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Biochimica et Biophysica Acta

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https://www.readbyqxmd.com/read/28636874/next-generation-matrix-metalloproteinase-inhibitors-novel-strategies-bring-new-prospects
#1
REVIEW
Maxim Levin, Yael Udi, Inna Solomonov, Irit Sagi
Enzymatic proteolysis of cell surface proteins and extracellular matrix (ECM) is critical for tissue homeostasis and cell signaling. These proteolytic activities are mediated predominantly by a family of proteases termed matrix metalloproteinases (MMPs). The growing evidence in recent years that ECM and non-ECM bioactive molecules (e.g., growth factors, cytokines, chemokines, on top of matrikines and matricryptins) have versatile functions redefines our view on the roles matrix remodeling enzymes play in many physiological and pathological processes, and underscores the notion that ECM proteolytic reaction mechanisms represent master switches in the regulation of critical biological processes and govern cell behavior...
June 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28634116/succinate-induced-neuronal-mitochondrial-fission-and-hexokinase-ii-malfunction-in-ischemic-stroke-therapeutical-effects-of-kaempferol
#2
Bin Wu, Hong Luo, Xu Zhou, Cai-Yi Cheng, Lin Lin, Bao-Lin Liu, Kang Liu, Ping Li, Hua Yang
Mitochondrial dysfunction is known as one of causative factors in ischemic stroke, leading to neuronal cell death. The present work was undertaken to investigate whether succinate induces neuron apoptosis by regulating mitochondrial morphology and function. In neurons, oxygen-glucose deprivation induced succinate accumulation due to the reversal of succinate dehydrogenase (SDH) activation, leading to mitochondrial fission. Kaempferol inhibited mitochondrial fission and maintained mitochondrial HK-II through activation of Akt, and thereby protected neurons from succinate-mediated ischemi injury...
June 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28634030/effects-of-membrane-curvature-and-ph-on-proton-pumping-activity-of-single-cytochrome-bo3-enzymes
#3
Mengqiu Li, Sanobar Khan, Honglin Rong, Roman Tuma, Nikos S Hatzakis, Lars J C Jeuken
The molecular mechanism of proton pumping by heme-copper oxidases (HCO) has intrigued the scientific community since it was first proposed. We have recently reported a novel technology that enables the continuous characterisation of proton transport activity of a HCO and ubiquinol oxidase from Escherichia coli, cytochrome bo3, for hundreds of seconds on the single enzyme level (Li et al. J Am Chem Soc 137 (2015) 16055-16063). Here, we have extended these studies by additional experiments and analyses of the proton transfer rate as a function of proteoliposome size and pH at the N- and P-side of single HCOs...
June 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28630024/proteolytic-control-of-interleukin-11-and-interleukin-6-biology
#4
REVIEW
Juliane Lokau, Maria Agthe, Charlotte M Flynn, Christoph Garbers
Interleukin-11 (IL-11) and IL-6 are secreted glycoproteins which fulfill important homeostatic functions. Activation of target cells occurs via membrane-bound IL-11 and IL-6 receptors (IL-11R and IL-6R, respectively). Formation of IL-11/IL-11R and IL-6/IL-6R complexes triggers the recruitment of a homodimer of the ubiquitously expressed signal-transducing β-receptor gp130 (classic signaling). IL-11R and IL-6R can be shed by several proteases, albeit with different preferences and specificities, and these soluble receptors (sIL-11R and sIL-6R) act as agonists and can activate in principle all cells via gp130...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28630007/rna-localization-making-its-way-to-the-center-stage
#5
REVIEW
Ashley Chin, Eric Lécuyer
Cells are highly organized entities that rely on intricate addressing mechanisms to sort their constituent molecules to precise subcellular locations. These processes are crucial for cells to maintain their proper organization and carry out specialized functions in the body, while genetic perturbations that clog up these addressing systems can contribute to disease aetiology. The trafficking of RNA molecules represents an important layer in the control of cellular organization, a process that is both highly prevalent and for which features of the regulatory machineries have been deeply conserved evolutionarily...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28630006/multiple-conformational-states-of-dnaa-protein-regulate-its-interaction-with-dnaa-boxes-in-the-initiation-of-dna-replication
