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Journal articles on the topic 'X-ray crystallography; Multi-clear NMR'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Cai, Kai, and John Markley. "NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis." Molecules 23, no. 9 (2018): 2213. http://dx.doi.org/10.3390/molecules23092213.

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Iron-sulfur (Fe-S) clusters, the ubiquitous protein cofactors found in all kingdoms of life, perform a myriad of functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. The biogenesis of Fe-S clusters is a multi-step process that involves the participation of many protein partners. Recent biophysical studies, involving X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and small angle X-ray scattering (SAXS), have greatly improved our understanding of these steps. In this review, afte

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2

Nöllmann, Marcelo, W. Marshall Stark, and Olwyn Byron. "A global multi-technique approach to study low-resolution solution structures." Journal of Applied Crystallography 38, no. 6 (2005): 874–87. http://dx.doi.org/10.1107/s0021889805026191.

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Finding the conformation of large macromolecular complexes has become an important problem in structural biology, which is not always soluble by high-resolution techniques such as X-ray crystallography and NMR spectroscopy. Solution biophysical properties can provide direct or indirect structural information on these large complexes. A general systematic approach to the construction of a structural model of the macromolecule consistent with all the experimental solution properties is currently lacking. In this paper, such an approach is presented, where generalized rigid-body modelling is comb

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3

Zhong, Tingshan, Jixing Zhao, and Hao Lei. "Trianionic binucleating bis(trityl)/aryloxide ligands and their lithium, magnesium, and zinc complexes." Canadian Journal of Chemistry 98, no. 8 (2020): 453–59. http://dx.doi.org/10.1139/cjc-2020-0139.

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A series of lithium complexes with trianionic bis(trityl)/aryloxide ligands were prepared by triple deprotonation of phenols with two ortho-diarylmethyl substituents. Transmetalation with one of the lithium complexes via salt metathesis resulted in the synthesis of corresponding Mg and Zn complexes, which showed distinct coordination stoichiometry and structures. The metal complexes were characterized by multi-nuclear NMR, UV–vis, and infrared spectroscopy. Additionally, the redox property of a trilithium compound was investigated by electrochemical methods. X-ray crystallography revealed that

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4

Smith, Gregory L., Hélène P. A. Mercier, and Gary J. Schrobilgen. "Synthesis of [F3S⋮NXeF][AsF6] and Structural Study by Multi-NMR and Raman Spectroscopy, Electronic Structure Calculations, and X-ray Crystallography." Inorganic Chemistry 46, no. 4 (2007): 1369–78. http://dx.doi.org/10.1021/ic061899+.

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5

Hynson, Robert M. G., Anthony P. Duff, Nigel Kirby, Stephan Mudie, and Lawrence K. Lee. "Differential ultracentrifugation coupled to small-angle X-ray scattering on macromolecular complexes." Journal of Applied Crystallography 48, no. 3 (2015): 769–75. http://dx.doi.org/10.1107/s1600576715005051.

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Small-angle X-ray scattering (SAXS) can provide accurate structural information and low-resolution shapes of macromolecules in solution. The technique is particularly amenable to large protein assemblies, which produce a strong scattering signal. Hence, SAXS can be a powerful tool to elucidate quaternary structure, especially when used in combination with high-resolution structural techniques such as X-ray crystallography and NMR. Sample requirements for SAXS experiments are stringent and only monodispersed samples can be satisfactorily analysed. Often, it is not possible to obtain a stable mo

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6

Han, Jeongmin, Iktae Kim, Jae-Hyun Park, et al. "A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction." International Journal of Molecular Sciences 21, no. 7 (2020): 2452. http://dx.doi.org/10.3390/ijms21072452.

