Probing the binding modes and dynamics of histidine on fumed silica surfaces by solid-state NMR

2020 ◽  
Vol 22 (36) ◽  
pp. 20349-20361
Author(s):  
Haley L. Swanson ◽  
Chengchen Guo ◽  
Michael Cao ◽  
J. Bennett Addison ◽  
Gregory P. Holland

Silica nanoparticles can be designed to exhibit a diverse range of morphologies (e.g. non-porous, mesoporous), physical properties (e.g. hydrophobic, hydrophilic) and a wide range of chemical and biomolecular surface functionalizations.

2006 ◽  
pp. 744 ◽  
Author(s):  
Liang Ouyang ◽  
Pedro M. Aguiar ◽  
Raymond J. Batchelor ◽  
Scott Kroeker ◽  
Daniel B. Leznoff

2021 ◽  
Author(s):  
Ulric B. le Paige ◽  
ShengQi Xiang ◽  
Marco M. R. M. Hendrix ◽  
Yi Zhang ◽  
Markus Weingarth ◽  
...  

Abstract. Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins to the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ~200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle x-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.


2015 ◽  
Vol 1 (11) ◽  
pp. e1501087 ◽  
Author(s):  
Chaowei Shi ◽  
Pascal Fricke ◽  
Lin Lin ◽  
Veniamin Chevelkov ◽  
Melanie Wegstroth ◽  
...  

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the speciesCaulobacter crescentusis not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR–derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.


2018 ◽  
Vol 11 (1) ◽  
pp. 485-508 ◽  
Author(s):  
Sharon E. Ashbrook ◽  
John M. Griffin ◽  
Karen E. Johnston

The sensitivity of nuclear magnetic resonance (NMR) spectroscopy to the local atomic-scale environment offers great potential for the characterization of a diverse range of solid materials. Despite offering more information than its solution-state counterpart, solid-state NMR has not yet achieved a similar level of recognition, owing to the anisotropic interactions that broaden the spectral lines and hinder the extraction of structural information. Here, we describe the methods available to improve the resolution of solid-state NMR spectra and the continuing research in this area. We also highlight areas of exciting new and future development, including recent interest in combining experiment with theoretical calculations, the rise of a range of polarization transfer techniques that provide significant sensitivity enhancements, and the progress of in situ measurements. We demonstrate the detailed information available when studying dynamic and disordered solids and discuss the future applications of solid-state NMR spectroscopy across the chemical sciences.


2006 ◽  
Vol 984 ◽  
Author(s):  
Paul Guerry ◽  
Donna L Carroll ◽  
Phillips N Gunawidjaja ◽  
Prodipta Bhattacharya ◽  
Daniela Carta ◽  
...  

AbstractTo understand amorphous and structurally disordered materials requires the application of a wide-range of advanced physical probe techniques and herein a combined methodology is outlined. The relatively short-range structural sensitivity of solid state NMR means that it is a core probe technique for characterizing such materials. The aspects of the solid state NMR contribution are emphasized here with examples given from a number of systems, with especial emphasis on the information available from 17O NMR in oxygen-containing materials. 17O NMR data for crystallization of pure sol-gel prepared oxides is compared, with new data presented from In2O3 and Sc2O3. Sol-gel formed oxide mixtures containing silica have been widely studied, but again the role and effect of the other added oxide varies widely. In a ternary ZrO2-TiO2-SiO2 silicate sol-gel the level of Q4 formation is dependent not only on the composition, as expected, but also the nature of the second added oxide. Sol-gel formed phosphates have been much less widely studied than silicates and some 31P NMR data from xerogel, sonogel and melt-quench glasses of the same composition are compared. The effect of small amounts of added antibacterial copper on phosphate glass networks is also explored.


Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1400 ◽  
Author(s):  
Robert Knitsch ◽  
Melanie Brinkkötter ◽  
Thomas Wiegand ◽  
Gerald Kehr ◽  
Gerhard Erker ◽  
...  

Modern solid-state NMR techniques offer a wide range of opportunities for the structural characterization of frustrated Lewis pairs (FLPs), their aggregates, and the products of cooperative addition reactions at their two Lewis centers. This information is extremely valuable for materials that elude structural characterization by X-ray diffraction because of their nanocrystalline or amorphous character, (pseudo-)polymorphism, or other types of disordering phenomena inherent in the solid state. Aside from simple chemical shift measurements using single-pulse or cross-polarization/magic-angle spinning NMR detection techniques, the availability of advanced multidimensional and double-resonance NMR methods greatly deepened the informational content of these experiments. In particular, methods quantifying the magnetic dipole–dipole interaction strengths and indirect spin–spin interactions prove useful for the measurement of intermolecular association, connectivity, assessment of FLP–ligand distributions, and the stereochemistry of adducts. The present review illustrates several important solid-state NMR methods with some insightful applications to open questions in FLP chemistry, with a particular focus on supramolecular associates.


Inorganics ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 70
Author(s):  
Graeme Hogarth ◽  
Damian C. Onwudiwe

Copper dithiocarbamate complexes have been known for ca. 120 years and find relevance in biology and medicine, especially as anticancer agents and applications in materials science as a single-source precursor (SSPs) to nanoscale copper sulfides. Dithiocarbamates support Cu(I), Cu(II) and Cu(III) and show a rich and diverse coordination chemistry. Homoleptic [Cu(S2CNR2)2] are most common, being known for hundreds of substituents. All contain a Cu(II) centre, being either monomeric (distorted square planar) or dimeric (distorted trigonal bipyramidal) in the solid state, the latter being held together by intermolecular C···S interactions. Their d9 electronic configuration renders them paramagnetic and thus readily detected by electron paramagnetic resonance (EPR) spectroscopy. Reaction with a range of oxidants affords d8 Cu(III) complexes, [Cu(S2CNR2)2][X], in which copper remains in a square-planar geometry, but Cu–S bonds shorten by ca. 0.1 Å. These show a wide range of different structural motifs in the solid-state, varying with changes in anion and dithiocarbamate substituents. Cu(I) complexes, [Cu(S2CNR2)2]−, are (briefly) accessible in an electrochemical cell, and the only stable example is recently reported [Cu(S2CNH2)2][NH4]·H2O. Others readily lose a dithiocarbamate and the d10 centres can either be trapped with other coordinating ligands, especially phosphines, or form clusters with tetrahedral [Cu(μ3-S2CNR2)]4 being most common. Over the past decade, a wide range of Cu(I) dithiocarbamate clusters have been prepared and structurally characterised with nuclearities of 3–28, especially exciting being those with interstitial hydride and/or acetylide co-ligands. A range of mixed-valence Cu(I)–Cu(II) and Cu(II)–Cu(III) complexes are known, many of which show novel physical properties, and one Cu(I)–Cu(II)–Cu(III) species has been reported. Copper dithiocarbamates have been widely used as SSPs to nanoscale copper sulfides, allowing control over the phase, particle size and morphology of nanomaterials, and thus giving access to materials with tuneable physical properties. The identification of copper in a range of neurological diseases and the use of disulfiram as a drug for over 50 years makes understanding of the biological formation and action of [Cu(S2CNEt2)2] especially important. Furthermore, the finding that it and related Cu(II) dithiocarbamates are active anticancer agents has pushed them to the fore in studies of metal-based biomedicines.


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