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Frontiers in Molecular Biosciences

Helena Tossavainen, Vytas Raulinaitis, Linda Kauppinen, Ulla Pentikäinen, Hannu Maaheimo, Perttu Permi
Lysostaphin from Staphylococcus simulans and its family enzymes rapidly acquire prominence as the next generation agents in treatment of S. aureus infections. The specificity of lysostaphin is promoted by its C-terminal cell wall targeting domain selectivity toward pentaglycine bridges in S. aureus cell wall. Scission of these cross-links is carried out by its N-terminal catalytic domain, a zinc-dependent endopeptidase. Understanding the determinants affecting the efficiency of catalysis and strength and specificity of interactions lies at the heart of all lysostaphin family enzyme applications...
2018: Frontiers in Molecular Biosciences
Arindam Datta, Robert M Brosh
Small molecules that deter the functions of DNA damage response machinery are postulated to be useful for enhancing the DNA damaging effects of chemotherapy or ionizing radiation treatments to combat cancer by impairing the proliferative capacity of rapidly dividing cells that accumulate replicative lesions. Chemically induced or genetic synthetic lethality is a promising area in personalized medicine, but it remains to be optimized. A new target in cancer therapy is DNA unwinding enzymes known as helicases...
2018: Frontiers in Molecular Biosciences
Vito Scalera, Nicola Giangregorio, Silvana De Leonardis, Lara Console, Emanuele Salvatore Carulli, Annamaria Tonazzi
The Mitochondrial Ascorbic Acid Transporter (MAT) from both rat liver and potato mitochondria has been reconstituted in proteoliposomes. The protein has a molecular mass in the range of 28-35 kDa and catalyzes saturable, temperature and pH dependent, unidirectional ascorbic acid transport. The transport activity is sodium independent and it is optimal at acidic pH values. It is stimulated by proton gradient, thus supporting that ascorbate is symported with H+ . It is efficiently inhibited by the lysine reagent pyridoxal phosphate and it is not affected by inhibitors of other recognized plasma and mitochondrial membranes ascorbate transporters GLUT1(glucose transporter-1) or SVCT2 (sodium-dependent vitamin C transporter-2)...
2018: Frontiers in Molecular Biosciences
Karim Housseini B Issa, Gilles Phan, Isabelle Broutin
Bacterial antibiotic resistance is a worldwide health problem that deserves important research attention in order to develop new therapeutic strategies. Recently, the World Health Organization (WHO) classified Pseudomonas aeruginosa as one of the priority bacteria for which new antibiotics are urgently needed. In this opportunistic pathogen, antibiotics efflux is one of the most prevalent mechanisms where the drug is efficiently expulsed through the cell-wall. This resistance mechanism is highly correlated to the expression level of efflux pumps of the resistance-nodulation-cell division (RND) family, which is finely tuned by gene regulators...
2018: Frontiers in Molecular Biosciences
Masatoshi Esaki, Ai Johjima-Murata, Md Tanvir Islam, Teru Ogura
The ATP-powered protein degradation machinery plays essential roles in maintaining protein homeostasis in all organisms. Robust proteolytic activities are typically sequestered within protein complexes to avoid the fatal removal of essential proteins. Because the openings of proteolytic chambers are narrow, substrate proteins must undergo unfolding. AAA superfamily proteins (ATPases associated with diverse cellular activities) are mostly located at these openings and regulate protein degradation appropriately...
2018: Frontiers in Molecular Biosciences
Laura Y Kim, William J Rice, Edward T Eng, Mykhailo Kopylov, Anchi Cheng, Ashleigh M Raczkowski, Kelsey D Jordan, Daija Bobe, Clinton S Potter, Bridget Carragher
Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user...
2018: Frontiers in Molecular Biosciences
Silvia Sacchi, Pamela Cappelletti, Giulia Murtas
The stereoselective flavoenzyme D-amino acid oxidase (DAAO) catalyzes the oxidative deamination of neutral and polar D-amino acids producing the corresponding α-keto acids, ammonia, and hydrogen peroxide. Despite its peculiar and atypical substrates, DAAO is widespread expressed in most eukaryotic organisms. In mammals (and humans in particular), DAAO is involved in relevant physiological processes ranging from D-amino acid detoxification in kidney to neurotransmission in the central nervous system, where DAAO is responsible of the catabolism of D-serine, a key endogenous co-agonist of N-methyl-D-aspartate receptors...
