of S82 phosphorylation through electrostatic interactions. We show using biophysical and bioinformatic analyses that the reverse mutation H80R prevents the effects of S82D phosphorylation on hNQO1 by modulating the local stability. Consistently, in rat NQO1 (rNQO1) which contains R80, the effects of phosphorylation were milder, resembling the behaviour found in hNQO1 when this residue was humanized in rNQO1 (by the R80H mutation). Thus, apparently neutral and evolutionarily divergent mutations may determine the functional response of mammalian orthologues towards phosphorylation. [ABSTRACT FROM AUTHOR]

In this article, we present a data-driven approach to obtain the static image of a scene, eliminating dynamic objects that might have been present at the time of traversing the scene with a camera. The general objective is to improve vision-based localization and mapping tasks in dynamic environments, where the presence (or absence) of different dynamic objects in different moments makes these tasks less robust. We introduce an end-to-end deep learning framework to turn images of an urban environment that include dynamic content, such as vehicles or pedestrians, into realistic static frames suitable for localization and mapping. This objective faces two main challenges: detecting the dynamic objects, and inpainting the static occluded background. The first challenge is addressed by the use of a convolutional network that learns a multiclass semantic segmentation of the image. The second challenge is approached with a generative adversarial model that, taking as input the original dynamic image and the computed dynamic/static binary mask, is capable of generating the final static image. This framework makes use of two new losses, one based on image steganalysis techniques, useful to improve the inpainting quality, and another one based on ORB features, designed to enhance feature matching between real and hallucinated image regions. To validate our approach, we perform an extensive evaluation on different tasks that are affected by dynamic entities, i.e.,visual odometry, place recognition, and multiview stereo, with the hallucinated images. Code has been made available on https://github.com/bertabescos/EmptyCities_SLAM. [ABSTRACT FROM AUTHOR]

The purpose of this work is to highlight the paramount importance of representing and quantifying uncertainty to correctly report the associated confidence of the robot's location estimate at each time step along its trajectory and therefore decide the correct course of action in an active SLAM mission. We analyze the monotonicity property of different decision-making criteria, both in 2-D and 3-D, with respect to the representation of uncertainty and of the orientation of the robot's pose. Monotonicity, the property that uncertainty increases as the robot moves, is essential for adequate decision making. We analytically show that, by using differential representations to propagate spatial uncertainties, monotonicity is preserved for all optimality criteria, A-opt, D-opt, and E-opt, and for Shannon's entropy. We also show that monotonicity does not hold for any criteria in absolute representations using Roll-Pitch-Yaw and Euler angles. Finally, using unit quaternions in absolute representations, the only criteria that preserve monotonicity are D-opt and Shannon's entropy. [ABSTRACT FROM AUTHOR]

Simultaneous localization and mapping (SLAM) consists in the concurrent construction of a model of the environment (the map), and the estimation of the state of the robot moving within it. The SLAM community has made astonishing progress over the last 30 years, enabling large-scale real-world applications and witnessing a steady transition of this technology to industry. We survey the current state of SLAM and consider future directions. We start by presenting what is now the de-facto standard formulation for SLAM. We then review related work, covering a broad set of topics including robustness and scalability in long-term mapping, metric and semantic representations for mapping, theoretical performance guarantees, active SLAM and exploration, and other new frontiers. This paper simultaneously serves as a position paper and tutorial to those who are users of SLAM. By looking at the published research with a critical eye, we delineate open challenges and new research issues, that still deserve careful scientific investigation. The paper also contains the authors’ take on two questions that often animate discussions during robotics conferences: Do robots need SLAM? and Is SLAM solved? [ABSTRACT FROM AUTHOR]