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Human SNF5 and BAF155 constitute the core subunit of multi-protein SWI/SNF chromatin-remodeling complexes that are required for ATP-dependent nucleosome mobility and transcriptional control. Human SNF5 (hSNF5) utilizes its repeat 1 (RPT1) domain to associate with the SWIRM domain of BAF155. Here, we employed X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and various biophysical methods in order to investigate the detailed binding mechanism between hSNF5 and BAF155. Multi-angle light scattering data clearly indicate that hSNF5171–258 and BAF155SWIRM are both monomeric in

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7

Vialemaringe, Marianne, Marie Jos�phe Bourgeois, Evelyne Montaudon, Christian Courseille, Bernard Barbe, and Isabelle Pianet. "Isofenchylic alcohol derived from a functionalized pinene oxide: unexpected formation and structural confirmation using multi-dimensional NMR spectroscopy and x-ray crystallography." Magnetic Resonance in Chemistry 38, no. 9 (2000): 785–88. http://dx.doi.org/10.1002/1097-458x(200009)38:9<785::aid-mrc734>3.0.co;2-5.

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8

Putnam, Christopher D., Michal Hammel, Greg L. Hura, and John A. Tainer. "X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution." Quarterly Reviews of Biophysics 40, no. 3 (2007): 191–285. http://dx.doi.org/10.1017/s0033583507004635.

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AbstractCrystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 Å to 10 Å resolution, but without the size limitations inherent in NMR and electron microscopy studies.

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9

Rath, Emma, Anthony Duff, Robert Knott, and W. Church. "Small-angle X-ray scattering of BAMLET protein-oleic acid complexes at pH 12." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C420. http://dx.doi.org/10.1107/s2053273314095795.

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BAMLET and HAMLET represent a new class of compound having unrealised potential for treating a broad spectrum of cancers and some multi-drug resistant bacterial infections (Brinkmann et al. 2013; Marks et al. 2013). These compounds are composed of protein (14 to 84 kDa) and oleic acid (282 Da), the latter being the main active component. Hypothesised molten-globularity makes structural determination by NMR and X-ray crystallography very challenging. We carried out small angle X-ray scattering (SAXS) on BAMLET at pH 12 (Rath et al. 2014), the pH at which the complex can be prepared. SAXS showed

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10

Duff, Michael R., Jasmina S. Redzic, Lucas P. Ryan, et al. "Structure, dynamics and function of the evolutionarily changing biliverdin reductase B family." Journal of Biochemistry 168, no. 2 (2020): 191–202. http://dx.doi.org/10.1093/jb/mvaa039.

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Abstract Biliverdin reductase B (BLVRB) family members are general flavin reductases critical in maintaining cellular redox with recent findings revealing that BLVRB alone can dictate cellular fate. However, as opposed to most enzymes, the BLVRB family remains enigmatic with an evolutionarily changing active site and unknown structural and functional consequences. Here, we applied a multi-faceted approach that combines X-ray crystallography, NMR and kinetics methods to elucidate the structural and functional basis of the evolutionarily changing BLVRB active site. Using a panel of three BLVRB i

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11

van Heel, Marin, Brent Gowen, Rishi Matadeen, et al. "Single-particle electron cryo-microscopy: towards atomic resolution." Quarterly Reviews of Biophysics 33, no. 4 (2000): 307–69. http://dx.doi.org/10.1017/s0033583500003644.

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1. Introduction 3082. Electron microscopy 3112.1 Specimen preparation 3112.2 The electron microscope 3112.3 Acceleration voltage, defocus, and the electron gun 3122.4 Magnification and data collection 3133. Digitisation and CTF correction 3173.1 The patchwork densitometer 3183.2 Particle selection 3203.3 Position dependent CTF correction 3213.4 Precision of CTF determination 3214. Single particles and angular reconstitution 3234.1 Preliminary filtering and centring of data 3234.2 Alignments using correlation functions 3244.3 Choice of first reference images 3244.4 Multi-reference alignment of

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12

Osz, Judit, Alastair G. McEwen, Maxime Bourguet, et al. "Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR." Nucleic Acids Research 48, no. 17 (2020): 9969–85. http://dx.doi.org/10.1093/nar/gkaa697.

