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Guohua Lv, Ashutosh Kumar, Yun Huang, David Eliezer
Fibrillar α-synuclein (AS) is the major component of Lewy bodies, the pathological hallmark of Parkinson's disease. Using solid-state nuclear magnetic resonance (ssNMR), we previously reported a structural characterization of mouse AS (mAS) fibrils and found that the secondary structure of the mAS fibrils is highly similar to a form of human AS (hAS) fibrils. Recently, a three-dimensional structure of these same hAS fibrils was determined by ssNMR and scanning transmission electron microscopy. Using medium- and long-range distance restraints obtained from ssNMR spectra, we found that the single protofilament structure of mAS fibrils is also similar to that of the hAS fibrils...
June 19, 2018: Biophysical Journal
Patrick C A van der Wel
Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry...
April 20, 2018: Emerging Topics in Life Sciences
Xiangyan Shi, Chinmayi Prasanna, Toshio Nagashima, Toshio Yamazaki, Konstantin Pervushin, Lars Nordenskiöld
Eukaryotic chromatin structure and dynamics play key roles in genomic regulation. In the current study, the secondary structure and intramolecular dynamics of human histone H4 (hH4) in the nucleosome core particle (NCP) and in a nucleosome array are determined by solid-state NMR (SSNMR). Secondary structure elements are successfully localized in the hH4 in the NCP precipitated with Mg2+. In particular, dynamics on nanosecond to microsecond and microsecond to millisecond timescales are elucidated, revealing diverse internal motions in the hH4 protein...
June 14, 2018: Angewandte Chemie
Patrick M J Szell, Gabriella Cavallo, Giancarlo Terraneo, Pierangelo Metrangolo, Bulat Gabidullin, David L Bryce
Halogen bonding is an increasingly important tool in crystal engineering, and measuring its influence on the local chemical and electronic environment is necessary to fully understand this interaction. We present a systematic crystallographic and solid-state NMR study of self-complementary halogen-bonded frameworks built from the halide salts (HCl, HBr, HI, HI3) of 2-iodoethynylpyridine and 3-iodoethynylpyridine. A series of single crystal X-ray structures reveals the formation of discrete charged dimers in the solid state, directed by simultaneous X- ···H-N+ hydrogen bonds and C-I···X- halogen bonds (X = Cl, Br, I)...
May 31, 2018: Chemistry: a European Journal
Dylan Steer, Sherry Leung, Hannah Meiselman, Daniel Topgaard, Cecilia Leal
The hierarchical assembly of lipids, as modulated by composition and environment, plays a significant role in the function of biological membranes and a myriad of diseases. Elevated concentrations of calcium ions and cardiolipin, an anionic tetra-alkyl lipid found in mitochondria and some bacterial cell membranes, have been implicated in pneumonia recently. However, their impact on the physicochemical properties of lipid assemblies in lungs and how it impairs alveoli function is still unknown. We use Small- and Wide- Angle X-ray Scattering (S/WAXS) and Solid-State Nuclear Magnetic Resonance (ssNMR) to probe the structure and dynamics of lung-mimetic multilamellar bodies (MLBs) in the presence of Ca2+ and cardiolipin...
May 30, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Carla I Nieto, Pilar Cabildo, M Ángeles García, Rosa M Claramunt, José Elguero, Ibon Alkorta
The X-ray crystal structure of 2-benzyl-1H-benzimidazole, 2BnBzIm, was determined at 293 K showing no dynamic phenomena (disorder) of any class. On the other hand, some 13 C NMR signals were absent in the CPMAS spectrum (100 MHz, 300 K). We decided to carry out variable-temperature SSNMR and discovered that the missing signals are ortho and meta carbons of the phenyl ring of the benzyl group. Line-shape analysis and the Eyring equation were used to determine the barrier, which was compared to the calculated (DFT) for the gas-phase that it is much lower...
