keyword
MENU ▼
Read by QxMD icon Read
search

Small molecule structure

keyword
https://www.readbyqxmd.com/read/28103010/a-fluorescent-hsp90-probe-demonstrates-the-unique-association-between-extracellular-hsp90-and-malignancy-in-vivo
#1
Lauren B Crowe, Philip F Hughes, David A Alcorta, Takuya Osada, Aaron P Smith, Juliane Totzke, David R Loiselle, Isaac D Lutz, Madhusudhana Gargesha, Debasish Roy, Jose Roques, David Darr, H Kim Lyerly, Neil L Spector, Timothy Aj Haystead
Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is correlated with malignancy. Development of small molecule probes that can detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a cell impermeable far-red fluorophore-tagged Hsp90 inhibitor to target eHsp90 in vivo. High resolution confocal and lattice light sheet microscopy show that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is actively internalized...
January 19, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28102674/2d-ir-spectroscopy-shows-that-optimised-dna-minor-groove-binding-of-hoechst33258-follows-an-induced-fit-model
#2
Lennart A I Ramakers, Gordon Hithell, John J May, Gregory M Greetham, Paul M Donaldson, Michael Towrie, Anthony W Parker, Glenn A Burley, Neil T Hunt
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region...
January 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28101864/filamentous-structure-of-hard-%C3%AE-keratins-in-the-epidermal-appendages-of-birds-and-reptiles
#3
R D Bruce Fraser, David A D Parry
The structures of avian and reptilian epidermal appendages, such as feathers, claws and scales, have been modelled using X-ray diffraction and electron microscopy data, combined with sequence analyses. In most cases, a family of closely related molecules makes up the bulk of the appendage, and each of these molecules contains a central β-rich 34-residue segment, which has been identified as the principal component of the framework of the 3.4 nm diameter filaments. The N- and C-terminal segments form the matrix component of the filament/matrix complex...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101857/fibrous-protein-structures-hierarchy-history-and-heroes
#4
John M Squire, David A D Parry
During the 1930s and 1940s the technique of X-ray diffraction was applied widely by William Astbury and his colleagues to a number of naturally-occurring fibrous materials. On the basis of the diffraction patterns obtained, he observed that the structure of each of the fibres was dominated by one of a small number of different types of molecular conformation. One group of fibres, known as the k-m-e-f group of proteins (keratin - myosin - epidermin - fibrinogen), gave rise to diffraction characteristics that became known as the α-pattern...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101541/inner-salt-shaped-small-molecular-photosensitizer-with-extremely-enhanced-two-photon-absorption-for-mitochondrial-targeted-photodynamic-therapy
#5
Wenbo Hu, Tingchao He, Rongcui Jiang, Jun Yin, Lin Li, Xiaomei Lu, Hui Zhao, Lei Zhang, Ling Huang, Handong Sun, Wei Huang, Quli Fan
Herein, we experimentally and theoretically demonstrate an unprecedentedly enhanced two-photon absorption in a small organic molecule by a simple introduction of an inner salt-shaped structure. Moreover, such an inner salt-shaped small molecule also exhibits superior singlet oxygen quantum yield and fascinating structure-inherent mitochondrial-targeting ability for highly efficient two-photon photodynamic therapy via a mitochondrial apoptosis pathway.
January 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28099808/dynamics-in-a-room-temperature-ionic-liquid-from-the-cation-perspective-2d-ir-vibrational-echo-spectroscopy
#6
Steven A Yamada, Heather E Bailey, Amr Tamimi, Chunya Li, Michael D Fayer
The dynamics of the room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf2) were investigated with two dimensional infrared (2D IR) vibrational echo spectroscopy and polarization selective pump-probe (PSPP) experiments. The CN stretch frequency of a modified Bmim+ cation (referred to hereafter as 2-SeCN-Bmim+), in which a SeCN moiety was substituted onto the C-2 position of the imidazolium ring, was used as a vibrational probe. A major result of the 2D IR experiments is the observation of a long timescale structural spectral diffusion component of 600 ps in addition to short and intermediate timescales similar to those measured for selenocyanate anion (SeCN‒) dissolved in BmimNTf2...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28098421/hexagonal-boron-nitride-h-bn-sheets-decorated-with-oli-ona-and-li2-f-molecules-for-enhanced-energy-storage
#7
Syeda Rabab Naqvi, Gollu Sankar Rao, Wei Luo, Rajeev Ahuja, Tanveer Hussain
First-principles electronic structure calculations were carried out on hexagonal boron nitride (h-BN) sheets functionalized with small molecules, such as OLi, ONa, and Li2 F, to study their hydrogen (H2 ) storage properties. We found that OLi and ONa strongly adsorb on h-BN sheets with reasonably large inter-adsorbent separations, which is desirable for H2 storage. Ab initio molecular dynamics (MD) simulations further confirmed the structural stability of OLi-BN and ONa-BN systems at 400 K. On the other hand, Li2 F molecules form clusters over the surface of h-BN at higher temperatures...
