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X-ray crystallography

Zhenyu Li, Huapeng Ruan, Lulu Wang, Caiping Liu, Li Xu
Two intermetalloid Matryoshka cluster anions [Sb@Pd12@Sb20](3-,4-) obtained from the reaction of KSb and Pd(PPh3)4 were isolated as [K(2,2,2-cryptand)](+) and [K(18-crown-6)](+) salt, respectively, and characterized by X-ray crystallography, EPR measurement and DFT theoretical calculations.
February 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Suraj Adhikary, Daniel J Deredge, Anu Nagarajan, Lucy R Forrest, Patrick L Wintrode, Satinder K Singh
Neurotransmitter:sodium symporters (NSSs) are integral membrane proteins responsible for the sodium-dependent reuptake of small-molecule neurotransmitters from the synaptic cleft. The symporters for the biogenic amines serotonin (SERT), dopamine (DAT), and norepinephrine (NET) are targets of multiple psychoactive agents, and their dysfunction has been implicated in numerous neuropsychiatric ailments. LeuT, a thermostable eubacterial NSS homolog, has been exploited as a model protein for NSS members to canvass the conformational mechanism of transport with a combination of X-ray crystallography, cysteine accessibility, and solution spectroscopy...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
Ahibur Rahaman, Carolina Gimbert-Suriñach, Arne Ficks, Graham E Ball, Mohan Bhadbhade, Matti Haukka, Lee Higham, Ebbe Nordlander, Stephen B Colbran
The influence of the substitution, orientation and structure of the phosphido bridges in [Fe2(CO)6(μ-PR2)2] electrocatalysts of proton reduction has been studied. The isomers e,a-[Fe2(CO)6{μ-P(Ar)H}2] (1a(Ar): Ar = Ph, 2'-methoxy-1,1'-binaphthyl (bn')), e,e-[Fe2(CO)6{μ-P(Ar)H}2] (1b(Ar): Ar = Ph, bn') were isolated from reactions of iron pentacarbonyl and the corresponding primary phosphine, syntheses that also afforded the phosphinidene-capped tri-iron clusters, [Fe3(CO)9(μ-CO)(μ3-Pbn')] (2) and [Fe3(CO)9(μ3-PAr)2] (3(Ar), Ar = Ph, bn')...
February 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Philipp Consentius, Bernhard Loll, Ulrich Gohlke, Claudia Alings, Carsten Mueller, Robert Müller, Christian Teutloff, Udo Heinemann, Martin Kaupp, Markus C Wahl, Thomas Risse
Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS)-spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information of the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature, while being characterized by a bent conformation at low temperature...
February 21, 2017: Journal of Physical Chemistry Letters
Michihiro Suga, Fusamichi Akita, Michihiro Sugahara, Minoru Kubo, Yoshiki Nakajima, Takanori Nakane, Keitaro Yamashita, Yasufumi Umena, Makoto Nakabayashi, Takahiro Yamane, Takamitsu Nakano, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Tetsunari Kimura, Takashi Nomura, Shinichiro Yonekura, Long-Jiang Yu, Tomohiro Sakamoto, Taiki Motomura, Jing-Hua Chen, Yuki Kato, Takumi Noguchi, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Eriko Nango, Rie Tanaka, Hisashi Naitow, Yoshinori Matsuura, Ayumi Yamashita, Masaki Yamamoto, Osamu Nureki, Makina Yabashi, Tetsuya Ishikawa, So Iwata, Jian-Ren Shen
Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure...
February 20, 2017: Nature
Jonathan N Jaworski, Scott D McCann, Ilia A Guzei, Shannon S Stahl
Palladium(II)-catalyzed oxidation reactions exhibit broad utility in organic synthesis; however, they often feature high catalyst loading and low turnover numbers relative to non-oxidative cross-coupling reactions. Insights into the fate of the Pd catalyst during turnover could help to address this limitation. Herein, we report the identification and characterization of a dimeric Pd(I) species in two prototypical Pd-catalyzed aerobic oxidation reactions: allylic C-H acetoxylation of terminal alkenes and intramolecular aza-Wacker cyclization...
February 20, 2017: Angewandte Chemie
Jimin Wang, Mikhail Askerka, Gary W Brudvig, Victor S Batista
Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods...
