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Biophysical Reviews

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https://www.readbyqxmd.com/read/29222808/-just-a-spoonful-of-sugar-import-of-sialic-acid-across-bacterial-cell-membranes
#1
REVIEW
Rachel A North, Christopher R Horne, James S Davies, Daniela M Remus, Andrew C Muscroft-Taylor, Parveen Goyal, Weixiao Yuan Wahlgren, S Ramaswamy, Rosmarie Friemann, Renwick C J Dobson
Eukaryotic cell surfaces are decorated with a complex array of glycoconjugates that are usually capped with sialic acids, a large family of over 50 structurally distinct nine-carbon amino sugars, the most common member of which is N-acetylneuraminic acid. Once made available through the action of neuraminidases, bacterial pathogens and commensals utilise host-derived sialic acid by degrading it for energy or repurposing the sialic acid onto their own cell surface to camouflage the bacterium from the immune system...
December 8, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29222807/long-non-coding-rna-expression-in-bladder-cancer
#2
REVIEW
Mohammad Taheri, Mir Davood Omrani, Soudeh Ghafouri-Fard
The advent of novel high-throughput sequencing methods has facilitated identification of non-coding RNAs with fundamental roles in cellular biological and pathological conditions. A group of these consisting of at least 200 nucleotides are called long non-coding RNAs (lncRNAs). Their participation in the pathogenesis of cancer has been highlighted in recent years. Bladder cancer, one of the most prevalent cancers worldwide, exhibits altered expression levels of several lncRNAs. Several in vitro and in vivo studies have assessed the effects of silencing RNAs on cancer cell phenotypes and in vivo tumor growth...
December 8, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29222806/identification-of-udp-glucose-binding-site-in-glycosyltransferase-domain-of-sucrose-phosphate-synthase-from-sugarcane-saccharum-officinarum-by-structure-based-site-directed-mutagenesis
#3
REVIEW
Widhi Dyah Sawitri, Siti Nurul Afidah, Atsushi Nakagawa, Toshiharu Hase, Bambang Sugiharto
Sucrose phosphate synthase (SPS) is believed to be the key enzyme for controlling the biosynthesis of sucrose. SPSs consist of a functional glycosyltransferase domain that shares conserved residues with the glycosyltransferase domain of sucrose biosynthesis-related protein. The formation of sucrose-6-phosphate is catalyzed by SPS with the transfer of a glycosyl group of uridine diphosphate glucose (UDP-G) as an activated donor sugar to a fructose-6-phosphate as a sugar acceptor. However, understanding of the mechanism of catalytic and substrate binding in SPS is very limited...
December 8, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29222805/the-present-and-future-of-the-japan-society-for-the-promotion-of-science-alumni-association-in-australia-jspsaaa
#4
LETTER
Graziella Caprarelli
No abstract text is available yet for this article.
December 8, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29214606/recent-progress-on-understanding-the-mechanisms-of-amyloid-nucleation
#5
REVIEW
Eri Chatani, Naoki Yamamoto
Amyloid fibrils are supramolecular protein assemblies with a fibrous morphology and cross-β structure. The formation of amyloid fibrils typically follows a nucleation-dependent polymerization mechanism, in which a one-step nucleation scheme has widely been accepted. However, a variety of oligomers have been identified in early stages of fibrillation, and a nucleated conformational conversion (NCC) mechanism, in which oligomers serve as a precursor of amyloid nucleation and convert to amyloid nuclei, has been proposed...
December 6, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29214605/creation-of-artificial-protein-protein-interactions-using-%C3%AE-helices-as-interfaces
#6
REVIEW
Sota Yagi, Satoshi Akanuma, Akihiko Yamagishi
Designing novel protein-protein interactions (PPIs) with high affinity is a challenging task. Directed evolution, a combination of randomization of the gene for the protein of interest and selection using a display technique, is one of the most powerful tools for producing a protein binder. However, the selected proteins often bind to the target protein at an undesired surface. More problematically, some selected proteins bind to their targets even though they are unfolded. Current state-of-the-art computational design methods have successfully created novel protein binders...