Biosurfactants are of growing interest as sustainable alternatives to fossil-fuel-derived chemical surfactants, particularly for the detergent industry. To realize this potential, it is necessary to understand how they affect proteins which they may encounter in their applications. However, knowledge of such interactions is limited. Here, we present a study of the interactions between the model protein apo-α-lactalbumin (apo-aLA) and the biosurfactant sophorolipid (SL) produced by the yeast Starmerella bombicola. SL occurs both as an acidic and a lactonic form; the lactonic form (lactSL) is sparingly soluble and has a lower critical micelle concentration (cmc) than the acidic form [nonacetylated acidic sophorolipid (acidSL)]. We show that acidSL affects apo-aLA in a similar way to the related glycolipid biosurfactant rhamnolipid (RL), with the important difference that RL is also active below the cmc in contrast to acidSL. Using isothermal titration calorimetry data, we show that acidSL has weak and saturable interactions with apo-aLA at low concentrations; due to the relatively low cmc of acidSL (which means that the monomer concentration is limited to ca. 0-1 mM SL), it is only possible to observe interactions with monomeric acidSL at high apo-aLA concentrations. However, the denaturation kinetics of apo-aLA in the presence of acidSL are consistent with a collaboration between monomeric and micellar surfactant species, similar to RL and non-ionic or zwitterionic surfactants. Inclusion of diacetylated lactonic sophorolipid (lactSL) as mixed micelles with acidSL lowers the cmc and this effectively reduces the rate of unfolding, emphasizing that SL like other biosurfactants is a gentle anionic surfactant. Our data highlight the potential of these biosurfactants for future use in the detergent and pharmaceutical industry. [ABSTRACT FROM AUTHOR]

We have previously demonstrated a crucial role of nuclear protein 1 ( NUPR1) in tumor development and progression. In this work, we report the functional characterization of a novel Nupr1-like isoform (NUPR1L) and its functional interaction with the protumoral factor NUPR1. Through the use of primary sequence analysis, threading, and homology-based molecular modeling, as well as expression and immunolocalization, studies reveal that NUPR1L displays properties, which are similar to member of the HMG-like family of chromatin regulators, including its ability to translocate to the cell nucleus and bind to DNA. Analysis of the NUPR1L promoter showed the presence of two p53-response elements at positions −37 and −7, respectively. Experiments using reporter assays combined with site-directed mutagenesis and using cells with controllable p53 expression demonstrate that both of these sequences are responsible for the regulation of NUPR1L expression by p53. Congruently, NUPR1L gene expression is activated in response to DNA damage induced by oxaliplatin treatment or cell cycle arrest induced by serum starvation, two well-validated methods to achieve p53 activation. Interestingly, expression of NUPR1L downregulates the expression of NUPR1, its closely related protumoral isoform, by a mechanism that involves the inhibition of its promoter activity. At the cellular level, overexpression of NUPR1L induces G1 cell cycle arrest and a decrease in their cell viability, an effect that is mediated, at least in part, by downregulating NUPR1 expression. Combined, these experiments constitute the first functional characterization of NUPR1L as a new p53-induced gene, which negatively regulates the protumoral factor NUPR1. J. Cell. Physiol. 230: 2936-2950, 2015. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Erb1 (Eukaryotic Ribosome Biogenesis 1) protein is essential for the maturation of the ribosomal 60S subunit. Functional studies in yeast and mammalian cells showed that altogether with Nop7 and Ytm1 it forms a stable subcomplex called PeBoW that is crucial for a correct rRNA processing. The exact function of the protein within the process remains unknown. The N-terminal region of the protein includes a well conserved region shown to be involved in PeBoW complex formation whereas the carboxy-terminal half was predicted to contain seven WD40 repeats. This first structural report on Erb1 from yeast describes the architecture of a seven-bladed β-propeller domain that revealed a characteristic extra motif formed by two α-helices and a β-strand that insert within the second WD repeat. We performed analysis of molecular surface and crystal packing, together with multiple sequence alignment and comparison of the structure with other β-propellers, in order to identify areas that are more likely to mediate protein-protein interactions. The abundance of many positively charged residues on the surface of the domain led us to investigate whether the propeller of Erb1 might be involved in RNA binding. Three independent assays confirmed that the protein interacted in vitro with polyuridilic acid (polyU), thus suggesting a possible role of the domain in rRNA rearrangement during ribosome biogenesis. [ABSTRACT FROM AUTHOR]

The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3) aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i) its thermal stability; and (ii) its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6522 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P212121, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation. [ABSTRACT FROM AUTHOR]