February 10, 2017: ACS Energy Lett
Jakub Pedziwiatr, Ion Ghiviriga, Khalil A Abboud, Adam S Veige
This report describes a synthetic protocols and the crystal structures involving a novel pincer-type H3[NNN] ligand, namely di-μ-bromido-μ-{2-(2,2-di-methylpropanimido-yl)-N-[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-bis-[(diethyl ether)lithium], [Li2Br2(C24H33N3)(C4H10O)2] (1) and a dinuclear metal complex, namely di-μ-bromido-2:3κ(4)Br:Br-bis-{2-(2,2-di-methylpropanimido-yl)-N-[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-1κ(3)N,N',N'';4κ(3)N,N',N''-tetra-μ-iso-propano-lato-1:2κ(4)O:O;3:4κ(4)O:O-diiso-propano-lato-1κO,4κO-2,3-dilithium-1,4-dititanium, [Li2Ti2Br2(C24H32N3)2(C3H7O)6] or {[NHNNH]Ti(O (i) Pr)3(LiBr)2}2 (2)...
February 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
Amit K Keshari, Ashok K Singh, Sudipta Saha
Thiazolopyrimidine derivatives containing bridgehead nitrogen atom are now-a-days attracting the attention of many medicinal chemists throughout the world to explore this framework for its potential. This biologically important scaffold is formed by the fusion of two aromatic rings, thiazole and pyrimidine, in such a way that one carbon atom at the ring junction is replaced by a nitrogen atom and is, therefore, being common for both the heterocyclic rings. One of the most common example of this type of fusion is thiazolo[3,2-a]pyrimidine which is being used perpetually with tremendous success in various field of therapeutic applications...
February 16, 2017: Mini Reviews in Medicinal Chemistry
Min Zhou, Hang-Ying Ma, Zhi-Hua Liu, Guang-Yu Yang, Gang Du, Yan-Qing Ye, Gan-Peng Li, Qiu-Fen Hu
(+)-Meyeniins A-C (1-3), a novel class of sulfur-containing hexahydroimidazo[1,5-c]thiazole derivatives, were isolated from the tubers of Lepidium meyenii cultivated in Lijiang, Yunnan Province, China. Guided by their biosynthetic hypothesis, a stereocontrolled biomimetic synthesis of meyeniins A-C and their individual enantiomers was efficiently accomplished by a combination of a condensation reaction and Edman degradation. The formation of high-quality crystals for X-ray crystallography occurred much more readily from a racemic mixture of (±)-meyeniin A than with the single enantiomer alone in this case...
February 17, 2017: Journal of Agricultural and Food Chemistry
Amandine Conte-Daban, Valentina Borghesani, Stéphanie Sayen, Emmanuel Guillon, Yves Journaux, Geoffrey Gontard, Laurent Lisnard, Christelle Hureau
Being able to easily determine the Cu(II) affinity for biomolecules of moderate affinity is important. Such biomolecules include amyloidogenic peptides, such as the well-known amyloid-β peptide involved in Alzheimer's disease. Here, we report the synthesis of a new water-soluble ratiometric Cu(II) dye with a moderate affinity (10(9) M(-1) at pH 7.1) and the characterizations of the Cu(II) corresponding complex by X-ray crystallography, EPR, and XAS spectroscopic methods. UV-vis competition was performed on the Aβ peptide as well as on a wide series of modified peptides, leading to an affinity value of 1...
February 7, 2017: Analytical Chemistry
Andrea E Prota, Katja Bargsten, Mariano Redondo, Amos B Smith Iii, Chia-Ping H Yang, Hayley M McDaid, Ian Paterson, Susan B Horwitz, José Fernando Díaz, Michel O Steinmetz
Microtubule-stabilizing agents (MSAs) are widely used in chemotherapy. Here, using X-ray crystallography we describe the detailed binding modes of two potent MSAs, (+)-discodermolide (DDM) and the DDM-paclitaxel-hybrid KS-1-199-32, in the taxane pocket of ß-tubulin. Both compounds bind in a very similar hairpin conformation as previously observed in solution. However, they differentially stabilize the M-loop of ß-tubulin: KS-1-199-32 induces an M-loop helical conformation that is not observed for DDM. In the context of the microtubule structure, both MSAs connect the ß-tubulin helices H6 and H7 and loop S9-S10 with the M-loop, which is similar to the structural effects elicited by epothilone A, but distinct from paclitaxel...
February 16, 2017: Chembiochem: a European Journal of Chemical Biology
Vicky Howe, Andrew J Brown
Biochemical methods can help elucidate the membrane topology of hydrophobic membrane proteins where X-ray crystallography is difficult or impractical, providing important structural data. Here, we describe the method of PEGylation, which uses a cysteine-reactive molecule, maleimide polyethylene glycol (mPEG), to determine the cytosolic accessibility of introduced cysteine residues. This accessibility is visualized using Western blotting to detect a band shift that indicates cysteine labeling by mPEG. Using scanning cysteine mutagenesis, followed by PEGylation, one can map the accessibility of the introduced cysteines, hence inferring the membrane topology of the protein...