December 6, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204887/molecular-evolution-of-an-oligomeric-biocatalyst-functioning-in-lysine-biosynthesis
#7
REVIEW
Tatiana P Soares da Costa, Belinda M Abbott, Anthony R Gendall, Santosh Panjikar, Matthew A Perugini
Dihydrodipicolinate synthase (DHDPS) is critical to the production of lysine through the diaminopimelate (DAP) pathway. Elucidation of the function, regulation and structure of this key class I aldolase has been the focus of considerable study in recent years, given that the dapA gene encoding DHDPS has been found to be essential to bacteria and plants. Allosteric inhibition by lysine is observed for DHDPS from plants and some bacterial species, the latter requiring a histidine or glutamate at position 56 (Escherichia coli numbering) over a basic amino acid...
December 5, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204886/membrane-mediated-amyloid-deposition-of-human-islet-amyloid-polypeptide
#8
REVIEW
Kenji Sasahara
Amyloid deposition of human islet amyloid polypeptide (hIAPP) within the islet of Langerhans is closely associated with type II diabetes mellitus. Accumulating evidence indicates that the membrane-mediated aggregation and subsequent deposition of hIAPP are linked to the dysfunction and death of insulin-producing pancreatic β-cells, but the molecular process of hIAPP deposition is poorly understood. In this review, I focus on recent in vitro studies utilizing model membranes to observe the membrane-mediated aggregation/deposition of hIAPP...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204885/bacteriophage-t4-long-tail-fiber-domains
#9
REVIEW
Paul Hyman, Mark van Raaij
Bacteriophage T4 initially recognizes its host cells using its long tail fibers. Long tail fibers consist of a phage-proximal and a phage-distal rod, each around 80 nm long and attached to each other at a slight angle. The phage-proximal rod is formed by a homo-trimer of gene product 34 (gp34) and is attached to the phage-distal rod by a monomer of gp35. The phage-distal rod consists of two protein trimers: a trimer of gp36, attached to gp35, although most of the phage-distal rod, including the receptor-binding domain, is formed by a trimer of gp37...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204884/structure-and-assembly-mechanism-of-virus-associated-pyramids
#10
REVIEW
Tessa E F Quax, Bertram Daum
Viruses have developed intricate molecular machines to infect, replicate within and escape from their host cells. Perhaps one of the most intriguing of these mechanisms is the pyramidal egress structure that has evolved in archaeal viruses, such as SIRV2 or STIV1. The structure and mechanism of these virus-associated pyramids (VAPs) has been studied by cryo-electron tomography and complementary biochemical techniques, revealing that VAPs are formed by multiple copies of a virus-encoded 10-kDa protein (PVAP) that integrate into the cell membrane and assemble into hollow, sevenfold symmetric pyramids...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204883/multiple-analyses-of-protein-dynamics-in-solution
#11
REVIEW
Tadayuki Ogawa, Nobutaka Hirokawa
The need for accurate description of protein behavior in solution has gained importance in various fields, including biophysics, biochemistry, structural biology, drug discovery, and antibody drugs. To achieve the desired accuracy, multiple precise analyses should be performed on the target molecule, compared, and effectively combined. This review focuses on the combination of multiple analyses in solution: size-exclusion chromatography (SEC), multi-angle light scattering (MALS), small-angle X-ray scattering (SAXS), analytical ultracentrifugation (AUC), and their complementary methods, such as atomic force microscopy (AFM) and mass spectrometry (MS)...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204882/multiscale-molecular-dynamics-simulations-of-rotary-motor-proteins
#12
REVIEW
Toru Ekimoto, Mitsunori Ikeguchi
Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204881/environment-transformable-sequence-structure-relationship-a-general-mechanism-for-proteotoxicity
#13
REVIEW
Jianxing Song
In his Nobel Lecture, Anfinsen stated "the native conformation is determined by the totality of interatomic interactions and hence by the amino acid sequence, in a given environment." As aqueous solutions and membrane systems co-exist in cells, proteins are classified into membrane and non-membrane proteins, but whether one can transform one into the other remains unknown. Intriguingly, many well-folded non-membrane proteins are converted into "insoluble" and toxic forms by aging- or disease-associated factors, but the underlying mechanisms remain elusive...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204880/formation-and-properties-of-amyloid-fibrils-of-prion-protein