NUPR1, a small chromatin protein, plays a critical role in cancer development, progression, and resistance to therapy. Here, using a combination of structural bioinformatics and molecular modeling methods, we report several novel findings that enhance our understanding of the biochemical function of this protein. We find that NUPR1 has been conserved throughout evolution, and over time it has undergone duplications and transpositions to form other transcriptional regulators. Using threading, homology-based molecular modeling, molecular mechanics calculations, and molecular dynamics simulations, we generated structural models for four of these proteins: NUPR1a, NUPR1b, NUPR2, and the NUPR-like domain of GTF2-I. Comparative analyses of these models combined with extensive linear motif identification reveal that these four proteins, though similar in their propensities for folding, differ in size, surface changes, and sites amenable for posttranslational modification. Lastly, taking NUPR1a as the paradigm for this family, we built models of a NUPR-DNA complex. Additional structural comparisons revealed that NUPR1 defines a new family of small-groove-binding proteins that share structural features with, yet are distinct from, helix-loop-helix AT-hook-containing HMG proteins. These models and inferences should lead to a better understanding of the function of this group of chromatin proteins, which play a critical role in the development of human malignant diseases. [ABSTRACT FROM AUTHOR]

The nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) is responsible for processing the non-structural region of the viral precursor polyprotein in infected hepatic cells. NS3 protease activity, located at the N-terminal domain, is a zinc-dependent serine protease. A zinc ion, required for the hydrolytic activity, has been considered as a structural metal ion essential for the structural integrity of the protein. In addition, NS3 interacts with another cofactor, NS4A, an accessory viral protein that induces a conformational change enhancing the hydrolytic activity. Biophysical studies on the isolated protease domain, whose behavior is similar to that of the full-length protein (e.g., catalytic activity, allosteric mechanism and susceptibility to inhibitors), suggest that a considerable global conformational change in the protein is coupled to zinc binding. Zinc binding to NS3 protease can be considered as a folding event, an extreme case of induced-fit binding. Therefore, NS3 protease is an intrinsically (partially) disordered protein with a complex conformational landscape due to its inherent plasticity and to the interaction with its different effectors. Here we summarize the results from a detailed biophysical characterization of this enzyme and present new experimental data. [ABSTRACT FROM AUTHOR]

The stress protein p8 is a small, highly basic, unfolded, and multifunctional protein. We have previously shown that most of its functions are exerted through interactions with other proteins, whose activities are thereby enhanced or repressed. In this work we describe another example of such mechanism, by which p8 binds and negatively regulates MSL1, a histone acetyl transferase (HAT)-associated protein, which in turn binds the DNA-damage-associated 53BP1 protein to facilitate DNA repair following DNA γ-irradiation. Contrary to the HAT-associated activity, MSL1-dependent DNA-repair activity is almost completely dependent on 53BP1 expression. The picture that has emerged from our findings is that 53BP1 could be a scaffold that gets the HAT MSL1-dependent DNA-repair activity to the sites of DNA damage. Finally, we also found that, although p8 expression is transiently activated after γ-irradiation, it is eventually submitted to sustained down-regulation, presumably to allow development of MSL1-associated DNA-repair activity. We conclude that interaction of MSL1 with 53BP1 brings MSL1-dependent HAT activity to the vicinity of damaged DNA. MSL1-dependent HAT activity, which is negatively regulated by the stress protein p8, induces chromatin remodeling and relaxation allowing access to DNA of the repair machinery. J. Cell. Physiol. 221: 594–602, 2009. © 2009 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

The hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease is responsible for the processing of the non-structural region of the viral precursor polyprotein in infected hepatic cells. HCV NS3 is a zinc-dependent serine protease. The zinc ion, which is bound far away from the active site and considered to have a structural role, is essential for the structural integrity of the protein; furthermore, the ion is required for the hydrolytic activity. Consequently, the NS3 zinc binding site has been considered for a long time as a possible target for drug discovery. As a first step towards this goal, the energetics of the NS3-zinc interaction and its effect on the NS3 conformation must be established and discussed. The thermodynamic characterization of zinc binding to NS3 protease by isothermal titration calorimetry and spectroscopy is presented here. Spectroscopic and calorimetric results suggest that a considerable conformational change in the protein is coupled to zinc binding. The energetics of the conformational change is comparable to that of the folding of a protein of similar size. Therefore, zinc binding to NS3 protease can be considered as a 'folding by binding' event. Proteins 2009. © 2009 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Hydantoin racemase enzyme plays a crucial role in the reaction cascade known as 'hydantoinase process.' In conjunction with a stereoselective hydantoinase and a stereospecific carbamoylase, it allows the total conversion from D,L-5-monosubstituted hydantoins, with a low rate of racemization, to optically pure D- or L-amino acids. Residues Cys76 and Cys181 belonging to hydantoin racemase from Sinorhizobium meliloti (SmeHyuA) have been proved to be involved in catalysis. Here, we report biophysical data of SmeHyuA Cys76 and Cys181 to alanine mutants, which point toward a two-base mechanism for the racemization of 5-monosubstituted hydantoins. The secondary and the tertiary structure of the mutants were not significantly affected, as shown by circular dichroism. Calorimetric and fluorescence experiments have shown that Cys76 is responsible for recognition and proton retrieval of D-isomers, while Cys181 is responsible for L-isomer recognition and racemization. This recognition process is further supported by measurements of protein stability followed by chemical denaturation in the presence of the corresponding compound. [ABSTRACT FROM AUTHOR]

