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Helix stabilization

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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/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
#2
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/29148740/effect-of-an-imposed-contact-on-secondary-structure-in-the-denatured-state-of-yeast-iso-1-cytochome-c
#3
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
#4
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/29138354/efficient-er-fusion-requires-a-dimerization-and-c-terminal-tail-mediated-membrane-anchoring-of-rhd3
#5
Jiaqi Sun, Huanquan Zheng
The endoplasmic reticulum (ER) is a network of tubules and sheets stretching throughout the eukaryotic cells. The formation of the ER requires homotypic membrane fusion, which is mediated by a family of Dynamin-like GTPase proteins. The Arabidopsis member ROOT HAIR DEFECTIVE3 (RHD3) has been demonstrated to mediate ER membrane fusion, but how exactly RHD3 is involved in the process is still unknown. Here we conducted systemic structure-function analyses of roles of different RHD3 domains in mediating ER fusion...
November 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29138096/one-single-salt-bridge-explains-the-different-cytolytic-activities-shown-by-actinoporins-sticholysin-i-and-ii-from-the-venom-of-stichodactyla-helianthus
#6
Esperanza Rivera-de-Torre, Juan Palacios-Ortega, Sara García-Linares, José G Gavilanes, Álvaro Martínez-Del-Pozo
Sticholysins I and II (StnI and StnII), α-pore forming toxins from the sea anemone Stichodactyla helianthus, are water-soluble toxic proteins which upon interaction with lipid membranes of specific composition bind to the bilayer, extend and insert their N-terminal α-helix, and become oligomeric integral membrane structures. The result is a pore that leads to cell death by osmotic shock. StnI and StnII show 93% of sequence identity, but also different membrane pore-forming activities. The hydrophobicity profile along the first 18 residues revealed differences which were canceled by substituting StnI amino acids 2 and 9...
November 11, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29136243/structure-and-electrical-properties-of-dna-nanotubes-embedded-in-lipid-bilayer-membranes
#7
Himanshu Joshi, Prabal K Maiti
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 μs long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane...
November 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29131541/rhombic-shaped-nanostructures-and-mechanical-properties-of-2d-dna-origami-constructed-with-different-crossover-nick-designs
#8
Zhipeng Ma, Yunfei Huang, Seongsu Park, Kentaro Kawai, Do-Nyun Kim, Yoshikazu Hirai, Toshiyuki Tsuchiya, Hirofumi Yamada, Osamu Tabata
DNA origami methods enable the fabrication of various nanostructures and nanodevices, but their effective use depends on an understanding of their structural and mechanical properties and the effects of basic structural features. Frequency-modulation atomic force microscopy is introduced to directly characterize, in aqueous solution, the crossover regions of sets of 2D DNA origami based on different crossover/nick designs. Rhombic-shaped nanostructures formed under the influence of flexible crossovers placed between DNA helices are observed in DNA origami incorporating crossovers every 3, 4, or 6 DNA turns...
November 13, 2017: Small
https://www.readbyqxmd.com/read/29129631/binding-of-calcium-and-target-peptide-to-calmodulin-like-protein-cml19-the-centrin-2-of-arabidopsis-thaliana
#9
Valentina La Verde, Matteo Trande, Mariapina D'Onofrio, Paola Dominici, Alessandra Astegno
Calmodulin-like protein 19 (CML19) is an Arabidopsis centrin that modulates nucleotide excision repair (NER) by binding to RAD4 protein, the Arabidopsis homolog of human Xeroderma pigmentosum complementation group C protein. Although the necessity of CML19 as a part of the RAD4 plant recognition complex for functional NER is known at a cellular level, little is known at a molecular level. Herein, we used a combination of biophysical and biochemical approaches to investigate the structural and ion and target-peptide binding properties of CML19...
November 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29129605/evolution-and-adaptation-of-single-pass-transmembrane-proteins
#10
Irina D Pogozheva, Andrei L Lomize
A comparative analysis of 6,039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication...
November 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29124702/impact-of-uv-radiation-on-genome-stability-and-human-health
#11
Sujit Roy
Gradual depletion of the atmospheric ozone layer during the past few years has increased the incidence of solar UV radiation specifically the UV-C on earth's surface is one of the major environmental concerns because of the harmful effects of this radiation in all forms of life. The solar UV radiation including the harmful wavelength range of UV-B (280-320 nm) represents a significant climatic stress for both animals and plants, causing damage to the fundamental biomolecules such as DNA, proteins and lipids, thus activating genotoxic stress and induces genome instability...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29116071/-crispr-cas9-editing-based-modeling-of-hypoxia-in-renal-cancer-cells
#12
N A Zhigalova, S V Zhenilo, A V Artemov, E B Prokhortchouk
Uncontrolled growth in the cell mass of malignant tumors induces intensive angiogenesis. However, the demands of the cancer cells for nutrients and oxygen remain only partially met. Hypoxia is a process that accompanies malignant transformation and evokes changes in the DNA methylation profile in solid tumors. To a certain extent, these changes, including the hypermethylation of tumor suppressor gene promoters, are related to the decrease in the activity of Tet proteins under the conditions of oxygen and free radical deficit...
