Unravelling the structural complexity of protein–lipid interactions with neutron reflectometry

2021 ◽  
Author(s):  
Luke A. Clifton
Keyword(s):  
Structural Information ◽  
Biological Membrane ◽  
Structural Complexity ◽  
Neutron Reflectometry ◽  
Antimicrobial Protein ◽  
Relative Distribution ◽  
Buried Structures ◽  
Lipid Interactions ◽  
Low Energies ◽  
Before And After

Neutron reflectometry (NR) is a large-facility technique used to examine structure at interfaces. In this brief review an introduction to the utilisation of NR in the study of protein–lipid interactions is given. Cold neutron beams penetrate matter deeply, have low energies, wavelengths in the Ångstrom regime and are sensitive to light elements. High differential hydrogen sensitivity (between protium and deuterium) enables solution and sample isotopic labelling to be utilised to enhance or diminish the scattering signal of individual components within complex biological structures. The combination of these effects means NR can probe buried structures such as those at the solid–liquid interface and encode molecular level structural information on interfacial protein–lipid complexes revealing the relative distribution of components as well as the overall structure. Model biological membrane sample systems can be structurally probed to examine phenomena such as antimicrobial mode of activity, as well as structural and mechanistic properties peripheral/integral proteins within membrane complexes. Here, the example of the antimicrobial protein α1-purothionin binding to a model Gram negative bacterial outer membrane is used to highlight the utilisation of this technique, detailing how changes in the protein/lipid distributions across the membrane before and after the protein interaction can be easily encoded using hydrogen isotope labelling.

scholarly journals The Principle of Maximal Simplicity for Modular Inorganic Crystal Structures

Crystals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1472
Author(s):  
Sergey V. Krivovichev
Keyword(s):  
Crystal Structures ◽  
Structure Prediction ◽  
Structural Information ◽  
Structural Complexity ◽  
Configurational Entropy ◽  
Sensu Stricto ◽  
Least Action ◽  
Inorganic Crystal ◽  
Principle Of Least Action ◽  
Structure Description

Modularity is an important construction principle of many inorganic crystal structures that has been used for the analysis of structural relations, classification, structure description and structure prediction. The principle of maximal simplicity for modular inorganic crystal structures can be formulated as follows: in a modular series of inorganic crystal structures, the most common and abundant in nature and experiments are those arrangements that possess maximal simplicity and minimal structural information. The latter can be quantitatively estimated using information-based structural complexity parameters. The principle is applied for the modular series based upon 0D (lovozerite family), 1D (biopyriboles) and 2D (spinelloids and kurchatovite family) modules. This principle is empirical and is valid for those cases only, where there are no factors that may lead to the destabilization of simplest structural arrangements. The physical basis of the principle is in the relations between structural complexity and configurational entropy sensu stricto (which should be distinguished from the entropy of mixing). It can also be seen as an analogy of the principle of least action in physics.

scholarly journals Adsorption Behavior and Relative Distribution of Cd2+ Adsorption Mechanisms by the Magnetic and Nonmagnetic Biochars Derived from Chicken Manure

2020 ◽  
Vol 17 (5) ◽  
pp. 1602 ◽  
Author(s):  
Fei Huang ◽  
Lu Zhang ◽  
Ren-Ren Wu ◽  
Si-Ming Zhang ◽  
Rong-Bo Xiao
Keyword(s):  
Ion Exchange ◽  
Magnetic Separation ◽  
Adsorption Process ◽  
Freundlich Isotherm ◽  
Chicken Manure ◽  
Relative Distribution ◽  
Order Kinetic ◽  
Practical Applications ◽  
Adsorption Mechanisms ◽  
Before And After

The present study investigated the adsorption of Cd2+ by nonmagnetic and magnetic biochars (CMB and M-CMB) derived from chicken manure, respectively. The adsorption characteristics were investigated as a function of initial pH, contact time, initial Cd2+ concentration and magnetic separation. Adsorption process of both biochars were better described by Pseudo-second-order kinetic equation and Freundlich isotherm model, which were spontaneous and endothermic in nature. It was found that maximum capacities were 60.69 and 41.07 mg/g obtained at the initial Cd2+ concentration of 180 mg/L for CMB and M-CMB, and the turbidity of adsorption-treated solution was reduced from 244.3 to 11.3 NTU after magnetic separation of 0.5 min. These indicated that M-CMB had lower adsorption capacity of Cd2+ than CMB, though it was successfully separated from the treated solutions. Furthermore, both biochars before and after adsorption were analyzed by SEM-EDS, XRD and FTIR. Adsorption mechanisms mainly included precipitation, ion-exchange, complexation and Cπ-coordination, in which precipitation and ion-exchange dominated the adsorption process by CMB, while in M-CMB, precipitation was always predominant mechanism, followed by ion-exchange. The two other mechanisms of complexation and Cπ-coordination were trivial in both biochars, jointly contributing 7.21% for CMB and 5.05% for M-CMB to total adsorption. The findings deepen our understanding of the mechanisms governing the adsorption process, which are also important for future practical applications in the removal of heavy metals from wastewater by the biochars.