In this paper we describe a new technique for the creation of featurebased stochastic maps using standard Polaroid sonar sensors. The fundamental contributions of our proposal are: (1) a perceptual grouping process that permits the robust identification and localization of environmental features, such as straight segments and corners, from the sparse and noisy sonar data; (2) a map joining technique that allows the system to build a sequence of independent limited-size stochastic maps and join them in a globally consistent way; (3) a robust mechanism to determine which features in a stochastic map correspond to the same environment feature, allowing the system to update the stochastic map accordingly, and perform tasks such as revisiting and loop closing. We demonstrate the practicality of this approach by building a geometric map of a medium size, real indoor environment, with several people moving around the robot. Maps built from laser data for the same experiment are provided for comparison. [ABSTRACT FROM AUTHOR]

Focuses on the problem associated with data association for simultaneous vehicle localization and map building of robots. Use of joint compatibility test in data association; Determination of the compatibility between sensor observation and map features; Impact of multitracking on robot complexity.

Studies the fusing range and intensity images for mobile robot localization. Integration of range points and intensity edges for mobile robot localization; Correspondence process for fusing vertical edges and images; Limitations inherent to the use of a priori maps for mobile robot localization.

Calafate (Berberis microphylla G. Forst) is a Patagonian barberry very rich in phenolic compounds. Our aim was to demonstrate, through in vitro models, that a comprehensive characterized calafate extract has a protective role against oxidative processes associated to cardiovascular disease development. Fifty-three phenolic compounds (17 of them not previously reported in calafate), were tentatively identified by Ultra-Liquid Chromatography with Diode Array Detector, coupled to Quadrupole-Time of Fly Mass Spectrometry (UHPLC-DAD-QTOF). Fatty acids profile and metals content were studied for the first time, by Gas Chromatography Mass Spectrometry (GC-MS) and Total X-ray Fluorescence (TXRF), respectively. Linolenic and linoleic acid, and Cu, Zn, and Mn were the main relevant compounds from these groups. The bioactivity of calafate extract associated to the cardiovascular protection was evaluated using Human Umbilical Vein Endothelial Cells (HUVECs) and human low density lipoproteins (LDL) to measure oxidative stress and lipid peroxidation. The results showed that calafate extract reduced intracellular Reactive Oxygen Species (ROS) production (51%) and completely inhibited LDL oxidation and malondialdehyde (MDA) formation. These findings demonstrated the potential of the relevant mix of compounds found in calafate extract on lipoperoxidation and suggest a promising protective effect for reducing the incidence of cardiovascular disease. [ABSTRACT FROM AUTHOR]

Disease associated genetic variations often cause intracellular enzyme inactivation, dysregulation and instability. However, allosteric communication of mutational effects to distant functional sites leading to loss-of-function remains poorly understood. We characterize here interdomain site-to-site communication by which a common cancer-associated single nucleotide polymorphism (c.C609T/p.P187S) reduces the activity and stability in vivo of NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a FAD-dependent, two-domain multifunctional stress protein acting as a Phase II enzyme, activating cancer pro-drugs and stabilizing p53 and p73α oncosuppressors. We show that p.P187S causes structural and dynamic changes communicated to functional sites far from the mutated site, affecting the FAD binding site located at the N-terminal domain (NTD) and accelerating proteasomal degradation through dynamic effects on the C-terminal domain (CTD). Structural protein:protein interaction studies reveal that the cancer-associated polymorphism does not abolish the interaction with p73α, indicating that oncosuppressor destabilization largely mirrors the low intracellular stability of p.P187S. In conclusion, we show how a single disease associated amino acid change may allosterically perturb several functional sites in an oligomeric and multidomain protein. These results have important implications for the understanding of loss-of-function genetic diseases and the identification of novel structural hot spots as targets for pharmacological intervention. [ABSTRACT FROM AUTHOR]