2017: Methods in Molecular Biology
Yunjun Shen, Yani Pan, Kang Zhang, Xuewei Liang, Jiyong Liu, Bernhard Spingler, Simon Duttwyler
The regioselective derivatization of the monocarba-closo-dodecaborate anion via catalytic B-H bond activation is reported. Amide directing groups in combination with rhodium and iridium catalysts allowed for the direct functionalization of cage boron vertices. Products comprising B-C, B-N and B-Cl bonds were synthesized. As a key intermediate of the B-H activation step, an iridium complex with a direct B-Ir interaction was isolated and fully characterized by spectroscopic methods as well as X-ray crystallography...
February 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Maxim V Ivanov, Khushabu Thakur, Anshul Bhatnagar, Rajendra Rathore
Chiral cation-radical salts hold significant promise as charge-transfer materials, chiroptical switches, and electron-transfer catalysts for enantioselective synthesis. Herein we demonstrate that the readily-available chiral 9,10-diphenyleanthracene derivative (i.e.(S)ANT) forms a robust cation radical, whose structure was elucidated by X-ray crystallography and DFT calculations. While (S)ANT was observed to racemize on a timescale (t1/2) of 1.1 hours, a computational conformational search and kinetic analysis of the racemization pathway led us to identify a simple methyl substituted (S)ANT derivative, which does not racemize (racemization t1/2 10(13)-10(17) years)...
February 16, 2017: Chemical Communications: Chem Comm
Hanna Kwon, Paul G Young, Christopher J Squire, Edward N Baker
The overall stability of globular protein structures is marginal, a balance between large numbers of stabilizing non-covalent interactions and a destabilizing entropic term. Higher stability can be engineered by introduction of disulfide bonds, provided the redox environment is controlled. The discovery of stabilizing isopeptide bond crosslinks, formed spontaneously between lysine and asparagine (or aspartic acid) side chains in certain bacterial cell-surface proteins suggests that such bonds could be introduced by protein engineering as an alternative protein stabilization strategy...
February 16, 2017: Scientific Reports
Cornelius Gati, Dominik Oberthuer, Oleksandr Yefanov, Richard D Bunker, Francesco Stellato, Elaine Chiu, Shin-Mei Yeh, Andrew Aquila, Shibom Basu, Richard Bean, Kenneth R Beyerlein, Sabine Botha, Sébastien Boutet, Daniel P DePonte, R Bruce Doak, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Daniel R James, Christopher Kupitz, Lukas Lomb, Marc Messerschmidt, Karol Nass, Kimberly Rendek, Robert L Shoeman, Dingjie Wang, Uwe Weierstall, Thomas A White, Garth J Williams, Nadia A Zatsepin, Petra Fromme, John C H Spence, Kenneth N Goldie, Johannes A Jehle, Peter Metcalf, Anton Barty, Henry N Chapman
To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling...
February 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
Suvrajit Maji, Rezvan Shahoei, Klaus Schulten, Joachim Frank
The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories...
February 15, 2017: Journal of Physical Chemistry. B
Simon Krautwald, Mate J Bezdek, Paul J Chirik
A cobalt-catalyzed method for the 1,1-diboration of terminal alkynes with bis(pinacolato)diboron (B2Pin2) is described. The reaction proceeds efficiently at 23 °C with excellent 1,1-selectivity and broad functional group tolerance. With the unsymmetrical diboron reagent PinB-BDan (Dan = naphthalene-1,8-diaminato), stereoselective 1,1-diboration provided products with two boron substituents that exhibit differential reactivity. One example prepared by diboration of 1-octyne was crystallized and its stereochemistry established by X-ray crystallography...
February 15, 2017: Journal of the American Chemical Society
Julian R Levell, Thomas Caferro, Gregg Chenail, Ina Dix, Julia Dooley, Brant Firestone, Pascal D Fortin, John Giraldes, Ty Gould, Joseph D Growney, Michael D Jones, Raviraj Kulathila, Fallon Lin, Gang Liu, Arne Mueller, Simon van der Plas, Kelly Slocum, Troy Smith, Remi Terranova, B Barry Touré, Viraj Tyagi, Trixie Wagner, Xiaoling Xie, Ming Xu, Fan S Yang, Liping X Zhou, Raymond Pagliarini, Young Shin Cho
High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl)amino)pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of IDH1(R132H). Synthesis of the four separate stereoisomers identified the (S,S)-diastereomer (IDH125, 1f) as the most potent isomer. This also showed reasonable cellular activity and excellent selectivity vs IDH1(wt). Initial structure-activity relationship exploration identified the key tolerances and potential for optimization. X-ray crystallography identified a functionally relevant allosteric binding site amenable to inhibitors, which can penetrate the blood-brain barrier, and aided rational optimization...
February 9, 2017: ACS Medicinal Chemistry Letters
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