#6
Meera J Patel, Lavesh Bhatia, Gulden Yilmaz, Esther E Biswas-Fiss, Subhasis B Biswas
DnaA protein is the initiator of genomic DNA replication in prokaryotes. It binds to specific DNA sequences in the origin of DNA replication and unwinds small AT-rich sequences downstream for the assembly of the replisome. The mechanism of activation of DnaA that enables it to bind and organize the origin DNA and leads to replication initiation remains unclear. In this study, we have developed double-labeled fluorescent DnaA probes to analyze conformational states of DnaA protein upon binding DNA, nucleotide, and Soj sporulation protein using Fluorescence Resonance Energy Transfer (FRET)...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28629946/phytol-induced-pathology-in-2-hydroxyacyl-coa-lyase-hacl1-deficient-mice-evidence-for-a-second-non-hacl1-related-lyase
#7
Serena Mezzar, Evelyn De Schryver, Stanny Asselberghs, Els Meyhi, Petruta L Morvay, Myriam Baes, Paul P Van Veldhoven
2-Hydroxyacyl-CoA lyase (HACL1) is a key enzyme of the peroxisomal α-oxidation of phytanic acid. To better understand its role in health and disease, a mouse model lacking HACL1 was investigated. Under normal conditions, these mice did not display a particular phenotype. However, upon dietary administration of phytol, phytanic acid accumulated in tissues, mainly in liver and serum of KO mice. As a consequence of phytanic acid (or a metabolite) toxicity, KO mice displayed a significant weight loss, absence of abdominal white adipose tissue, enlarged and mottled liver and reduced hepatic glycogen and triglycerides...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28629864/structure-function-relationships-in-human-d-aspartate-oxidase-characterisation-of-variants-corresponding-to-known-single-nucleotide-polymorphisms
#8
Masumi Katane, Ryo Kanazawa, Risa Kobayashi, Megumi Oishi, Kazuki Nakayama, Yasuaki Saitoh, Tetsuya Miyamoto, Masae Sekine, Hiroshi Homma
D-Aspartate oxidase (DDO) is a degradative enzyme that is stereospecific for the acidic amino acid D-aspartate, an endogenous agonist of the N-methyl-D-aspartate (NMDA) receptor. Dysregulation of NMDA receptor-mediated neurotransmission has been implicated in the onset of various neuropsychiatric disorders including schizophrenia and in chronic pain. Thus, appropriate regulation of the amount of D-aspartate is believed to be important for maintaining proper neural activity in the nervous system. Herein, the effects of the non-synonymous single nucleotide polymorphisms (SNPs) R216Q and S308N on several properties of human DDO were examined...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28629863/the-unfolding-mechanism-of-monomeric-mutant-sod1-by-simulated-force-spectroscopy
#9
Mona Habibi, Jörg Rottler, Steven S Plotkin
Mechanical unfolding of mutated apo, disulfide-reduced, monomeric superoxide dismutase 1 protein (SOD1) has been simulated via force spectroscopy techniques, using both an all-atom (AA), explicit solvent model and a coarse-grained heavy-atom Gō (HA-Gō) model. The HA-Gō model was implemented at two different pulling speeds for comparison. The most-common sequence of unfolding in the AA model agrees well with the most-common unfolding sequence of the HA-Gō model, when the same normalized pulling rate was used...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28629718/changes-in-podocyte-trpc-channels-evoked-by-plasma-and-sera-from-patients-with-recurrent-fsgs-and-by-putative-glomerular-permeability-factors
#10
Eun Young Kim, Hila Roshanravan, Stuart E Dryer
Primary forms of focal and segmental glomeruloslerosis (FSGS) are driven by circulating factors that cause dysfunction or loss podocytes. Rare genetic forms of FSGS can be caused by mutations in TRPC6, which encodes a Ca(2+)-permeable cationic channel expressed in mesangial cells and podocytes; and NPHS2, which encodes podocin, a TRPC6-binding protein expressed in podocyte slit diaphragm domains. Here we observed that exposing immortalized mouse podocytes to serum or plasma from recurrent FSGS patients for 24h increased the steady-state cell-surface abundance of TRPC6, accompanied by an increase in currents through endogenous TRPC6 channels evoked by a hypoosmotic stretch stimulus...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625917/the-cholangiocyte-primary-cilium-in-health-and-disease