scholarly journals Multi-scale statistical analysis of coronal solar activity

2016 ◽  
Vol 23 (4) ◽  
pp. 175-188
Author(s):  
Diana Gamborino ◽  
Diego del-Castillo-Negrete ◽  
Julio J. Martinell
Keyword(s):  
Structural Information ◽  
Active Regions ◽  
Orthogonal Decomposition ◽  
Multi Scale ◽  
Level Of Activity ◽  
Before And After ◽  
Temperature Maps ◽  
Proper Orthogonal ◽  
Scale Behavior ◽  
Region Information

Abstract. Multi-filter images from the solar corona are used to obtain temperature maps that are analyzed using techniques based on proper orthogonal decomposition (POD) in order to extract dynamical and structural information at various scales. Exploring active regions before and after a solar flare and comparing them with quiet regions, we show that the multi-scale behavior presents distinct statistical properties for each case that can be used to characterize the level of activity in a region. Information about the nature of heat transport is also to be extracted from the analysis.

Inspecting historical vaulted ceilings by means of physical and chemical analyses: an integrated approach combining active infrared thermography and reflectance spectroscopy

2020 ◽  
Vol 62 (3) ◽  
pp. 144-151 ◽  
Author(s):  
S Sfarra ◽  
E Cheilakou ◽  
P Theodorakeas ◽  
C Ibarra-Castanedo ◽  
H Zhang ◽  
...  
Keyword(s):  
Infrared Thermography ◽  
Near Infrared ◽  
Diffuse Reflectance Spectroscopy ◽  
Central Italy ◽  
Integrated Approach ◽  
Reflectance Spectroscopy ◽  
Fibre Optics ◽  
Buried Structures ◽  
Before And After ◽  
Physical And Chemical

The present study discusses the experimental physicochemical results obtained from the historical vaulted ceilings of an ancient church located in central Italy. Infrared thermography (IRT) in the active configuration was used to map subsurface defects caused by a seismic event and to discover buried structures, while the visible and near-infrared (VIS-NIR) fibre-optics diffuse reflectance spectroscopy (FORS) technique was applied to identify the pigments of wall paintings decorating the vault. Historical photographs are useful to readers in order to clarify the state of conservation before and after the earthquake that took place in 2009. The combination of the experimental results can be useful in restoration processes.

Crystal chemistry of natural layered double hydroxides: 4. Crystal structures and evolution of structural complexity of quintinite polytypes from the Kovdor alkaline-ultrabasic massif, Kola peninsula, Russia

2018 ◽  
Vol 82 (2) ◽  
pp. 329-346 ◽  
Author(s):  
Elena S. Zhitova ◽  
Sergey V. Krivovichev ◽  
Viktor N. Yakovenchuk ◽  
Gregory Yu. Ivanyuk ◽  
Yakov A. Pakhomovsky ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Information ◽  
Structural Complexity ◽  
Configurational Entropy ◽  
Direct Methods ◽  
Stacking Sequence ◽  
Layer Stacking ◽  
Complete Layer ◽  
Double Hydroxide ◽  
Double Hydroxides

