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https://www.readbyqxmd.com/read/29150976/salt-bridge-interactions-within-the-%C3%AE-2-integrin-%C3%AE-7-helix-mediate-force-induced-binding-and-shear-resistance-ability
#1
Xiao Zhang, Linda Li, Ning Li, Xinyu Shu, Lüwen Zhou, Shouqin Lü, Shenbao Chen, Debin Mao, Mian Long
The functional performance of αI domain α7 helix in β2 integrin activation depends on the allostery of the α7 helix, which axially slides down; therefore, it is critical to elucidate what factors regulate the allostery. In this study, we determined that there were two conservative salt bridge interaction pairs that constrain both the upper and bottom ends of the α7 helix. Molecular Dynamics (MD) simulations for three β2 integrin members of LFA-1 (αL β2 ), Mac-1 (αM β2 ) and αx β2 indicated that the magnitude of the salt bridge interaction is related to the stability of the αI domain and the strength of the corresponding force-induced allostery...
November 18, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29150496/alginate-lyases-diversity-of-three-dimensional-structures-and-catalytic-mechanisms
#2
Fei Xu, Peng Wang, Yu-Zhong Zhang, Xiu-Lan Chen
Alginate is a linear polysaccharide mainly produced by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units, β-d-mannuronate (M) and its C5 epimer α-l-guluronate (G). Alginate lyases are polysaccharide lyases (PL) that degrade alginate via a β-elimination reaction. These enzymes play an important role in marine carbon recycling, and also have widespread industrial applications. So far, more than 1774 alginate lyase sequences have been identified and are distributed into 7 PL families...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150442/functional-analyses-of-a-human-vascular-tumor-fos-variant-identify-a-novel-degradation-mechanism-and-a-link-to-tumorigenesis
#3
David G P van Ijzendoorn, Zary Forghany, Frauke Liebelt, Alfred C Vertegaal, Aart G Jochemsen, Judith V M G Bovée, Karoly Szuhai, David A Baker
Epithelioid hemangioma is a locally aggressive vascular neoplasm, found in bones and soft tissue, whose cause is currently unknown, but may involve oncogene activation. FOS was one of the earliest viral oncogenes to be characterized and normal cellular FOS forms part of the activator protein 1 (AP-1) transcription factor complex which plays a pivotal role in cell growth, differentiation and survival as well as the DNA damage response. Despite this, to date, a causal link between aberrant FOS function and naturally occurring tumors has not been established...
November 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29150441/co-ii-and-ni-ii-binding-of-the-escherichia-coli-transcriptional-repressor-rcnr-orders-its-n-terminus-alters-helix-dynamics-and-reduces-dna-affinity
#4
Hsin-Ting Huang, Cedric E Bobst, Jeffrey S Iwig, Peter T Chivers, Igor A Kaltashov, Michael J Maroney
RcnR, a transcriptional regulator in Escherichia coli, derepresses the expression of the export proteins RcnAB upon binding Ni(II) or Co(II). Lack of structural information has precluded elucidation of the allosteric basis for the decreased DNA affinity in RcnR's metal-bound states. Here, using hydrogen-deuterium exchange coupled with MS (HDX-MS), we probed the RcnR structure in the presence of DNA, the cognate metal ions Ni(II) and Co(II), or the noncognate metal ion Zn(II). We found that cognate metal binding altered the flexibility from the N-terminus through helix 1 and modulated the RcnR-DNA interaction...