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Abstract Retinoic acid receptors (RARs) as a functional heterodimer with retinoid X receptors (RXRs), bind a diverse series of RA-response elements (RAREs) in regulated genes. Among them, the non-canonical DR0 elements are bound by RXR–RAR with comparable affinities to DR5 elements but DR0 elements do not act transcriptionally as independent RAREs. In this work, we present structural insights for the recognition of DR5 and DR0 elements by RXR–RAR heterodimer using x-ray crystallography, small angle x-ray scattering, and hydrogen/deuterium exchange coupled to mass spectrometry. We solved the cr

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13

Zhong, Yu-Jie, Jian-Hong Liao, Tzu-Hao Chiu, et al. "Intercluster exchanges leading to hydride-centered bimetallic clusters: a multi-NMR, X-ray crystallographic, and DFT study." Dalton Transactions 50, no. 13 (2021): 4727–34. http://dx.doi.org/10.1039/d1dt00072a.

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The tendency to reach dynamic equilibrium of intercluster reaction, Ag<sub>7</sub>(H) and Cu<sub>7</sub>(H), in solution is driven by a stepwise, one-metal exchange process, which has been illustrated by 2D EXSY NMR experiments.

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14

Wylie, Andrew, Joseph Schoepfer, Giuliano Berellini, et al. "ABL001, a Potent Allosteric Inhibitor of BCR-ABL, Prevents Emergence of Resistant Disease When Administered in Combination with Nilotinib in an in Vivo Murine Model of Chronic Myeloid Leukemia." Blood 124, no. 21 (2014): 398. http://dx.doi.org/10.1182/blood.v124.21.398.398.

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Abstract Background: Chronic myelogenous leukemia (CML) and a subset of acute lymphoblastic leukemia (ALL) are caused by the t(9;22)(q34;q11.2) chromosome translocation, resulting in fusion of the BCR and ABL1 genes on the Philadelphia chromosome to encode constitutively active ABL1 kinase. Despite the dramatic progress made over the past decade with tyrosine kinase inhibitors (TKIs) in the treatment of CML, allogeneic stem cell transplant is considered the only proven curative therapy. To achieve cure or benefit from treatment-free remissions with pharmacologically-based therapies, it is esti

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15

Newman, Jane D., Meghan M. Russell, Lixin Fan, Yun-Xing Wang, Giovanni Gonzalez-Gutierrez, and Julia C. van Kessel. "The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences." Nucleic Acids Research 49, no. 10 (2021): 5967–84. http://dx.doi.org/10.1093/nar/gkab387.

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Abstract Quorum sensing gene expression in vibrios is regulated by the LuxR/HapR family of transcriptional factors, which includes Vibrio vulnificus SmcR. The consensus binding site of Vibrio LuxR/HapR/SmcR proteins is palindromic but highly degenerate with sequence variations at each promoter. To examine the mechanism by which SmcR recognizes diverse DNA sites, we generated SmcR separation-of-function mutants that either repress or activate transcription but not both. SmcR N55I is restricted in recognition of single base-pair variations in DNA binding site sequences and thus is defective at t

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16

Vogel, Dominik, Sigurdur Rafn Thorkelsson, Emmanuelle R. J. Quemin, et al. "Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein." Nucleic Acids Research 48, no. 10 (2020): 5749–65. http://dx.doi.org/10.1093/nar/gkaa253.

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Abstract The Bunyavirales order contains several emerging viruses with high epidemic potential, including Severe fever with thrombocytopenia syndrome virus (SFTSV). The lack of medical countermeasures, such as vaccines and antivirals, is a limiting factor for the containment of any virus outbreak. To develop such antivirals a profound understanding of the viral replication process is essential. The L protein of bunyaviruses is a multi-functional and multi-domain protein performing both virus transcription and genome replication and, therefore, is an ideal drug target. We established expression

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17

Efremov, Andrey N., Vladimir V. Sharutin, Olga K. Sharutina, Pavel V. Andreev, and Oleg S. Eltsov. "SYNTHESIS AND STRUCTURE OF METHYLTRIPHENYLPHOSPHONIUM DICYANODIBROMOAURATE [Ph3PCH3] [Au(CN)2Br2]." IZVESTIYA VYSSHIKH UCHEBNYKH ZAVEDENII KHIMIYA KHIMICHESKAYA TEKHNOLOGIYA 63, no. 3 (2020): 10–15. http://dx.doi.org/10.6060/ivkkt.20206303.6097.