January 18, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28098290/in-situ-ligand-exchange-mediated-0d-1d-transformation-of-a-polyoxovanadate
#8
M Wendt, P Polzin, J van Leusen, C Näther, P Kögerler, W Bensch
The antimonato-polyoxovanadate {Ni(II)(en)3}3[VSbO42(H2O)]·ca.15H2O was utilized as a synthon for the solvothermal in situ generation of the new compound {Ni(II)(phen)3}2[{Ni(II)(en)2}VSbO42(H2O)]·19H2O, a rearrangement induced by ligand metathesis. While in the precursor structure cations and anions are isolated, the solid-state structure of the product is characterized by 1D chains consisting of alternating [V15Sb6O42(H2O)](6-) cluster shells and [Ni(en)2](2+) units covalently linked to neighboring clusters via terminal oxygen atoms...
January 18, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28098282/b40-cluster-stability-reactivity-and-its-planar-structural-precursor
#9
Yang Yang, Zhuhua Zhang, Evgeni S Penev, Boris I Yakobson
We report a comprehensive first-principles study of the structural and chemical properties of the recently discovered B40 cage. It is found to be highly reactive and can exothermically dimerize, regardless of the orientation, by overcoming a small energy barrier ≃0.06 eV. The energy gap of the system varies widely with the aggregation of the increasing number of B40 cages, from 3.14 eV in a single B40, to 1.54 eV in the dimer, to 1.25 eV in the trimer. We also explore a recipe for protecting the B40 cage by sheathing it within a carbon shell and identify carbon nanotubes with a radius of ∼6 Å as optimal hosts for an isolated cage...
January 18, 2017: Nanoscale
https://www.readbyqxmd.com/read/28098154/structural-basis-of-ligand-interaction-with-atypical-chemokine-receptor-3
#10
Martin Gustavsson, Liwen Wang, Noortje van Gils, Bryan S Stephens, Penglie Zhang, Thomas J Schall, Sichun Yang, Ruben Abagyan, Mark R Chance, Irina Kufareva, Tracy M Handel
Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097765/a-false-positive-screening-hit-in-fragment-based-lead-discovery-watch-out-for-the-red-herring
#11
Jonathan Cramer, Johannes Schiebel, Tobias Wulsdorf, Kristof Grohe, Eszter Eva Najbauer, Frederik R Ehrmann, Nedyalka Radeva, Nina Zitzer, Uwe Linne, Rasmus Linser, Andreas Heine, Gerhard Klebe
With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false-positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease endothiapepsin (EP) across multiple screening assays...
January 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28097059/the-complete-chloroplast-genome-sequence-of-an-endemic-monotypic-genus-hagenia-rosaceae-structural-comparative-analysis-gene-content-and-microsatellite-detection
#12
Andrew W Gichira, Zhizhong Li, Josphat K Saina, Zhicheng Long, Guangwan Hu, Robert W Gituru, Qingfeng Wang, Jinming Chen
Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H...