#11
REVIEW
Adrian P Mansini, Estanislao Peixoto, Kristen M Thelen, Cesar Gaspari, Sujeong Jin, Sergio A Gradilone
Cholangiocytes, like most cells, express primary cilia extending from their membranes. These organelles function as antennae which detect stimuli from bile and transmit the information into cells regulating several signaling pathways involved in secretion, proliferation and apoptosis. The ability of primary cilia to detect different signals is provided by ciliary associated proteins which are expressed in its membrane. Defects in the structure and/or function of these organelles lead to cholangiociliopathies that result in cholangiocyte hyperproliferation, altered fluid secretion and absorption...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625916/er-stress-disturbs-sr-er-mitochondria-ca-2-transfer-implications-in-duchenne-muscular-dystrophy
#12
Marion Pauly, Claire Angebault-Prouteau, Haikel Dridi, Cécile Notarnicola, Valérie Scheuermann, Alain Lacampagne, Stefan Matecki, Jérémy Fauconnier
Besides its role in calcium (Ca(2+)) homeostasis, the sarco-endoplamic reticulum (SR/ER) controls protein folding and is tethered to mitochondria.Under pathophysiological conditions the unfolded protein response (UPR) is associated with disturbance in SR/ER-mitochondria crosstalk. Here, we investigated whether ER stress altered SR/ER-mitochondria links, Ca(2+) handling and muscle damage in WT (Wild Type) and mdx mice, the murine model of Duchenne Muscular Dystrophy (DMD). In WT mice, the SR/ER-mitochondria links were decreased in isolated FDB muscle fibers after injection of ER stress activator tunicamycin (TM)...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625915/high-fat-diet-induced-obesity-increases-myocardial-injury-and-alters-cardiac-stat3-signaling-in-mice-after-polymicrobial-sepsis
#13
Theodore DeMartini, Marchele Nowell, Jeanne James, Lauren Williamson, Patrick Lahni, Hui Shen, Jennifer M Kaplan
Little is known about how obesity affects the heart during sepsis and we sought to investigate the obesity-induced cardiac effects that occur during polymicrobial sepsis. Six-week old C57BL/6 mice were randomized to a high fat (HFD) (60% kcal fat) or normal diet (ND) (16% kcal fat). After 6 wks of feeding, mice were anesthetized with isoflurane and polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Plasma and cardiac tissue were obtained for analysis. Echocardiography was performed on a separate cohort of mice at 0 and 18h after CLP...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625737/insights-into-the-conformations-and-dynamics-of-intrinsically-disordered-proteins-using-single-molecule-fluorescence
#14
REVIEW
Gregory-Neal Gomes, Claudiu C Gradinaru
Most proteins are not static structures, but many of them are found in a dynamic state, exchanging conformations on various time scales as a key aspect of their biological function. An entire spectrum of structural disorder exists in proteins and obtaining a satisfactory quantitative description of these states remains a challenge. Single-molecule fluorescence spectroscopy techniques are uniquely suited for this task, by measuring conformations without ensemble averaging and kinetics without interference from asynchronous processes...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625736/use-of-bioconjugation-with-cytochrome-p450-enzymes
#15
REVIEW
Julie Ducharme, Karine Auclair
Bioconjugation, defined as chemical modification of biomolecules, is widely employed in biological and biophysical studies. It can expand functional diversity and enable applications ranging from biocatalysis, biosensing and even therapy. This review summarizes how chemical modifications of cytochrome P450 enzymes (P450s or CYPs) have contributed to improving our understanding of these enzymes. Genetic modifications of P450s have also proven very useful but are not covered in this review. Bioconjugation has served to gain structural information and investigate the mechanism of P450s via photoaffinity labeling, mechanism-based inhibition (MBI) and fluorescence studies...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625689/multiple-and-complex-influences-of-connexins-and-pannexins-on-cell-death
#16
REVIEW