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Methyltriphenylphosphonium dicyanodibromoaurate (1) [Ph3PMe]+[Au(CN)2Br2]– was synthesized by the reaction of potassium dicyanodibromoaurate with methyltriphenylphosphonium bromide in an aqueous solution and was structurally characterized. The complex is a yellow-colored, air-resistant crystalline substance with a clear melting point. The structure of the compound was established by IR spectroscopy, NMR spectroscopy and X-ray diffraction analysis. An intense absorption band was observed in the IR spectrum of compound at 2220 cm−1, corresponding to the stretching vibrations of cyano groups. The

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18

Brookes, Emre, Javier Pérez, Barbara Cardinali, Aldo Profumo, Patrice Vachette, and Mattia Rocco. "Fibrinogen species as resolved by HPLC-SAXS data processing within theUltraScan Solution Modeler(US-SOMO) enhanced SAS module." Journal of Applied Crystallography 46, no. 6 (2013): 1823–33. http://dx.doi.org/10.1107/s0021889813027751.

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Fibrinogen is a large heterogeneous aggregation/degradation-prone protein playing a central role in blood coagulation and associated pathologies, whose structure is not completely resolved. When a high-molecular-weight fraction was analyzed by size-exclusion high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS), several composite peaks were apparent and because of the stickiness of fibrinogen the analysis was complicated by severe capillary fouling. Novel SAS analysis tools developed as a part of theUltraScan Solution Modeler(US-SOMO; http://somo.uthscsa.edu/), an ope

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19

Smith, Gregory L., Helene P. A. Mercier, and Gary J. Schrobilgen. "Synthesis of [F3SNXeF][AsF6] and Structural Study by Multi-NMR and Raman Spectroscopy, Electronic Structure Calculations, and X-Ray Crystallography." ChemInform 38, no. 21 (2007). http://dx.doi.org/10.1002/chin.200721015.

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20

Gandhi, Amit K., Zhen-Yu J. Sun, Walter M. Kim, et al. "Structural basis of the dynamic human CEACAM1 monomer-dimer equilibrium." Communications Biology 4, no. 1 (2021). http://dx.doi.org/10.1038/s42003-021-01871-2.

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AbstractHuman (h) carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) function depends upon IgV-mediated homodimerization or heterodimerization with host ligands, including hCEACAM5, hTIM-3, PD-1, and a variety of microbial pathogens. However, there is little structural information available on how hCEACAM1 transitions between monomeric and dimeric states which in the latter case is critical for initiating hCEACAM1 activities. We therefore mutated residues within the hCEACAM1 IgV GFCC′ face including V39, I91, N97, and E99 and examined hCEACAM1 IgV monomer-homodimer exchange us

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21

Lambrughi, Matteo, Emiliano Maiani, Burcu Aykac Fas, et al. "Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs." Frontiers in Molecular Biosciences 8 (June 28, 2021). http://dx.doi.org/10.3389/fmolb.2021.676235.

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Ubiquitin is a small protein at the heart of many cellular processes, and several different protein domains are known to recognize and bind ubiquitin. A common motif for interaction with ubiquitin is the Ubiquitin Interacting Motif (UIM), characterized by a conserved sequence signature and often found in multi-domain proteins. Multi-domain proteins with intrinsically disordered regions mediate interactions with multiple partners, orchestrating diverse pathways. Short linear motifs for binding are often embedded in these disordered regions and play crucial roles in modulating protein function.

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22

Okezue, Mercy, Susan Bogdanowich-Knipp, Daniel Smith, et al. "Salts and Polymorph Screens for Bedaquiline." AAPS PharmSciTech 22, no. 7 (2021). http://dx.doi.org/10.1208/s12249-021-02106-7.

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AbstractBedaquiline is used to treat multi-resistant tuberculosis in adults. The fumarate salt is commercially available and used in the product Sirturo. To provide open access to bedaquiline molecule once the patent on the chemical substance expires, new salts were screened. This work offers additional information on the bedaquiline system, as new salts may present better pharmacokinetic properties. The current studies focus on the attempted isolation of the acetate, benzoate, benzenesulfonate, hydrobromide, succinate, hydrochloride, tartrate, lactate, maleate, malate, and mesylate salts of b

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