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https://www.readbyqxmd.com/read/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#1
Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, Ruth Nussinov
Computational prediction and design of membrane protein-protein interactions facilitate biomedical engineering and biotechnological applications. Due to their antimicrobial activity, human defensins play an important role in the innate immune system. Human defensins are attractive pharmaceutical targets due to their small size, broad activity spectrum, reduced immunogenicity, and resistance to proteolysis. Protein engineering based modification of defensins can improve their pharmaceutical properties. Here we present an approach to computationally probe defensins' oligomerization states in the membrane...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913684/transporter-oligomerization-form-and-function
#2
REVIEW
Yilmaz Alguel, Alexander D Cameron, George Diallinas, Bernadette Byrne
Transporters are integral membrane proteins with central roles in the efficient movement of molecules across biological membranes. Many transporters exist as oligomers in the membrane. Depending on the individual transport protein, oligomerization can have roles in membrane trafficking, function, regulation and turnover. For example, our recent studies on UapA, a nucleobase ascorbate transporter, from Aspergillus nidulans, have revealed both that dimerization of this protein is essential for correct trafficking to the membrane and the structural basis of how one UapA protomer can affect the function of the closely associated adjacent protomer...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913663/resistance-of-dynamin-related-protein-1-oligomers-to-disassembly-impairs-mitophagy-resulting-in-myocardial-inflammation-and-heart-failure
#3
Thomas J Cahill, Vincenzo Leo, Matthew Kelly, Alexander Stockenhuber, Nolan W Kennedy, Leyuan Bao, Grazia M Cereghetti, Andrew R Harper, Gabor Czibik, Chunyan Liao, Mohammed Bellahcene, Violetta Steeples, Sahar Ghaffari, Arash Yavari, Alice Mayer, Joanna Poulton, David J P Ferguson, Luca Scorrano, Nishani T Hettiarachchi, Chris Peers, John Boyle, R Blake Hill, Alison Simmons, Hugh Watkins, T Neil Dear, Houman Ashrafian
No abstract text is available yet for this article.
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27911757/local-and-use-dependent-effects-of-%C3%AE-amyloid-oligomers-on-nmda-receptor-function-revealed-by-optical-quantal-analysis
#4
Brooke L Sinnen, Aaron B Bowen, Emily S Gibson, Matthew J Kennedy
: Beta amyloid (Aβ) triggers the elimination of excitatory synaptic connections in the CNS, an early manifestation of Alzheimer's disease. Oligomeric assemblies of Aβ peptide associate with excitatory synapses resulting in synapse elimination through a process that requires NMDA-type glutamate receptor activation. Whether Aβ affects synaptic NMDA receptor (NMDAR) function directly and acts locally at synapses to which it has bound and whether synaptic activity influences Aβ synaptic binding and synaptotoxicity have remained fundamental questions...
November 9, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27909051/the-chaperone-activity-and-substrate-spectrum-of-human-small-heat-shock-proteins
#5
Evgeny V Mymrikov, Marina Daake, Bettina Richter, Martin Haslbeck, Johannes Buchner
Small heat shock proteins (sHsps) are a ubiquitous family of molecular chaperones that suppress the unspecific aggregation of miscellaneous proteins. Multicellular organisms contain a large number of different sHsps, raising questions as to whether they function redundantly or are specialized in terms of substrates and mechanism. To gain insight into this issue, we undertook a comparative analysis of the 8 major human sHsps on the aggregation of both model proteins and cytosolic lysates under standardized conditions...
November 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27908246/inhibition-of-chaperonin-groel-by-a-monomer-of-ovine-prion-protein-and-its-oligomeric-forms
#6
S S Kudryavtseva, Y Y Stroylova, I A Zanyatkin, T Haertle, V I Muronetz
The possibility of inhibition of chaperonin functional activity by amyloid proteins was studied. It was found that the ovine prion protein PrP as well as its oligomeric and fibrillar forms are capable of binding with the chaperonin GroEL. Besides, GroEL was shown to promote amyloid aggregation of the monomeric and oligomeric PrP as well as PrP fibrils. The monomeric PrP was shown to inhibit the GroEL-assisted reactivation of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The oligomers of PrP decelerate the GroEL-assisted reactivation of GAPDH, and PrP fibrils did not affect this process...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27906971/nullomers-and-high-order-nullomers-in-genomic-sequences
#7
Davide Vergni, Daniele Santoni
A nullomer is an oligomer that does not occur as a subsequence in a given DNA sequence, i.e. it is an absent word of that sequence. The importance of nullomers in several applications, from drug discovery to forensic practice, is now debated in the literature. Here, we investigated the nature of nullomers, whether their absence in genomes has just a statistical explanation or it is a peculiar feature of genomic sequences. We introduced an extension of the notion of nullomer, namely high order nullomers, which are nullomers whose mutated sequences are still nullomers...