May 28, 2018: Magnetic Resonance in Chemistry: MRC
Xiaoyan Ding, Chao Sun, Haolin Cui, Sijin Chen, Yujiao Gao, Yanan Yang, Juan Wang, Xiao He, Dinu Iuga, Fang Tian, Anthony Watts, Xin Zhao
Tyrosine 185 (Y185), one of the aromatic residues within the retinal (Ret) chromophore binding pocket in helix F of bacteriorhodopsin (bR), is highly conserved among the microbial rhodopsin family proteins. Many studies have investigated the functions of Y185, but its underlying mechanism during the bR photocycle remains unclear. To address this research gap, in situ two-dimensional (2D) magic-angle spinning (MAS) solid-state NMR (ssNMR) of specifically labelled bR, combined with light-induced transient absorption change measurements, dynamic light scattering (DLS) measurements, titration analysis and site-directed mutagenesis, was used to elucidate the functional roles of Y185 during the bR photocycle in the native membrane environment...
May 22, 2018: Biochimica et Biophysica Acta
Alexander A Shcherbakov, Mei Hong
The ability to simultaneously measure many long-range distances is critical to efficient and accurate determination of protein structures by solid-state NMR (SSNMR). So far, the most common distance constraints for proteins are 13 C-15 N distances, which are usually measured using the rotational-echo double-resonance (REDOR) technique. However, these measurements are restricted to distances of up to ~ 5 Å due to the low gyromagnetic ratios of 15 N and 13 C. Here we present a robust 2D 13 C-19 F REDOR experiment to measure multiple distances to ~ 10 Å...
May 21, 2018: Journal of Biomolecular NMR
Suresh K Vasa, Petra Rovó, Rasmus Linser
Solid-state nuclear magnetic resonance (ssNMR) is a spectroscopic technique that is used for characterization of molecular properties in the solid phase at atomic resolution. In particular, using the approach of magic-angle spinning (MAS), ssNMR has seen widespread applications for topics ranging from material sciences to catalysis, metabolomics, and structural biology, where both isotropic and anisotropic parameters can be exploited for a detailed assessment of molecular properties. High-resolution detection of protons long represented the holy grail of the field...
May 15, 2018: Accounts of Chemical Research
Yiling Xiao, Dan McElheny, Minako Hoshi, Yoshitaka Ishii
Intense efforts have been made to understand the molecular structures of misfolded amyloid β (Aβ) in order to gain insight into the pathological mechanism of Alzheimer's disease. Solid-state NMR spectroscopy (SSNMR) is considered a primary tool for elucidating the structures of insoluble and noncrystalline amyloid fibrils and other amyloid assemblies. In this chapter, we describe a detailed protocol to obtain the first atomic model of the 42-residue human Aβ peptide Aβ(1-42) in structurally homogeneous amyloid fibrils from our recent SSNMR study (Nat Struct Mol Biol 22:499-505, 2015)...
2018: Methods in Molecular Biology
Ujjayini Ghosh, Wai-Ming Yau, Robert Tycko
Fibrils formed by 40- and 42-residue amyloid-β (Aβ40 and Aβ42) peptides exhibit molecular-level structural polymorphisms. A recent screen of fibrils derived from brain tissue of Alzheimer's disease patients revealed a single predominant Aβ40 polymorph. We present solid state nuclear magnetic resonance (ssNMR) data that define its coexisting structurally ordered and disordered segments.
May 15, 2018: Chemical Communications: Chem Comm
Gayathri Kollamaram, Denise M Croker, Gavin M Walker, Alvaro Goyanes, Abdul W Basit, Simon Gaisford
Fused deposition modelling (FDM) is the most commonly investigated 3D printing technology for the manufacture of personalized medicines, however, the high temperatures used in the process limit its wider application. The objective of this study was to print low-melting and thermolabile drugs by reducing the FDM printing temperature. Two immediate release polymers, Kollidon VA64 and Kollidon 12PF were investigated as potential candidates for low-temperature FDM printing. Ramipril was used as the model low melting temperature drug (109 °C); to the authors' knowledge this is the lowest melting point drug investigated to date by FDM printing...
July 10, 2018: International Journal of Pharmaceutics
Irina Matlahov, Patrick C A van der Wel
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments' sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chance to measure dynamics in great detail...
April 24, 2018: Methods: a Companion to Methods in Enzymology
Songhwan Hwang, Pascal Fricke, Maximilian Zinke, Karin Giller, Joseph S Wall, Dietmar Riedel, Stefan Becker, Adam Lange
Intra-neuronal aggregation of α-synuclein into fibrils is the molecular basis for α-synucleinopathies, such as Parkinson's disease. The atomic structure of human α-synuclein (hAS) fibrils was recently determined by Tuttle et al. using solid-state NMR (ssNMR). The previous study found that hAS fibrils are composed of a single protofilament. Here, we have investigated the structure of mouse α-synuclein (mAS) fibrils by STEM and isotope-dilution ssNMR experiments. We found that in contrast to hAS, mAS fibrils consist of two or even three protofilaments which are connected by rather weak interactions in between them...