AbstractTwo quintinite polytypes, 3R and 2T, which are new for the Kovdor alkaline-ultrabasic complex, have been structurally characterized. The crystal structure of quintinite-2T was solved by direct methods and refined to R1 = 0.048 on the basis of 330 unique reflections. The structure is trigonal, P$\bar 3$c1, a = 5.2720(6), c = 15.113(3) Å and V = 363.76(8) Å3. The crystal structure consists of [Mg2Al(OH)6]+ brucite-type layers with an ordered distribution of Mg2+ and Al3+ cations according to the $\sqrt 3 $ × $\sqrt 3 $ superstructure with the layers stacked according to a hexagonal type. The complete layer stacking sequence can be described as …=Ab1C = Cb1A=…. The crystal structure of quintinite-3R was solved by direct methods and refined to R1 = 0.022 on the basis of 140 unique reflections. It is trigonal, R$\bar 3$m, a = 3.063(1), c = 22.674(9) Å and V = 184.2(1) Å3. The crystal structure is based upon double hydroxide layers [M2+,3+(OH)2] with disordered distribution of Mg, Al and Fe and with the layers stacked according to a rhombohedral type. The stacking sequence of layers can be expressed as …=АB = BC = CA=… The study of morphologically different quintinite generations grown on one another detected the following natural sequence of polytype formation: 2H → 2T → 1M that can be attributed to a decrease of temperature during crystallization. According to the information-based approach to structural complexity, this sequence corresponds to the increasing structural information per atom (IG): 1.522 → 1.706 → 2.440 bits, respectively. As the IG value contributes negatively to the configurational entropy of crystalline solids, the evolution of polytypic modifications during crystallization corresponds to the decreasing configurational entropy. This is in agreement with the general principle that decreasing temperature corresponds to the appearance of more complex structures.

scholarly journals The Antifungal Mechanism of Amphotericin B Elucidated in Ergosterol and Cholesterol-Containing Membranes Using Neutron Reflectometry

Nanomaterials ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2439
Author(s):  
Robin Delhom ◽  
Andrew Nelson ◽  
Valerie Laux ◽  
Michael Haertlein ◽  
Wolfgang Knecht ◽  
...  
Keyword(s):  
Side Effects ◽  
Amphotericin B ◽  
Antifungal Drug ◽  
Neutron Reflectometry ◽  
Antifungal Effect ◽  
Neutron Reflection ◽  
Before And After ◽  
Lipid Chain ◽  
Molecular Origin ◽  
Membrane Thinning

We have characterized and compared the structures of ergosterol- and cholesterol-containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes before and after interaction with the amphiphilic antifungal drug amphotericin B (AmB) using neutron reflection. AmB inserts into both pure POPC and sterol-containing membranes in the lipid chain region and does not significantly perturb the structure of pure POPC membranes. By selective per-deuteration of the lipids/sterols, we show that AmB extracts ergosterol but not cholesterol from the bilayers and inserts to a much higher degree in the cholesterol-containing membranes. Ergosterol extraction by AmB is accompanied by membrane thinning. Our results provide new insights into the mechanism and antifungal effect of AmB in these simple models of fungal and mammalian membranes and help understand the molecular origin of its selectivity and toxic side effects.

The Effects of Bankruptcy on the Predictability of Price Formation Processes on Warsaw’s Stock Market

e-Finanse ◽  
2016 ◽  
Vol 12 (1) ◽  
pp. 32-42
Author(s):  
Paweł Fiedor ◽  
Artur Hołda
Keyword(s):  
Stock Returns ◽  
Stock Exchange ◽  
Large Body ◽  
Structural Complexity ◽  
Price Formation ◽  
Formation Processes ◽  
Before And After ◽  
History Of ◽  
Definition Of ◽  
Window Approach

AbstractIn this study we investigate how bankruptcy affects the market behaviour of prices of stocks on Warsaw’s Stock Exchange. As the behaviour of prices can be seen in a myriad of ways, we investigate a particular aspect of this behaviour, namely the predictability of these price formation processes. We approximate their predictability as the structural complexity of logarithmic returns. This method of analysing predictability of price formation processes using information theory follows closely the mathematical definition of predictability, and is equal to the degree to which redundancy is present in the time series describing stock returns. We use Shannon’s entropy rate (approximating Kolmogorov-Sinai entropy) to measure this redundancy, and estimate it using the Lempel-Ziv algorithm, computing it with a running window approach over the entire price history of 50 companies listed on the Warsaw market which have gone bankrupt in the last few years. This enables us not only to compare the differences between predictability of price formation processes before and after their filing for bankruptcy, but also to compare the changes in predictability over time, as well as divided into different categories of companies and bankruptcies. There exists a large body of research analysing the efficiency of the whole market and the predictability of price changes en large, but only a few detailed studies analysing the influence of external stimulion the efficiency of price formation processes. This study fills this gap in the knowledge of financial markets, and their response to extreme external events.