September 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29109186/insights-into-biofilm-dispersal-regulation-from-the-crystal-structure-of-the-pas-ggdef-eal-region-of-rbda-from-pseudomonas-aeruginosa
#13
Chong Liu, Chong Wai Liew, Yee Hwa Wong, Siok Thing Tan, Wee Han Poh, Sony M S Manimekalai, Sreekanth Rajan, Lingyi Xin, Zhao-Xun Liang, Gerhard Grüber, Scott A Rice, Julien Lescar
RbdA is a positive Regulator of biofilm dispersal of Pseudomonas aeruginosa Its cytoplasmic region (cRbdA) comprises a N-terminal PAS domain followed by a diguanylate cyclase (GGDEF) and an EAL domain, whose phosphodiesterase activity is allosterically stimulated by GTP binding to the GGDEF domain. We report crystal structures of cRbdA and of two binary complexes: with GTP/Mg(2+) bound to the GGDEF active site and with the EAL domain bound to the c-di-GMP substrate. These structures unveil a 2-fold symmetric dimer, stabilized by a closely packed N-terminal PAS domain and a non-canonical EAL dimer...
November 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29108002/structural-basis-of-antifreeze-activity-of-a-bacterial-multi-domain-antifreeze-protein
#14
Chen Wang, Svetlana Pakhomova, Marcia E Newcomer, Brent C Christner, Bing-Hao Luo
Antifreeze proteins (AFPs) enhance the survival of organisms inhabiting cold environments by affecting the formation and/or structure of ice. We report the crystal structure of the first multi-domain AFP that has been characterized. The two ice binding domains are structurally similar. Each consists of an irregular β-helix with a triangular cross-section and a long α-helix that runs parallel on one side of the β-helix. Both domains are stabilized by hydrophobic interactions. A flat plane on the same face of each domain's β-helix was identified as the ice binding site...
2017: PloS One
https://www.readbyqxmd.com/read/29097312/insights-on-the-conformational-dynamics-of-human-frataxin-through-modifications-of-loop-1
#15
Martín E Noguera, Martín Aran, Clara Smal, Diego S Vazquez, María Georgina Herrera, Ernesto A Roman, Nadine Alaimo, Mariana Gallo, Javier Santos
Human frataxin (FXN) is a highly conserved mitochondrial protein involved in iron homeostasis and activation of the iron-sulfur cluster assembly. FXN deficiency causes the neurodegenerative disease Friedreich's Ataxia. Here, we investigated the effect of alterations in loop-1, a stretch presumably essential for FXN function, on the conformational stability and dynamics of the native state. We generated four loop-1 variants, carrying substitutions, insertions and deletions. All of them were stable and well-folded proteins...
October 30, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29096508/links-between-the-charge-model-and-bonded-parameter-force-constants-in-biomolecular-force-fields
#16
David S Cerutti, Karl T Debiec, David A Case, Lillian T Chong
The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model...
October 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29094215/insulin-resistance-and-glycine-metabolism-in-humans
#17
REVIEW
M Adeva-Andany, G Souto-Adeva, E Ameneiros-Rodríguez, C Fernández-Fernández, C Donapetry-García, A Domínguez-Montero
Plasma glycine level is low in patients with obesity or diabetes and the improvement of insulin resistance increases plasma glycine concentration. In prospective studies, hypoglycinemia at baseline predicts the risk of developing type 2 diabetes and higher serum glycine level is associated with decreased risk of incident type 2 diabetes. Consistently, plasma glycine concentration is lower in the lean offspring of parents with type 2 diabetes compared to healthy subjects. Among patients with type 2 diabetes, hypoglycinemia occurs before clinical manifestations of the disease, but the pathophysiological mechanisms underlying glycine deficit and its potential clinical repercussions are unclear...
November 1, 2017: Amino Acids
https://www.readbyqxmd.com/read/29079572/a-pivotal-role-for-a-conserved-bulky-residue-at-the-%C3%AE-1-helix-of-the-%C3%AE-i-integrin-domain-in-ligand-binding
#18
Zhengli Wang, Aye Myat Myat Thinn, Jieqing Zhu
The ligand-binding βI and αI domains of integrin are the best-studied von Willebrand factor A (VWA) domains undergoing significant conformational changes for affinity regulation. In both βI and αI domains, the α1- and α7-helixes work in concert to shift the metal-ion-dependent-adhesion-site between the resting and active states. An absolutely conserved Gly in the middle of the α1-helix of βI helps maintain the resting βI conformation, while the homologous position in the αI α1-helix contains a conserved Phe...
October 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29077417/phosphorylation-versus-o-glcnacylation-computational-insights-into-the-differential-influences-of-the-two-competitive-post-translational-modifications
#19
Lata Rani, Sairam S Mallajosyula
Phosphorylation and O-GlcNAcylation are rapidly cycling intracellular protein post-translational modifications (PTMs) that can compete for the same serine (S) and threonine (T) sites. Limited crystal structure information is available on the direct influence of these PTMs on the underlying protein structure, especially for O-GlcNAcylation. NMR and CD studies show that these competitive-PTMs can have the same or differential influence on the overall secondary structure. In Tau derived peptide fragments, it was found that phosphorylation stabilized PPII conformations while O-GlcNAcylation destabilized the same...
November 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29065339/reduced-graphene-oxide-bifeo3-nanohybrids-based-signal-on-photoelectrochemical-sensing-system-for-prostate-specific-antigen-detection-coupling-with-magnetic-microfluidic-device
#20
Qian Zhou, Youxiu Lin, Kangyao Zhang, Meijin Li, Dianping Tang
A novel magnetic controlled photoelectrochemical (PEC) sensing system was designed for sensitive detection of prostate-specific antigen (PSA) using reduced graphene oxide-functionalized BiFeO3 (rGO-BiFeO3) as the photoactive material and target-triggered hybridization chain reaction (HCR) for signal amplification. Remarkably enhanced PEC performance could be obtained by using rGO-BiFeO3 as the photoelectrode material due to its accelerated charge transfer and improved the visible light absorption. Additionally, efficient and simple operation could be achieved by introducing magnetic controlled flow-through device...
October 16, 2017: Biosensors & Bioelectronics
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