2018: Frontiers in Molecular Biosciences
Chitra Narayanan, David N Bernard, Khushboo Bafna, Donald Gagné, Pratul K Agarwal, Nicolas Doucet
Enzyme catalysis is a complex process involving several steps along the reaction coordinates, including substrate recognition and binding, chemical transformation, and product release. Evidence continues to emerge linking the functional and evolutionary role of conformational exchange processes in optimal catalytic activity. Ligand binding changes the conformational landscape of enzymes, inducing long-range conformational rearrangements. Using functionally distinct members of the pancreatic ribonuclease superfamily as a model system, we characterized the structural and conformational changes associated with the binding of two mononucleotide ligands...
2018: Frontiers in Molecular Biosciences
Massimiliano Meli, Maria Gasset, Giorgio Colombo
The self-assembly of proteins and peptides into amyloids is a key feature of an increasing number of diseases. Amyloid fibrils display a unique surface reactivity endowing the sequestration of molecules such as MicroRNAs, which can be the active moiety of the toxic action. To test this hypothesis we studied the recognition between a model RNA and two different steric zipper spines using molecular dynamics simulations. We found that the interaction occurs and displays peptide-sequence dependence. Interestingly, interactions with polar zipper surfaces such as the formed by SNQNNF are more stable and favor the formation of β-barrel like complexes resembling the structures of toxic oligomers...
2018: Frontiers in Molecular Biosciences
Kenji Ohe, Shinsuke Miyajima, Tomoko Tanaka, Yuriko Hamaguchi, Yoshihiro Harada, Yuta Horita, Yuki Beppu, Fumiaki Ito, Takafumi Yamasaki, Hiroki Terai, Masayoshi Mori, Yusuke Murata, Makito Tanabe, Ichiro Abe, Kenji Ashida, Kunihisa Kobayashi, Munechika Enjoji, Takashi Nomiyama, Toshihiko Yanase, Nobuhiro Harada, Toshiaki Utsumi, Akila Mayeda
Objectives: The high-mobility group A protein 1a (HMGA1a) protein is known as a transcription factor that binds to DNA, but recent studies have shown it exerts novel functions through RNA-binding. We were prompted to decipher the mechanism of HMGA1a-induced alternative splicing of the estrogen receptor alpha (ERα) that we recently reported would alter tamoxifen sensitivity in MCF-7 TAMR1 cells. Methods: Endogenous expression of full length ERα66 and its isoform ERα46 were evaluated in MCF-7 breast cancer cells by transient expression of HMGA1a and an RNA decoy (2'-O-methylated RNA of the HMGA1a RNA-binding site) that binds to HMGA1a...
2018: Frontiers in Molecular Biosciences
Mark S Roe, Ben Wahab, Zsolt Török, Ibolya Horváth, László Vigh, Chrisostomos Prodromou
Chaperones play a pivotal role in protein homeostasis, but with age their ability to clear aggregated and damaged protein from cells declines. Tau pathology is a driver of a variety of neurodegenerative disease and in Alzheimer's disease (AD) it appears to be precipitated by the formation of amyloid-β (Aβ) aggregates. Aβ-peptide appears to trigger Tau hyperphosphorylation, formation of neurofibrillary tangles and neurotoxicity. Recently, dihydropyridine derivatives were shown to upregulate the heat shock response (HSR) and provide a neuroprotective effect in an APPxPS1 AD mouse model...
2018: Frontiers in Molecular Biosciences
Andrew L Lee, Paul J Sapienza
Thymidylate synthase (TS) is a homodimeric enzyme with evidence for negative regulation of one protomer while the other protomer acts on substrate, so called half-the-sites reactivity. The mechanisms by which multisubunit allosteric proteins communicate between protomers is not well understood, and the simplicity of dimeric systems has advantages for observing conformational and dynamic processes that functionally connect distance-separated active sites. This review considers progress in overcoming the inherent challenges of accurate thermodynamic and atomic-resolution characterization of interprotomer communication mechanisms in symmetric protein dimers, with TS used as an example...
2018: Frontiers in Molecular Biosciences
G A Nagana Gowda, Gregory A Barding, Jin Dai, Haiwei Gu, Daciana H Margineantu, David M Hockenbery, Daniel Raftery
The Warburg effect is a well-known phenomenon in cancer, but the glutamine addiction in which cancer cells utilize glutamine as an alternative source of energy is less well known. Recent efforts have focused on preventing cancer cell proliferation associated with glutamine addiction by targeting glutaminase using the inhibitor BPTES (bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide). In the current study, an investigation of the BPTES induced changes in metabolism was made in two human breast cancer cell lines, MCF7 (an estrogen receptor dependent cell line) and MDA-MB231 (a triple negative cell line), relative to the non-cancerous cell line, MCF10A...