April 17, 2018: Journal of Structural Biology
Abathodharanan Narayanan, Ravishankar Kartik, Elanchezhian Sangeetha, Raghavachari Dhamodharan
A new superabsorbent with maximum water absorption capacity of ∼1250 g/g is prepared by hydrothermal synthesis from sustainable and biodegradable resources such as chitosan, citric acid and urea (denoted as 'CHCAUR'). CHCAUR is characterized extensively by various analytical techniques such as PXRD, SSNMR, FTIR, and TGA. Pure and saline water absorption study showed that CHCAUR could be a better adsorbent compared to the super absorbent polymer (SAP) used in commercial diaper material. The mechanism of water absorption is shown to arise out of a combination of electrostatic attraction of water to the ionic crosslinks and the presence of macropores as well as undulated surface due to the formation of nanofibrous bundles...
July 1, 2018: Carbohydrate Polymers
Alexander Marchanka, Christoph Kreutz, Teresa Carlomagno
Nucleic acids play key roles in most biological processes, either in isolation or in complex with proteins. Often they are difficult targets for structural studies, due to their dynamic behavior and high molecular weight. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) provides a unique opportunity to study large biomolecules in a non-crystalline state at atomic resolution. Application of ssNMR to RNA, however, is still at an early stage of development and presents considerable challenges due to broad resonances and poor dispersion...
April 12, 2018: Journal of Biomolecular NMR
Antoine Loquet, Nadia El Mammeri, Jan Stanek, Mélanie Berbon, Benjamin Bardiaux, Guido Pintacuda, Birgit Habenstein
The amyloid fold is structurally characterized by a typical cross-β architecture, which is under debate to represent an energy-favourable folding state that many globular or natively unfolded proteins can adopt. Being initially solely associated with amyloid fibrils observed in the propagation of several neurodegenerative disorders, the discovery of non-pathological (or "functional") amyloids in many native biological processes has recently further intensified the general interest invested in those cross-β supramolecular assemblies...
April 1, 2018: Methods: a Companion to Methods in Enzymology
Erika L Buckle, June S Lum, Adrienne M Roehrich, Robert E Stote, Branden Vandermoon, Martin Dracinsky, Shaun F Filocamo, Gary P Drobny
A biomimetic approach to the formation of titania (TiO2 ) nanostructures is desirable because of the mild conditions required in this form of production. We have identified a series of serine-lysine peptides as candidates for the biomimetic production of TiO2 nanostructures. We have assayed these peptides for TiO2 -precipitating activity upon exposure to titanium bis(ammonium lactato)dihydroxide and have characterized the resulting coprecipitates using scanning electron microscopy. A subset of these assayed peptides efficiently facilitates the production of TiO2 nanospheres...
May 3, 2018: Journal of Physical Chemistry. B
Yue Zhang, Bryan E G Lucier, Michael Fischer, Zhehong Gan, Paul D Boyle, Bligh Desveaux, Yining Huang
Methane is a promising clean and inexpensive energy alternative to traditional fossil fuels, however, its low volumetric energy density at ambient conditions has made devising viable, efficient methane storage systems very challenging. Metal-organic frameworks (MOFs) are promising candidates for methane storage. In order to improve the methane storage capacity of MOFs, a better understanding of the methane adsorption, mobility, and host-guest interactions within MOFs must be realized. In this study, methane adsorption within α-Mg3 (HCO2 )6 , α-Zn3 (HCO2 )6 , SIFSIX-3-Zn, and M-MOF-74 (M=Mg, Zn, Ni, Co) has been comprehensively examined...
March 25, 2018: Chemistry: a European Journal
M E Ward, M A Daniëls, E C van Kappel, M M Maurice, M Baldus
We report solid-state Nuclear Magnetic Resonance (ssNMR) studies on amyloid-like protein complexes formed by DIX domains that mediate key protein interactions in the Wnt signalling pathway. Our results provide insight into the 3D fold of the self-associated Axin-DIX domain and identify a potential lipid cofactor.
April 17, 2018: Chemical Communications: Chem Comm
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