2016: PloS One
https://www.readbyqxmd.com/read/27906600/role-of-polysaccharide-and-lipid-in-lipopolysaccharide-induced-prion-protein-conversion
#8
Carol L Ladner-Keay, Marcia LeVatte, David S Wishart
Conversion of native cellular prion protein (PrP(c)) from an α-helical structure to a toxic and infectious β-sheet structure (PrP(Sc)) is a critical step in the development of prion disease. There are some indications that the formation of PrP(Sc) is preceded by a β-sheet rich PrP (PrP(β)) form which is non-infectious, but is an intermediate in the formation of infectious PrP(Sc). Furthermore the presence of lipid cofactors is thought to be critical in the formation of both intermediate-PrP(β) and lethal, infectious PrP(Sc)...
December 1, 2016: Prion
https://www.readbyqxmd.com/read/27905353/-twenty-five-years-of-the-amyloid-hypothesis-of-alzheimer-disease-advances-failures-and-new-perspectives
#9
O S Levin, E E Vasenina
Amyloid hypothesis of Alzheimer's disease (AD) has been long the primary one. During the 25-year history the concept has been dramatically changed. Accumulation of β-amyloid is associated not only with the disruption of its synthesis (as it seemed after the discovery of genetic mechanisms of some familial cases of AD) but rather with the disruption of its clearance and elimination from the brain tissue via the microcirculatory system. It has been recognized that soluble oligomers of β-amyloid, but not senile plaques that consisted of insoluble conjugates described by A...
2016: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/27905107/co-operative-suppression-of-inflammatory-responses-in-human-dendritic-cells-by-plant-proanthocyanidins-and-products-from-the-parasitic-nematode-trichuris-suis
#10
Andrew R Williams, Elsenoor J Klaver, Lisa C Laan, Aina Ramsay, Christos Fryganas, Rolf Difborg, Helene Kringel, Jess D Reed, Irene Mueller-Harvey, Søren Skov, Irma van Die, Stig M Thamsborg
Interactions between dendritic cells (DCs) and environmental, dietary and pathogen antigens play a key role in immune homeostasis and regulation of inflammation. Dietary polyphenols such as proanthocyanidins (PAC) may reduce inflammation, and we therefore hypothesized that PAC may suppress lipopolysaccharide (LPS) -induced responses in human DCs and subsequent T helper type 1 (Th1) -type responses in naive T cells. Moreover, we proposed that, because DCs are likely to be exposed to multiple stimuli, the activity of PAC may synergise with other bioactive molecules that have anti-inflammatory activity, e...
November 7, 2016: Immunology
https://www.readbyqxmd.com/read/27904924/sequential-lignin-depolymerization-by-combination-of-biocatalytic-and-formic-acid-formate-treatment-steps
#11
Christoph A Gasser, Monika Čvančarová, Erik M Ammann, Andreas Schäffer, Patrick Shahgaldian, Philippe F-X Corvini
Lignin, a complex three-dimensional amorphous polymer, is considered to be a potential natural renewable resource for the production of low-molecular-weight aromatic compounds. In the present study, a novel sequential lignin treatment method consisting of a biocatalytic oxidation step followed by a formic acid-induced lignin depolymerization step was developed and optimized using response surface methodology. The biocatalytic step employed a laccase mediator system using the redox mediator 1-hydroxybenzotriazole...
November 30, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27904835/a-novel-dominant-d109a-cryab-mutation-in-a-family-with-myofibrillar-myopathy-affects-%C3%AE-b-crystallin-structure
#12
Jakub P Fichna, Anna Potulska-Chromik, Przemysław Miszta, Maria Jolanta Redowicz, Anna M Kaminska, Cezary Zekanowski, Sławomir Filipek
Myofibrillar myopathy (MFM) is a group of inherited muscular disorders characterized by myofibrils dissolution and abnormal accumulation of degradation products. So far causative mutations have been identified in nine genes encoding Z-disk proteins, including αB-crystallin (CRYAB), a small heat shock protein (also called HSPB5). Here, we report a case study of a 63-year-old Polish female with a progressive lower limb weakness and muscle biopsy suggesting a myofibrillar myopathy, and extra-muscular multisystemic involvement, including cataract and cardiomiopathy...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/27904493/beta-2-adrenergic-receptor-activation-enhances-neurogenesis-in-alzheimer-s-disease-mice
#13
Gao-Shang Chai, Yang-Yang Wang, Amina Yasheng, Peng Zhao
Impaired hippocampal neurogenesis is one of the early pathological features of Alzheimer's disease. Enhancing adult hippocampal neurogenesis has been pursued as a potential therapeutic strategy for Alzheimer's disease. Recent studies have demonstrated that environmental novelty activates β2-adrenergic signaling and prevents the memory impairment induced by amyloid-β oligomers. Here, we hypothesized that β2-adrenoceptor activation would enhance neurogenesis and ameliorate memory deficits in Alzheimer's disease...
October 2016: Neural Regeneration Research
https://www.readbyqxmd.com/read/27904093/nonequilibrium-molecular-switching-of-chiral-helicene-oligomers-in-double-helix-formation
#14
Masanori Shigeno
 Molecular switching is the phenomenon in which a molecular structural change occurs reversibly in response to an external stimulus or energy. It plays an important role in biology, in which it is used for sensing environmental changes. In contrast to well-studied equilibrium molecular switching involving thermodynamically stable states, nonequilibrium molecular switching involving a metastable state is a notable chemical phenomenon and is the theme of this study. Sulfonamido- and aminomethylenehelicene oligomers show a reversible structural change from a double helix to a random coil in dilute solution...