Long-term dynamics of organic matter and elements exported as coarse particulates from two Caribbean montane watersheds

2012 ◽  
Vol 28 (2) ◽  
pp. 127-139 ◽  
Author(s):  
T. Heartsill Scalley ◽  
F. N. Scatena ◽  
S. Moya ◽  
A. E. Lugo
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
Headwater Streams ◽  
Structural Complexity ◽  
Base Flow ◽  
Coarse Particulate Organic Matter ◽  
North East ◽  
Storm Flow ◽  
Before And After

Abstract:In heterotrophic streams the retention and export of coarse particulate organic matter and associated elements are fundamental biogeochemical processes that influence water quality, food webs and the structural complexity of forested headwater streams. Nevertheless, few studies have documented the quantity and quality of exported organic matter over multiple years and under a range of conditions that includes both droughts and hurricanes. This study quantifies the export of coarse particulate organic matter (CPOM, > 12.7 mm), over 18 y in two headwater streams in north-east Puerto Rico. Daily exports ranged from 0 to over 170 g ha−1 d−1 and averaged 7.39 g ha−1 d−1, with similar amounts coming from leaves (3.5 g ha−1 d−1) and wood (3.2 g ha−1 d−1). Export of coarse particulate organic carbon was 3.0 g ha−1 d−1 which constitutes only 1.32% of carbon exports. Most litter falling into the streams was processed in place as only 2.3% of the leaf litter falling directly into these perennial channels was exported as CPOM. On average, 6 wk y−1 had no exports while events transporting more than 10 g ha−1 d−1 occurred every 2.8 mo. Instead of a single annual pulse as observed in deciduous systems, there were annual peaks in CPOM exports during May and September and less export during the drier period from December to February. Ratios of C:N in the exported material were highest in the driest month and lowest during rainy months, while leaf fluxes for nitrogen, phosphorus and calcium were highest in rainy months and lowest during February. Although median daily exports and exports during low- and base-flow periods were similar before and after Hugo, after 16 y exports during moderate- and high-flow periods were still less than those in the 2 y prior to the hurricane. Our observations indicate a system with high rates of internal processing that quickly returns to median daily conditions following hurricanes but requires several decades for storm-flow exports to return to pre-disturbance conditions and indicates that the long-term pattern of CPOM export is associated with the level of maturity of watershed vegetation.

Using Neutron Reflectometry to Characterize Antimicrobial Protein Surface Coatings

2017 ◽  
Vol 121 (24) ◽  
pp. 5908-5916 ◽  
Author(s):  
Peter W. Akers ◽  
Andrew J. Dingley ◽  
Simon Swift ◽  
Andrew R. J. Nelson ◽  
Julie Martin ◽  
...  
Keyword(s):  
Neutron Reflectometry ◽  
Surface Coatings ◽  
Antimicrobial Protein ◽  
Protein Surface

Thermal Expansion and Glass Transition Behaviour of Thin Polymer Films with and without a Free Surface Via Neutron Reflectometry

1998 ◽  
Vol 543 ◽  
Author(s):  
D. J. Pochan ◽  
E. K. Lin ◽  
S. Satija ◽  
S. Z. D. Cheng ◽  
Wen-Li Wu
Keyword(s):  
Thermal Expansion ◽  
Glass Transition ◽  
Free Surface ◽  
Film Thickness ◽  
Coefficient Of Thermal Expansion ◽  
Neutron Reflectometry ◽  
Bilayer Films ◽  
Fluorinated Polyimide ◽  
Expansion Behavior ◽  
Before And After

AbstractThe thermal expansion of thin deuterated polystyrene (dPS) films supported on energetically repulsive, fluorinated polyimide (PI) substrates (PI/dPS bilayer) was measured via neutron reflectometry as a function of initial dPS film thickness. Film thickness was measured before and after capping with a top layer of the same repulsive, high glass transition polyimide that comprised the substrate layer (PI/dPS/PI trilayer) in an attempt to observe any effects of the dPS free surface in the bilayer geometry. Bulk thermal expansion behavior, characterized by a discontinuous change in coefficient of thermal expansion (CTE) at the glass transition (Tg), is observed in films with thickness > 70 rim. For thicknesses between 70 nm and 40 nm a transition is seen from bulk behavior in bilayer films to glassy thermal behavior in the trilayer films persisting up to 20 °C above the bulk Tg. In films with thickness < 40 nm the bulk glassy CTE persists well above the bulk Tg for both bilayer and trilayer films

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