2018: Frontiers in Molecular Biosciences
Yury S Polikanov, Nikolay A Aleksashin, Bertrand Beckert, Daniel N Wilson
The ribosome is one of the major targets in the cell for clinically used antibiotics. However, the increase in multidrug resistant bacteria is rapidly reducing the effectiveness of our current arsenal of ribosome-targeting antibiotics, highlighting the need for the discovery of compounds with new scaffolds that bind to novel sites on the ribosome. One possible avenue for the development of new antimicrobial agents is by characterization and optimization of ribosome-targeting peptide antibiotics. Biochemical and structural data on ribosome-targeting peptide antibiotics illustrates the large diversity of scaffolds, binding interactions with the ribosome as well as mechanism of action to inhibit translation...
2018: Frontiers in Molecular Biosciences
Pierce T O'Neil, Alexandra J Machen, Benjamin C Deatherage, Caleb Trecazzi, Alexander Tischer, Venkata R Machha, Matthew T Auton, Michael R Baldwin, Tommi A White, Mark T Fisher
The nucleotide-free chaperonin GroEL is capable of capturing transient unfolded or partially unfolded states that flicker in and out of existence due to large-scale protein dynamic vibrational modes. In this work, three short vignettes are presented to highlight our continuing advances in the application of GroEL biosensor biolayer interferometry (BLI) technologies and includes expanded uses of GroEL as a molecular scaffold for electron microscopy determination. The first example presents an extension of the ability to detect dynamic pre-aggregate transients in therapeutic protein solutions where the assessment of the kinetic stability of any folded protein or, as shown herein, quantitative detection of mutant-type protein when mixed with wild-type native counterparts...
2018: Frontiers in Molecular Biosciences
Sofie V Hellsten, Rekha Tripathi, Mikaela M Ceder, Robert Fredriksson
Amino acid sensing and signaling is vital for cells, and both gene expression and protein levels of amino acid transporters are regulated in response to amino acid availability. Here, the aim was to study the regulation of all members of the SLC38 amino acid transporter family, Slc38a1-11 , in mouse brain cells following amino acid starvation. We reanalyzed microarray data for the immortalized hypothalamic cell line N25/2 subjected to complete amino acid starvation for 1, 2, 3, 5, or 16 h, focusing specifically on the SLC38 family...
2018: Frontiers in Molecular Biosciences
Priya Kalra, Abhijeet Dhiman, William C Cho, John G Bruno, Tarun K Sharma
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX...
2018: Frontiers in Molecular Biosciences
Shinsuke Ishigaki, Gen Sobue
Fused in sarcoma (FUS) is an RNA binding protein that regulates RNA metabolism including alternative splicing, transcription, and RNA transportation. FUS is genetically and pathologically involved in frontotemporal lobar degeneration (FTLD)/amyotrophic lateral sclerosis (ALS). Multiple lines of evidence across diverse models suggest that functional loss of FUS can lead to neuronal dysfunction and/or neuronal cell death. Loss of FUS in the nucleus can impair alternative splicing and/or transcription, whereas dysfunction of FUS in the cytoplasm, especially in the dendritic spines of neurons, can cause mRNA destabilization...
2018: Frontiers in Molecular Biosciences
Ana Galán-Cobo, Elena Arellano-Orden, Rocío Sánchez Silva, José Luis López-Campos, César Gutiérrez Rivera, Lourdes Gómez Izquierdo, Nela Suárez-Luna, María Molina-Molina, José A Rodríguez Portal, Miriam Echevarría
Activation of the epithelial-mesenchymal transition process (EMT) by which alveolar cells in human lung tissue undergo differentiation giving rise to a mesenchymal phenotype (fibroblast/miofibroblasts) has been well recognized as a key element in the origin of idiopathic pulmonary fibrosis (IPF). Here we analyzed expression of AQP1 in lung biopsies of patients diagnosed with IPF, and compared it to biopsies derived from patients with diverse lung pneumonies, such as hypersensitivity pneumonitis, sarcoidosis or normal lungs...
2018: Frontiers in Molecular Biosciences
Miguel Arbesú, Guillermo Iruela, Héctor Fuentes, João M C Teixeira, Miquel Pons
Structural disorder is an essential ingredient for function in many proteins and protein complexes. Fuzzy complexes describe the many instances where disorder is maintained as a critical element of protein interactions. In this minireview we discuss how intramolecular fuzzy interactions function in signaling complexes. Focussing on the Src family of kinases, we argue that the intrinsically disordered domains that are unique for each of the family members and display a clear fingerprint of long range interactions in Src, might have critical roles as functional sensor or effectors and mediate allosteric communication via fuzzy interactions...
2018: Frontiers in Molecular Biosciences
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