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https://www.readbyqxmd.com/read/29792795/tuning-the-morphology-of-nanostructured-peptide-films-by-introduction-of-a-secondary-structure-conformational-constraint-a-case-study-of-hierarchical-self-assembly
#1
Marta De Zotti, Beatrice Muzzi, Emanuela Gatto, Benedetta Di Napoli, Claudia Mazzuca, Antonio Palleschi, Ernesto Placidi, Fernando Formaggio, Claudio Toniolo, Mariano Venanzi
Peptide self-assembly is ubiquitous in nature. It governs the organization of proteins, controlling their folding kinetics and preserving their structure stability and bioactivity. In this connection, model oligopeptides may give important insights on the molecular mechanisms and elementary forces driving the formation of supramolecular structures. In this contribution we show that a single residue substitution, i.e. Aib (α-aminoisobutyric acid) in place of Ala at position 4 of an -(L-Ala)5- homo-oligomer, strongly alters the aggregation process...
May 24, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29791461/a-discrete-mathematical-model-for-the-aggregation-of-%C3%AE-amyloid
#2
Maher A Dayeh, George Livadiotis, Saber Elaydi
Dementia associated with the Alzheimer's disease is thought to be correlated with the conversion of the β - Amyloid (Aβ) peptides from soluble monomers to aggregated oligomers and insoluble fibrils. We present a discrete-time mathematical model for the aggregation of Aβ monomers into oligomers using concepts from chemical kinetics and population dynamics. Conditions for the stability and instability of the equilibria of the model are established. A formula for the number of monomers that is required for producing oligomers is also given...
2018: PloS One
https://www.readbyqxmd.com/read/29790563/backbone-conformation-affects-duplex-initiation-and-duplex-propagation-in-hybridisation-of-synthetic-h-bonding-oligomers
#3
Giulia Iadevaia, Diego Núñez-Villanueva, Alexander E Stross, Christopher A Hunter
Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene...
May 23, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29790112/an-automated-high-throughput-method-for-interpreting-the-tandem-mass-spectra-of-glycosaminoglycans
#4
Jiana Duan, I Jonathan Amster
The biological interactions between glycosaminoglycans (GAGs) and other biomolecules are heavily influenced by structural features of the glycan. The structure of GAGs can be assigned using tandem mass spectrometry (MS2 ), but analysis of these data, to date, requires manually interpretation, a slow process that presents a bottleneck to the broader deployment of this approach to solving biologically relevant problems. Automated interpretation remains a challenge, as GAG biosynthesis is not template-driven, and therefore, one cannot predict structures from genomic data, as is done with proteins...
May 22, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29789820/structural-mechanisms-of-oligomer-and-amyloid-fibril-formation-by-the-prion-protein
#5
Ishita Sengupta, Jayant B Udgaonkar
Misfolding and aggregation of the prion protein is responsible for multiple neurodegenerative diseases. Works from several laboratories on folding of both the WT and multiple pathogenic mutant variants of the prion protein have identified several structurally dissimilar intermediates, which might be potential precursors to misfolding and aggregation. The misfolded aggregates themselves are morphologically distinct, critically dependent on the solution conditions under which they are prepared, but always β-sheet rich...
May 23, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29789539/proteasomal-degradation-of-the-histone-acetyl-transferase-p300-contributes-to-beta-cell-injury-in-a-diabetes-environment
#6
Lucie Ruiz, Tatyana Gurlo, Magalie A Ravier, Anne Wojtusciszyn, Julia Mathieu, Matthew R Brown, Christophe Broca, Gyslaine Bertrand, Peter C Butler, Aleksey V Matveyenko, Stéphane Dalle, Safia Costes
In type 2 diabetes, amyloid oligomers, chronic hyperglycemia, lipotoxicity, and pro-inflammatory cytokines are detrimental to beta-cells, causing apoptosis and impaired insulin secretion. The histone acetyl transferase p300, involved in remodeling of chromatin structure by epigenetic mechanisms, is a key ubiquitous activator of the transcriptional machinery. In this study, we report that loss of p300 acetyl transferase activity and expression leads to beta-cell apoptosis, and most importantly, that stress situations known to be associated with diabetes alter p300 levels and functional integrity...