November 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29150433/tyrosine-phosphorylation-of-munc18-1-inhibits-synaptic-transmission-by-preventing-snare%C3%A2-assembly
#5
Marieke Meijer, Bernhard Dörr, Hanna Ca Lammertse, Chrysanthi Blithikioti, Jan Rt van Weering, Ruud Fg Toonen, Thomas H Söllner, Matthijs Verhage
Tyrosine kinases are important regulators of synaptic strength. Here, we describe a key component of the synaptic vesicle release machinery, Munc18-1, as a phosphorylation target for neuronal Src family kinases (SFKs). Phosphomimetic Y473D mutation of a SFK phosphorylation site previously identified by brain phospho-proteomics abolished the stimulatory effect of Munc18-1 on SNARE complex formation ("SNARE-templating") and membrane fusion in vitro Furthermore, priming but not docking of synaptic vesicles was disrupted in hippocampal munc18-1-null neurons expressing Munc18-1Y473D Synaptic transmission was temporarily restored by high-frequency stimulation, as well as by a Munc18-1 mutation that results in helix 12 extension, a critical conformational step in vesicle priming...
November 17, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29150077/unique-arginine-array-improves-cytosolic-localization-of-hydrocarbon-stapled-peptides
#6
Kim Quach, Jonathan LaRochelle, Xiao-Han Li, Elizabeth Rhoades, Alanna Schepartz
We have previously reported that miniature proteins containing a distinct array of 5 arginine residues on a folded α-helix - a penta-arg motif - traffic with high efficiency from endosomes into the cytosol and nucleus of mammalian cells. Here we evaluate whether a penta-arg motif can improve the intracellular trafficking of an otherwise impermeant hydrocarbon-stapled peptide, SAH-p53-4(Rho). We prepared a panel of SAH-p53-4(Rho) variants containing penta-arg sequences with different spacings and axial arrangement and evaluated their overall uptake (as judged by flow cytometry) and their intracellular access (as determined by fluorescence correlation spectroscopy, FCS)...
November 7, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29149705/toll-like-receptor-4-deficiency-increases-resistance-in-sepsis-induced-immune-dysfunction
#7
Chao Cao, Yanfen Chai, Songtao Shou, Jun Wang, Ying Huang, Tao Ma
Sepsis constitutes a serious life-threatening syndrome associated with complications of deregulated inflammatory response against endotoxin/lipopolysaccharide (LPS)-mediated severe infection. Toll-like receptor 4 (TLR4) plays a critical role in the activation of innate immunity through recognition of LPS. However, the impact of TLR4 signaling on the development of sepsis-induced immune dysfunction remains unclear. The aim of this study was to investigate the effect of TLR4 on regulatory T cells (Tregs) and its potential mechanism...
November 14, 2017: International Immunopharmacology
https://www.readbyqxmd.com/read/29149637/antiviral-potential-of-natural-compounds-against-influenza-virus-hemagglutinin
#8
S Kannan, P Kolandaivel
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29149090/computational-methods-for-modeling-aptamers-and-designing-riboswitches
#9
REVIEW
Sha Gong, Yanli Wang, Zhen Wang, Wenbing Zhang
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29149026/non-catalytic-roles-of-the-topoisomerase-ii%C3%AE-c-terminal-domain
#10
REVIEW
Duncan J Clarke, Yoshiaki Azuma
DNA Topoisomerase IIα (Topo IIα) is a ubiquitous enzyme in eukaryotes that performs the strand passage reaction where a double helix of DNA is passed through a second double helix. This unique reaction is critical for numerous cellular processes. However, the enzyme also possesses a C-terminal domain (CTD) that is largely dispensable for the strand passage reaction but is nevertheless important for the fidelity of cell division. Recent studies have expanded our understanding of the roles of the Topo IIα CTD, in particular in mitotic mechanisms where the CTD is modified by Small Ubiquitin-like Modifier (SUMO), which in turn provides binding sites for key regulators of mitosis...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29148767/role-of-the-benzodioxole-group-in-the-interactions-between-the-natural-alkaloids-chelerythrine-and-coptisine-and-the-human-telomeric-g-quadruplex-dna-a-multiapproach-investigation
#11
F Papi, M Ferraroni, R Rigo, S Da Ros, C Bazzicalupi, C Sissi, P Gratteri
The binding properties toward the human telomeric G-quadruplex of the two natural alkaloids coptisine and chelerythrine were studied using spectroscopic techniques, molecular modeling, and X-ray diffraction analysis. The results were compared with reported data for the parent compounds berberine and sanguinarine. Spectroscopic studies showed modest, but different rearrangements of the DNA-ligand complexes, which can be explained considering particular stereochemical features for these alkaloids, in spite of the similarity of their skeletons...