2017: PeerJ
https://www.readbyqxmd.com/read/28096378/biosynthesis-of-the-microtubule-destabilizing-diterpene-pseudolaric-acid-b-from-golden-larch-involves-an-unusual-diterpene-synthase
#13
Sibongile Mafu, Prema Sambandaswami Karunanithi, Teresa Ann Palazzo, Bronwyn Lee Harrod, Selina Marakana Rodriguez, Iris Natalie Mollhoff, Terrence Edward O'Brien, Shen Tong, Oliver Fiehn, Dean J Tantillo, Jörg Bohlmann, Philipp Zerbe
The diversity of small molecules formed via plant diterpene metabolism offers a rich source of known and potentially new biopharmaceuticals. Among these, the microtubule-destabilizing activity of pseudolaric acid B (PAB) holds promise for new anticancer agents. PAB is found, perhaps uniquely, in the coniferous tree golden larch (Pseudolarix amabilis, Pxa). Here we describe the discovery and mechanistic analysis of golden larch terpene synthase 8 (PxaTPS8), an unusual diterpene synthase (diTPS) that catalyzes the first committed step in PAB biosynthesis...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28094510/nanoporous-gold-based-electrode-morphology-libraries-for-investigating-structure-property-relationships-in-nucleic-acid-based-electrochemical-biosensors
#14
Zimple Matharu, Pallavi Daggumati, Ling Wang, Tatiana S Dorofeeva, Zidong Li, Erkin Seker
Nanoporous gold (np-Au) electrode coatings significantly enhance performance of electrochemical nucleic acid biosensors due to their three-dimensional nanoscale network, high electrical conductivity, facile surface functionalization, and biocompatibility. Contrary to planar electrodes, the np-Au electrodes also exhibit sensitive detection in the presence of common biofouling media due to their porous structure. However, the pore size of the nano-matrix plays a critical role in dictating the extent of biomolecular capture and transport...
January 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28093469/assembly-of-the%C3%A2-elongated-collagen-prolyl-4-hydroxylase-%C3%AE-2%C3%AE-2-heterotetramer%C3%A2-around-a-central-%C3%AE-2-dimer
#15
Kristian Koski, Jothi Anantharajan, Petri Kursula, Prathusha Dhavala, Abhinandan Venkatesha Murthy, Ulrich Bergmann, Johanna Myllyharju, Rik K Wierenga
COLLAGEN PROLYL 4-HYDROXYLASE C-P4H, AN Α2Β2 HETEROTETRAMER, IS A CRUCIAL ENZYME FOR COLLAGEN SYNTHESIS THE Α SUBUNIT CONSISTS OF AN N TERMINAL DIMERIZATION DOMAIN, A CENTRAL PEPTIDE-SUBSTRATE-BINDING PSB DOMAIN, AND A C TERMINAL CATALYTIC CAT DOMAIN THE Β SUBUNIT ALSO KNOWN AS PROTEIN DISULFIDE ISOMERASE PDI ACTS AS A CHAPERONE, STABILIZING THE FUNCTIONAL CONFORMATION OF C-P4H C-P4H HAS BEEN STUDIED FOR DECADES, BUT ITS STRUCTURE HAS REMAINED ELUSIVE HERE, WE PRESENT : A THREE-DIMENSIONAL SMALL-ANGLE X-RAY SCATTERING SAXS MODEL OF THE ENTIRE HUMAN C-P4H-I HETEROTETRAMER C-P4H IS AN ELONGATED, BILOBAL, SYMMETRIC MOLECULE WITH A LENGTH OF 290 Å THE DIMERIZATION DOMAINS FROM THE TWO A SUBUNITS FORM A PROTEIN-PROTEIN DIMER INTERFACE, ASSEMBLED AROUND THE CENTRAL ANTIPARALLEL COILED-COIL INTERFACE OF THEIR N TERMINAL Α HELICES THIS REGION FORMS A THIN WAIST IN THE BILOBAL TETRAMER THE TWO PSB/CAT UNITS, EACH COMPLEXED WITH A PDI/Β SUBUNIT, FORM TWO BULKY LOBES POINTING OUTWARD FROM THIS WAIST REGION, SUCH THAT THE PDI/Β SUBUNITS LOCATE AT THE FAR ENDS OF THE ΒΑΑΒ COMPLEX THE PDI/Β SUBUNIT INTERACTS EXTENSIVELY WITH THE CAT DOMAIN THE ASYMMETRIC SHAPE OF TWO TRUNCATED C-P4H-I VARIANTS, ALSO CHARACTERIZED IN THIS STUDY, AGREES WITH THIS ASSEMBLY FURTHERMORE, DATA FROM THESE TRUNCATED VARIANTS SHOW THAT DIMERIZATION BETWEEN THE A SUBUNITS HAS AN IMPORTANT ROLE IN ACHIEVING THE CORRECT PSB-CAT ASSEMBLY COMPETENT FOR CATALYTIC ACTIVITY KINETIC ASSAYS WITH VARIOUS PROLINE-RICH PEPTIDE SUBSTRATES AND INHIBITORS SUGGEST THAT IN THE COMPETENT ASSEMBLY, THE PSB DOMAIN BINDS TO THE PROCOLLAGEN SUBSTRATE DOWNSTREAM FROM THE CAT DOMAIN...