May 22, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29789410/a-randomised-open-label-parallel-group-phase-2-study-of-antisense-oligonucleotide-therapy-in-acromegaly
#7
Peter J Trainer, John Newell-Price, John Ayuk, Simon Aylwin, D Aled Rees, Wm Drake, Philippe Chanson, Thierry Brue, Susan M Webb, Carmen Fajardo Montañana, Javier Aller, Ann I McCormack, David J Torpy, George Tachas, Lynne Atley, David Ryder, Martin Bidlingmaier
OBJECTIVE: ATL1103 is a second-generation antisense oligomer targeting the human GH receptor. This phase 2 randomised, open-label, parallel-group study assessed the potential of ATL1103 as a treatment for acromegaly. DESIGN: 26 patients with active acromegaly (IGF-I >130% upper limit of normal) were randomised to subcutaneous ATL1103 200 mg either once- or twice-weekly for 13 weeks, and monitored for a further 8-week washout period. METHODS: The primary efficacy measures were change in IGF-I at week 14, compared to baseline and between cohorts...
May 22, 2018: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29788274/arabidopsis-skp1-like-protein-13-ask13-positively-regulates-seed-germination-and-seedling-growth-under-abiotic-stresses
#8
Venkateswara Rao, Bhanu Prakash Petla, Pooja Verma, Prafull Salvi, Nitin Uttam Kamble, Sharboni Ghosh, Harmeet Kaur, Saurabh C Saxena, Manoj Majee
SKP1 (S-Phase Kinase Associated Protein1) proteins are key members of the SCF (SKP-Cullin-F-box protein) E3 ligase complexes that ubiquitinate the target proteins and play diverse roles in plant biology. However, as compared to other members of the SCF complex, study of SKP1-like proteins is very limited in plants. In the present work, we report that Arabidopsis SKP1-like protein13 (ASK13) is differentially regulated in different organs, during seed development and germination, and is upregulated in response to abiotic stresses...
May 18, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29788004/juvenile-traumatic-brain-injury-results-in-cognitive-deficits-associated-with-impaired-endoplasmic-reticulum-stress-and-early-tauopathy
#9
Michael J Hylin, Ryan C Holden, Aidan C Smith, Aric F Logsdon, Rabia Qaiser, Brandon P Lucke-Wold
The leading cause of death in the juvenile population is trauma, and in particular neurotrauma. The juvenile brain response to neurotrauma is not completely understood. Endoplasmic reticulum (ER) stress has been shown to contribute to injury expansion and behavioral deficits in adult rodents and furthermore has been seen in adult postmortem human brains diagnosed with chronic traumatic encephalopathy. Whether endoplasmic reticulum stress is increased in juveniles with traumatic brain injury (TBI) is poorly delineated...
May 22, 2018: Developmental Neuroscience
https://www.readbyqxmd.com/read/29787346/-slipped-sandwich-model-for-chitin-and-chitosan-perception-in-arabidopsis
#10
Ekaterina Gubaeva, Airat Gubaev, Rebacca Melcher, Stefan Cord-Landwehr, Ratna Singh, Nour Eddine El Gueddari, Bruno Maria Moerschbacher
Chitin, a linear polymer of N-acetyl-D-glucosamine, and chitosans, fully or partially deacetylated derivatives of chitin, are known to elicit defense reactions in higher plants. We compared the ability of chitin and chitosan oligomers and polymers (chitin oligomers with degree of polymerization 3 to 8; chitosan oligomers with degree of acetylation 0% to 35% and degree of polymerization 3 to 15; chitosan polymers with degree of acetylation 1% to 60% and degree of polymerization ~1300) to elicit an oxidative burst indicative of induced defense reactions in A...