Jérôme Gilleron, Diane Carette, Dominique Segretain, Georges Pointis
Cell death is a fundamental process for organogenesis, immunity and cell renewal. During the last decades a broad range of molecular tools were identified as important players for several different cell death pathways (apoptosis, pyroptosis, necrosis, autosis…). Aside from these direct regulators of cell death programs, several lines of evidence proposed connexins and pannexins as potent effectors of cell death. In the present review we discussed the potential roles played by connexins, pannexins and innexins in the different cell death programs at different scales from gap junction intercellular communication to protein-protein interactions...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625421/insights-into-the-anticancer-properties-of-the-first-antimicrobial-peptide-from-archaea
#17
Rosa Gaglione, Luciano Pirone, Biancamaria Farina, Salvatore Fusco, Giovanni Smaldone, Martina Aulitto, Eliana Dell'Olmo, Emanuela Roscetto, Annarita Del Gatto, Roberto Fattorusso, Eugenio Notomista, Laura Zaccaro, Angela Arciello, Emilia Pedone, Patrizia Contursi
BACKGROUND: The peptide VLL-28, identified in the sequence of an archaeal protein, the transcription factor Stf76 from Sulfolobus islandicus, was previously identified and characterized as an antimicrobial peptide, possessing a broad-spectrum antibacterial activity. METHODS: Through a combined approach of NMR and Circular Dichroism spectroscopy, Dynamic Light Scattering, confocal microscopy and cell viability assays, the interaction of VLL-28 with the membranes of both parental and malignant cell lines has been characterized and peptide mechanism of action has been studied...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28625420/formation-and-remodeling-of-the-brain-extracellular-matrix-in-neural-plasticity-roles-of-chondroitin-sulfate-and-hyaluronan
#18
REVIEW
Shinji Miyata, Hiroshi Kitagawa
BACKGROUND: The extracellular matrix (ECM) of the brain is rich in glycosaminoglycans such as chondroitin sulfate (CS) and hyaluronan. These glycosaminoglycans are organized into either diffuse or condensed ECM. Diffuse ECM is distributed throughout the brain and fills perisynaptic spaces, whereas condensed ECM selectively surrounds parvalbumin-expressing inhibitory neurons (PV cells) in mesh-like structures called perineuronal nets (PNNs). The brain ECM acts as a non-specific physical barrier that modulates neural plasticity and axon regeneration...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28624556/a-64-bp-sequence-containing-the-gaaga-motif-is-essential-for-camv-35s-promoter-methylation-in-gentian
#19
Asahi Shimada, Azusa Okumura, Satoshi Yamasaki, Yuji Iwata, Nozomu Koizumi, Masahiro Nishihara, Kei-Ichiro Mishiba
This study investigated sequence specificity and perenniality of DNA methylation in the cauliflower mosaic virus (CaMV) 35S promoter of transgenic gentian (Gentiana triflora×G. scabra) plants. Unlike conventional transgene silencing models, 35S promoter hypermethylation in gentian is species-specific and occurs irrespective of the T-DNA copy number and genomic location. Modified 35S promoters were introduced into gentian, and single-copy transgenic lines were selected for methylation analysis. Modified 35S promoter lacking a core (-90) region [35S(Δcore)] in gentian conferred hypermethylation and high levels of de novo methylation of the CpHpH/CpCpG sites in the 35S enhancer regions (-298 to -241 and -148 to -85)...
June 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28624497/new-paradigms-for-the-hedgehog-signaling-network-in-mammary-gland-development-and-breast-cancer
#20
REVIEW
Teresa Monkkonen, Michael T Lewis
The Hedgehog signaling network regulates organogenesis, cell fate, proliferation, survival, and stem cell self-renewal in many mammalian tissues. Aberrant activation of the Hedgehog signaling network is present in ~25% of all cancers, including breast. Altered expression of Hedgehog network genes in the mammary gland can elicit phenotypes at many stages of development. However, synthesizing a cohesive mechanistic model of signaling at different stages of development has been difficult. Emerging data suggest that this difficulty is due, in part, to non-canonical and tissue compartment-specific (i...
June 14, 2017: Biochimica et Biophysica Acta
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