January 16, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28092703/enantioselective-three-component-amination-of-enecarbamates-enables-the-synthesis-of-structurally-complex-small-molecules
#16
Audrey Dumoulin, Guillaume Bernadat, Géraldine Masson
The control of asymmetric synthesis tools represents a major challenge, especially when it comes to the synthesis of bioactive molecules. In this context, the asymmetric synthesis of 1,2-diamines through amination of enecarbamates has appeared to us as a highly efficient and tunable approach. Indeed, reactivity of the latter species could be exploited to realize a double functionalization via an electrophilic amination followed by nucleophilic trapping. Herein, we describe a chiral phosphoric acid-catalyzed electrophilic amination of enecarbamates with dibenzylazodicarboxylate and oxygenated or thiol-containing nucleophiles affording stable precursors of α-hydrazinoimines in high yields and with almost complete enantioselectivities (up to >99%)...
January 16, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28092434/3d-probed-lipid-dynamics-in-small-unilamellar-vesicles
#17
Meng-Hsuan Chao, Yen-Ting Lin, Namasivayam Dhenadhayalan, Hsin-Lung Lee, Hsin-Yen Lee, King-Chuen Lin
Single-molecule fluorescence correlation spectroscopy overcomes the resolution barrier of optical microscopy (10≈-20 nm) and is utilized to look into lipid dynamics in small unilamellar vesicles (SUVs; diameter < 100 nm). The fluorescence trajectories of lipid-like tracer 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine (DiD) in the membrane bilayers are acquired at a single-molecule level. The autocorrelation analysis yields the kinetic information on lipid organization, oxygen transport, and lateral diffusion in SUVs' membrane...
January 16, 2017: Small
https://www.readbyqxmd.com/read/28092358/recurrent-rna-motifs-as-scaffolds-for-genetically-encodable-small-molecule-biosensors
#18
Ely B Porter, Jacob T Polaski, Makenna M Morck, Robert T Batey
Allosteric RNA devices are increasingly being viewed as important tools capable of monitoring enzyme evolution, optimizing engineered metabolic pathways, facilitating gene discovery and regulators of nucleic acid-based therapeutics. A key bottleneck in the development of these platforms is the availability of small-molecule-binding RNA aptamers that robustly function in the cellular environment. Although aptamers can be raised against nearly any desired target through in vitro selection, many cannot easily be integrated into devices or do not reliably function in a cellular context...
January 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28090745/side-group-induced-polymorphism-in-self-assembled-monolayers-3-5-bis-trifluoromethyl-benzenethiolate-films-on-au-111
#19
Asif Bashir, Eric Sauter, Najd Al-Refaie, Michael Rohwerder, Michael Zharnikov, Waleed Azzam
The structure and molecular organization of self-assembled monolayers (SAMs) depend on a complex interplay of intermolecular and molecule-substrate interactions, so that even a small change of molecular composition can results in noticeable changes in the SAM structure. Here we show that the decoration of the most basic aromatic SAM constituent, benzenethiol, with two trifluromethyl groups leads to distinct polymorphism in the respective SAMs, with the appearance of a specific structural phase or a combination of several different phases being dependent on the parameters of the preparation procedure...
January 15, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28089448/structural-basis-for-the-interaction-of-a-human-small-heat-shock-protein-with-the-14-3-3-universal-signaling-regulator
#20
Nikolai N Sluchanko, Steven Beelen, Alexandra A Kulikova, Stephen D Weeks, Alfred A Antson, Nikolai B Gusev, Sergei V Strelkov
By interacting with hundreds of protein partners, 14-3-3 proteins coordinate vital cellular processes. Phosphorylation of the small heat shock protein, HSPB6, within its intrinsically disordered N-terminal domain activates its interaction with 14-3-3, ultimately triggering smooth muscle relaxation. After analyzing the binding of an HSPB6-derived phosphopeptide to 14-3-3 using isothermal calorimetry and X-ray crystallography, we have determined the crystal structure of the complete assembly consisting of the 14-3-3 dimer and full-length HSPB6 dimer and further characterized this complex in solution using fluorescence spectroscopy, small-angle X-ray scattering, and limited proteolysis...
December 30, 2016: Structure
keyword
keyword
110097
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"