May 22, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29786756/backbone-nmr-assignments-of-hypf-n-under-conditions-generating-toxic-and-non-toxic-oligomers
#11
Jayneil R Patel, Yingqi Xu, Claudia Capitini, Fabrizio Chiti, Alfonso De Simone
The HypF protein is involved in the maturation and regulation of hydrogenases. The N-terminal domain of HypF (HypF-N) has served as a key model system to study the pathways of protein amyloid formation and the nature of the toxicity of pre-fibrilar protein oligomers. This domain can aggregate into two forms of oligomers having significantly different toxic effects when added to neuronal cultures. Here, NMR assignments of HypF-N backbone resonances are presented in its native state and under the conditions favouring the formation of toxic and non-toxic oligomers...
May 21, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29786666/dopamine-receptor-subtypes-differentially-regulate-autophagy
#12
Dongmei Wang, Xinmiao Ji, Juanjuan Liu, Zhiyuan Li, Xin Zhang
Some dopamine receptor subtypes were reported to participate in autophagy regulation, but their exact functions and mechanisms are still unclear. Here we found that dopamine receptors D2 and D3 (D2-like family) are positive regulators of autophagy, while dopamine receptors D1 and D5 (D1-like family) are negative regulators. Furthermore, dopamine and ammonia, the two reported endogenous ligands of dopamine receptors, both can induce dopamine receptor internalization and degradation. In addition, we found that AKT (protein kinase B)-mTOR (mechanistic target of rapamycin) and AMPK (AMP-activated protein kinase) pathways are involved in DRD3 (dopamine receptor D3) regulated autophagy...
May 22, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29783772/acid-sphingomyelinase-promotes-cellular-internalization-of-clostridium-perfringens-iota-toxin
#13
Masahiro Nagahama, Masaya Takehara, Kazuaki Miyamoto, Kazumi Ishidoh, Keiko Kobayashi
Clostridium perfringens iota-toxin is a binary actin-ADP-ribosylating toxin composed of the enzymatic component Ia and receptor binding component Ib. Ib binds to a cell surface receptor, forms Ib oligomer in lipid rafts, and associates with Ia. The Ia-Ib complex then internalizes by endocytosis. Here, we showed that acid sphingomyelinase (ASMase) facilitates the cellular uptake of iota-toxin. Inhibitions of ASMase and lysosomal exocytosis by respective blockers depressed cell rounding induced by iota-toxin...
May 20, 2018: Toxins
https://www.readbyqxmd.com/read/29782982/process-optimization-purification-and-characterization-of-a-novel-acidic-thermostable-chitinase-from-humicola-grisea
#14
Manish Kumar, Amandeep Brar, V Vivekanand, Nidhi Pareek
An extracellular acidic and thermostable chitinase (HgChi) from thermophilic Humicola grisea was purified and characterized. Enhancement in chitinase production (Qp  = 2.9662 Ul-1  h-1 ) was achieved through derivation of optimum fermentation conditions via central composite design. H. grisea observed to produce various isoforms of chitinase, among which the major expressed form has molecular mass of about 50 kDa. Purified chitinases exhibited optimal activity at pH 3.0 and 70 °C. Chitinase showed notable stability at increasing temperatures...
May 18, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29782825/characterization-of-an-n-terminal-mutant-of-%C3%AE-a-crystallin-%C3%AE-a-r21q-associated-with-congenital-cataract
#15
Ashutosh S Phadte, Puttur Santhoshkumar, K Krishna Sharma
Several mutations associated with congenital cataracts in human beings target conserved arginine residues in αA-crystallin. The N-terminal region of αA-crystallin is a "mutational hotspot," with multiple cataract-related mutations reported in this region. Two mutations at arginine 21 in the N-terminal domain of αA-crystallin - αA-R21L and αA-R21W have been associated with congenital cataract. A third mutant of R21, αA-R21Q, was recently identified to be associated with congenital cataract in a South Australian family...
May 18, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29782818/antimicrobial-activity-profiles-of-amphiphilic-xanthone-derivatives-are-a-function-of-their-molecular-oligomerization
#16
Jun-Jie Koh, Shuimu Lin, Yang Bai, Wendy Wan Ling Sin, Thet Tun Aung, Jianguo Li, Verma Chandra, Konstantin Pervushin, Roger W Beuerman, Shouping Liu
Currently, membrane-targeting small antimicrobial peptidomimetics (SAP) are important in antibiotic development because bacteria appear to develop resistance to these surface-active compounds less readily. However, the molecular membrane-targeting action of SAPs has received little attention. In this study, we investigated the effect of oligomerization of amphiphilic xanthone, a model SAP, on its antimicrobial properties against both Gram-positive and Gram-negative bacteria. First, oligomer formation by an amphiphilic xanthone, compound 2 (also coded as AM052), was investigated via solution-state nuclear magnetic resonance (NMR) spectroscopy...