November 17, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/29148758/synthesis-and-structure-of-feet-to-feet-connected-bisresorcinarenes
#12
Daisuke Shimoyama, Toshiaki Ikeda, Ryo Sekiya, Takeharu Haino
Bisresorcinarenes 1a-d were obtained in excellent yields, and 1e was finally obtained in 50% yield. X-ray diffraction analysis showed that 1a and 1b adopted helical conformations, whereas the two resorcinarenes of 1c-e were in parallel orientations in which the clefts of the aliphatic chains entrapped one or two solvent molecules. The conformational study revealed that the helix interconversion between the (P)- and (M)-helical conformers depended on the length of the aliphatic chains. 1a had the largest energetic barrier to helix interconversion, while in 1b, its more flexible aliphatic chains lowered its energetic barriers...
November 17, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29148740/effect-of-an-imposed-contact-on-secondary-structure-in-the-denatured-state-of-yeast-iso-1-cytochome-c
#13
Travis A Danielson, Jessica M Stine, Tanveer A Dar, Klara Briknarova, Bruce E Bowler
There is considerable evidence that long-range interactions stabilize residual protein structure under denaturing conditions. However, evaluation of the effect of a specific contact on structure in the denatured state has been difficult. Iso-1-cytochrome c variants with a Lys54-->His mutation form a particularly stable His-heme loop in the denatured state, suggestive of loop-induced residual structure. We have used multidimensional NMR methods to assign (1)H and (15)N backbone amide and (13)C backbone and side chain chemical shifts in the denatured state of iso-1-cytochrome c carrying the Lys54-->His mutation in 3 and 6 M guanidine hydrochloride and at both pH 6...
November 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/29148735/stereoselective-stabilization-of-polymeric-vitamin-e-conjugate-micelles
#14
Min Gao, Jian Deng, Huiying Chu, Yu Tang, Zheng Wang, Yanjun Zhao, Guohui Li
Vitamin E (α-tocopherol) (TPGS) micelle is a robust nanocarrier in delivering hydrophobic active pharmaceutical ingredients, but is suffering from poor stability that is essential in terms of pharmaceutical and biomedical applications. Taking advantage of the chirality of vitamin E, this work reports the stereoselective stabilization of polymer-vitamin E conjugate micelles. Vitamin E was covalently linked to multivalent methoxy poly(ethylene glycol)-co-poly(glutamic acid), generating amphiphilic conjugates that could self-assemble into micelles...
November 17, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/29148699/controlling-ligand-spacing-on-surface-polyproline-based-fluorous-microarray-as-a-tool-in-spatial-specificity-analysis-and-inhibitor-development-for-carbohydrate-protein-interactions
#15
Tse-Hsueh Lin, Cin-Hao Lin, Ying-Jie Liu, Chun Yi Huang, Yen-Cheng Lin, Sheng-Kai Wang
Multivalent carbohydrate-protein interactions are essential for many biological processes. Convenient characterization for multivalent binding property of proteins will aid the development of molecules to manipulate these processes. We exploited the polyproline helix II (PPII) structure as molecular scaffolds to adjust the distances between glycan ligand attachment sites at 9, 18, and 27 Å on a peptide scaffold. Optimized fluorous groups were also introduced to the peptide scaffold for immobilization to the microarray surface through fluorous interaction to control the orientation of the helical scaffolds...
November 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29147837/development-of-saap3d-force-field-and-the-application-to-replica-exchange-monte-carlo-simulation-for-chignolin-and-c-peptide
#16
Michio Iwaoka, Toshiki Suzuki, Yuya Shoji, Kenichi Dedachi, Taku Shimosato, Toshiya Minezaki, Hironobu Hojo, Hiroyuki Onuki, Hiroshi Hirota
Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2)...