#14
REVIEW
Kei-Ichi Yamaguchi, Kazuo Kuwata
Amyloid fibrils formed from prion protein (PrP) are associated with prion diseases. In this review we discuss a number of extrinsic and intrinsic experimental factors related to the formation of PrP amyloid fibrils in vitro. We first examined the effects of ultrasonic power on the induction of amyloid fibrillation from PrP. The most important conclusion drawn from the results is that an applied ultrasonic power of approximately 2 W enhanced the nucleation of amyloid fibrils efficiently but that more powerful ultrasonication led to retardation of growth...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204879/reconstitution-of-membrane-tethering-mediated-by-rab-family-small-gtpases
#15
REVIEW
Joji Mima
Membrane tethering is one of the most critical steps to determine the spatiotemporal specificity of membrane trafficking, which is the process to selectively transport proteins, lipids, and other biological molecules to the appropriate locations in eukaryotic cells, such as subcellular organelles, the plasma membrane, and the extracellular space. Based on genetic, cell biological, biochemical, and structural studies, Rab-family small GTPases and a number of Rab-interacting proteins (termed Rab effectors), including coiled-coil tethering proteins and multisubunit tethering complexes, have been proposed to be key protein components for membrane tethering...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204878/gliadins-from-wheat-grain-an-overview-from-primary-structure-to-nanostructures-of-aggregates
#16
REVIEW
Reiko Urade, Nobuhiro Sato, Masaaki Sugiyama
Gliadins are well-known wheat grain proteins, particularly important in food science. They were studied as early as the 1700s. Despite their long history, it has been difficult to identify their higher-order structure as they aggregate in aqueous solution. Consequently, most studies have been performed by extracting the proteins in 70% ethanol or dilute acidic solutions. The carboxy-terminal half of α- and γ-gliadins have α-helix-rich secondary structures stabilized with intramolecular disulfide bonds, which are present in either aqueous ethanol or pure water...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29204877/how-multi-scale-structural-biology-elucidated-context-dependent-variability-in-ectodomain-conformation-along-with%C3%A2-the-ligand-capture-and-release-cycle-for-ldlr-family-members
#17
REVIEW
Terukazu Nogi
The low-density lipoprotein receptor (LDLR) and its homologs capture and internalize lipoproteins into the cell. Due to the fact that LDLR family members possess a modular ectodomain that undergoes dynamic conformational changes, multi-scale structural analysis has been performed so as to understand the ligand capture and release mechanism. For example, crystallographic analyses have provided models for both the entire ectodomain and high-resolution structures of individual modules. In addition, nuclear magnetic resonance spectroscopic analyses have shown the rigidity and flexibility of inter-module linkers to restrict the mobility of ectodomain...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29198082/protein-solvent-interaction
#18
REVIEW
Tsutomu Arakawa
Protein folding and assembly can be manipulated in in vitro systems by co-solvents at high concentrations. A number of co-solvents that enhance protein stability and assembly have been shown to be excluded from the protein surface. Such co-solvent exclusion has been demonstrated by dialysis experiments and shown to be correlated with their effects on protein stability and assembly.
December 2, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29198081/anaerobic-crystallization-of-proteins
#19
REVIEW
Miki Senda, Toshiya Senda
Crystallization has been a bottleneck in the X-ray crystallography of proteins. Although many techniques have been developed to overcome this obstacle, the impurities caused by chemical reactions during crystallization have not been sufficiently considered. Oxidation of proteins, which can lead to poor reproducibility of the crystallization, is a prominent example. Protein oxidization in the crystallization droplet causes inter-molecular disulfide bridge formation, formation of oxidation film, and precipitation of proteins...
December 2, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29196935/serial-femtosecond-crystallography-at-the-sacla-breakthrough-to-dynamic-structural-biology
#20
REVIEW
Eiichi Mizohata, Takanori Nakane, Yohta Fukuda, Eriko Nango, So Iwata
X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca...
December 1, 2017: Biophysical Reviews
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