May 18, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29780983/the-predictive-power-of-aromaticity-quantitative-correlation-between-aromaticity-and-ionization-potentials-and-homo-lumo-gaps-in-oligomers-of-benzene-pyrrole-furan-and-thiophene
#17
Renana Gershoni-Poranne, Anuja P Rahalkar, Amnon Stanger
Aromaticity is a central and ubiquitous concept in organic chemistry, and is used extensively to explain various phenomena. Yet, aromaticity cannot be observed or measured as a property in its own right and, to date, only qualitative and semi-quantitative relationships have been described between aromaticity and an observable property. We now demonstrate for the first time a robust quantitative relationship between the HOMO-LUMO gap and adiabatic ionization potential of a polycyclic aromatic hydrocarbon oligomer - both measurable physical quantities - and its aromaticity, as quantified by the Nucleus Independent Chemical Shift (NICS) index...
May 21, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29780454/phosphate-phosphate-oligomerization-drives-higher-order-co-assemblies-with-stacks-of-cyanostar-macrocycles
#18
Elisabeth M Fatila, Maren Pink, Eric B Twum, Jonathan A Karty, Amar H Flood
The importance of phosphate in biology and chemistry has long motivated investigation of its recognition. Despite this interest, phosphate's facile oligomerization is only now being examined following the discovery of complexes of anion-anion dimers of hydroxyanions. Here we address how oligomerization dictates phosphate's recognition properties when engaged with planar cyanostar macrocycles that can also oligomerize by stacking. The crystal structure of cyanostar with phosphate shows an unprecedented tetrameric stack of cyanostar macrocycles threaded by a phosphate trimer, [H2 PO4 ···H2 PO4 ···H2 PO4 ]3- ...
March 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29779787/a-thermodynamic-funnel-drives-bacterial-lipopolysaccharide-transfer-in-the-tlr4-pathway
#19
Roland G Huber, Nils A Berglund, Vasileios Kargas, Jan K Marzinek, Daniel A Holdbrook, Syma Khalid, Thomas J Piggot, Artur Schmidtchen, Peter J Bond
The Gram-negative bacterial outer membrane contains lipopolysaccharide, which potently stimulates the mammalian innate immune response. This involves a relay of specialized complexes culminating in transfer of lipopolysaccharide from CD14 to Toll-like receptor 4 (TLR4) and its co-receptor MD-2 on the cell surface, leading to activation of downstream inflammatory responses. In this study we develop computational models to trace the TLR4 cascade in near-atomic detail. We demonstrate through rigorous thermodynamic calculations that lipopolysaccharide molecules traversing the receptor cascade fall into a thermodynamic funnel...
April 25, 2018: Structure
https://www.readbyqxmd.com/read/29779213/differential-toxicity-of-tdp-43-isoforms-depends-on-their-sub-mitochondrial-localization-in-neuronal-cells
#20
Illari Salvatori, Alberto Ferri, Silvia Scaricamazza, Ilaria Giovannelli, Alessia Serrano, Simona Rossi, Nadia D'Ambrosi, Mauro Cozzolino, Andrea Di Giulio, Sandra Moreno, Cristiana Valle, Maria Teresa Carrì
TAR DNA binding protein 43 (TDP-43) is an RNA binding protein and a major component of protein aggregates found in Amyotrophic Lateral Sclerosis and several other neurodegenerative diseases. TDP-43 exists as a full length protein and as two shorter forms of 25 and 35 kDa. Full length mutant TDP-43s found in ALS patients re-localize from the nucleus to the cytoplasm and in part to mitochondria, where they exert a toxic role associated with neurodegeneration. However, induction of mitochondrial damage by TDP-43 fragments is yet to be clarified...
May 20, 2018: Journal of Neurochemistry
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