November 17, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29147531/catalysis-of-a-1-3-dipolar-reaction-by-distorted-dna-incorporating-a-heterobimetallic-platinum-ii-and-copper-ii-complex
#17
Iván Rivilla, Abel de Cózar, Thomas Schäfer, Frank J Hernandez, Alexander M Bittner, Aitziber Eleta-Lopez, Ali Aboudzadeh, José I Santos, José I Miranda, Fernando P Cossío
A novel catalytic system based on covalently modified DNA is described. This catalyst promotes 1,3-dipolar reactions between azomethine ylides and maleimides. The catalytic system is based on the distortion of the double helix of DNA by means of the formation of Pt(ii) adducts with guanine units. This distortion, similar to that generated in the interaction of DNA with platinum chemotherapeutic drugs, generates active sites that can accommodate N-metallated azomethine ylides. The proposed reaction mechanism, based on QM(DFT)/MM calculations, is compatible with thermally allowed concerted (but asynchronous) [π4s + π2s] mechanisms leading to the exclusive formation of racemic endo-cycloadducts...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29146595/the-cartilage-specific-lectin-c-type-lectin-domain-family-3-member-a-clec3a-enhances-tissue-plasminogen-activator-mediated-plasminogen-activation
#18
Daniela Lau, Dzemal Elezagic, Gabriele Hermes, Matthias Mörgelin, Alexander P Wohl, Manuel Koch, Ursula Hartmann, Stefan Höllriegl, Raimund Wagener, Mats Paulsson, Thomas Streichert, Andreas R Klatt
C-type lectin domain family 3 member A (CLEC3A) is a poorly characterized protein belonging to the superfamily of C-type lectins. Its closest homologue tetranectin binds to the kringle 4 domain of plasminogen and enhances its association with tissue plasminogen activator (tPA) thereby enhancing plasmin production, but whether CLEC3A contributes to plasminogen activation is unknown. Here, we recombinantly expressed murine and human full-length CLEC3As as well as truncated forms of CLEC3A in HEK-293 EBNA cells...
November 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29146444/snps-in-the-toll1-receptor-of-litopenaeus-vannamei-are-associated-with-immune-response
#19
Defu Yao, Huimin Su, Jinghua Zhu, Xianliang Zhao, Jude Juventus Aweya, Fan Wang, Mingqi Zhong, Yueling Zhang
Tolls and Toll-like receptors (TLRs) are important regulators in the innate immune system and their genetic variations usually affect the host's susceptibility/resistance to pathogen infections. In this study, we report on the single nucleotide polymorphisms (SNPs) of Toll1 in Litopenaeus vannamei (LvToll1) and how this is associated with immune response. PCR-DGGE analysis revealed genetic polymorphisms in LvToll1 at both the genomic DNA (gDNA) and cDNA levels. Using high-throughput sequencing, 223 SNPs were identified at the gDNA level, of which 145 were non-synonymous SNP (nsSNP), with 3 nsSNPs having frequency over 1%...
November 13, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29146337/characterization-antioxidant-and-hypoglycemic-activities-of-degraded-polysaccharides-from-blackcurrant-ribes-nigrum-l-fruits
#20
Yaqin Xu, Xiaojie Niu, Ningyue Liu, Yankang Gao, Libo Wang, Gang Xu, Xingguo Li, Yu Yang
In this study, the degradation of polysaccharides from blackcurrant (BCP) was investigated. Two low-molecular-weight polysaccharides (DBCP-1, DBCP-2) were obtained using Fe(2+) with different concentrations of H2O2 solution. IR spectra showed DBCPs had obvious characteristic peaks of polysaccharides. GC analysis confirmed DBCPs were composed of the same monosaccharide units as BCP but with different molar ratios. NMR analysis indicated DBCPs and BCP had similar glycosidic linkage patterns. The surface area of fragmented structure in DBCPs was reduced compared to BCP, and they had no triple helix structure...
March 15, 2018: Food Chemistry
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