2016: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/27903721/cross-talk-between-brain-innate-immunity-and-serotonin-signaling-underlies-depressive-like-behavior-induced-by-alzheimer-s-amyloid-%C3%AE-oligomers-in-mice
#15
Jose Henrique Ledo, Estefania P Azevedo, Danielle Beckman, Felipe C Ribeiro, Luis E Santos, Daniela S Razolli, Grasielle C Kincheski, Helen M Melo, Maria Bellio, Antonio L Teixeira, Licio A Velloso, Debora Foguel, Fernanda G De Felice, Sergio T Ferreira
: Considerable clinical and epidemiological evidence links Alzheimer's disease (AD) and depression. However, the molecular mechanisms underlying this connection are largely unknown. We reported recently that soluble Aβ oligomers (AβOs), toxins that accumulate in AD brains and are thought to instigate synapse damage and memory loss, induce depressive-like behavior in mice. Here, we report that the mechanism underlying this action involves AβO-induced microglial activation, aberrant TNF-α signaling, and decreased brain serotonin levels...
November 30, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27901539/colloidal-molecules-assembled-from-binary-spheres-under-an-ac-electric-field
#16
Kelley Lynch Heatley, Fuduo Ma, Ning Wu
Colloidal particles are envisioned as analogues of atoms and molecules, however they often lack the complexities present in their counterparts. In this work, we report the assembly of colloidal molecules from a binary mixture of polystyrene spheres (1, 1.6, 2, and 4 μm) under an alternating current electric field. The rich family of assembled oligomers typically consists of a large sphere that is closely surrounded by a number of smaller petal particles, driven by the dipolar attraction between large and small particles...
November 30, 2016: Soft Matter
https://www.readbyqxmd.com/read/27901138/understanding-the-self-assembly-of-amino-ester-based-benzene-1-3-5-tricarboxamides-using-molecular-dynamics-simulations
#17
Karteek K Bejagam, Richard C Remsing, Michael L Klein, Sundaram Balasubramanian
Amino ester-based benzene-1,3,5-tricarboxamides (BTAs) are widely studied experimentally for their facile self-assembly, which leads to strong three-fold hydrogen bonded supramolecular polymers. Understanding the supramolecular assembly of these BTAs is complicated by the presence of two types of dimers, based on the nature of the intermolecular hydrogen bonding pattern: amide-amide (AA) and amide-carboxylate (AC). AA dimers form three hydrogen bonds between the two molecules, are typical of BTA stacks, and act as a basic building block of assembly...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27901087/polymorphism-of-fibrillar-structures-depending-on-the-size-of-assembled-a%C3%AE-17-42-peptides
#18
Mookyung Cheon, Mooseok Kang, Iksoo Chang
The size of assembled Aβ17-42 peptides can determine polymorphism during oligomerization and fibrillization, but the mechanism of this effect is unknown. Starting from separate random monomers, various fibrillar oligomers with distinct structural characteristics were identified using discontinuous molecular dynamics simulations based on a coarse-grained protein model. From the structures observed in the simulations, two characteristic oligomer sizes emerged, trimer and paranuclei, which generated distinct structural patterns during fibrillization...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27901067/a-chitin-deacetylase-from-the-endophytic-fungus-pestalotiopsis-sp-efficiently-inactivates-the-elicitor-activity-of-chitin-oligomers-in-rice-cells
#19
Stefan Cord-Landwehr, Rebecca L J Melcher, Stephan Kolkenbrock, Bruno M Moerschbacher
To successfully survive in plants, endophytes need strategies to avoid being detected by the plant immune system, as the cell walls of endophytes contain easily detectible chitin. It is possible that endophytes "hide" this chitin from the plant immune system by modifying it, or oligomers derived from it, using chitin deacetylases (CDA). To explore this hypothesis, we identified and expressed a CDA from Pestalotiopsis sp. (PesCDA), an endophytic fungus, in E. coli and characterized this enzyme and its chitosan oligomer products...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900617/new-and-evolving-concepts-regarding-the-prognosis-and-treatment-of-cardiac-amyloidosis
#20
REVIEW
Stefano Perlini, Roberta Mussinelli, Francesco Salinaro
Systemic amyloidoses are rare and proteiform diseases, caused by extracellular accumulation of insoluble misfolded fibrillar proteins. Prognosis is dictated by cardiac involvement, which is especially frequent in light chain (AL) and in transthyretin variants (ATTR, both mutated, (ATTRm), and wild-type, (ATTRwt)). Recently, ATTRwt has emerged as a potentially relevant cause of a heart failure with preserved ejection fraction (HFpEF). Cardiac amyloidosis is an archetypal example of restrictive cardiomyopathy, with signs and symptoms of global heart failure and diastolic dysfunction...
November 29, 2016: Current Heart Failure Reports
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