scholarly journals Identifying hydrophobic protein patches to inform protein interaction interfaces

2021 ◽  
Vol 118 (6) ◽  
pp. e2018234118
Author(s):  
Nicholas B. Rego ◽  
Erte Xi ◽  
Amish J. Patel
Keyword(s):  
Protein Interactions ◽  
Large Fraction ◽  
Hydration Shell ◽  
Protein Hydration ◽  
Chemical Compositions ◽  
Protein Patterns ◽  
Computational Framework ◽  
Hydrophobic Residues ◽  
Hydrophobic Protein

Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.

Extraction and Characterization of Cellulose from Empty Fruit Bunch (EFB) Fiber

2014 ◽  
Vol 68 (5) ◽  
Author(s):  
Norzita Ngadi ◽  
Nurul Saadiah Lani
Keyword(s):  
Large Fraction ◽  
Natural Fibers ◽  
Alkaline Treatment ◽  
Chemical Compositions ◽  
Empty Fruit Bunch ◽  
X Ray Diffraction ◽  
Efficient Treatment ◽  
Mechanical Methods ◽  
Scientific Attention

In recent years, the use of cellulose fibers in many fields has attracted significant scientific attention due to consumer and environmentally benign, especially in plastic industry, which has been used as cost–cutting fillers and hence provides the possibility of reinforcing polymers. Cellulose can be extracted from natural fibers by chemical and mechanical methods. However, the existing procedures either produce low yields and not environment friendly or energy efficient. The objective of this study was to develop a novel process that uses ionic liquid followed by alkaline method to extract cellulose from empty fruit bunch (EFB) fiber. Subsequently, the properties of original fiber and cellulose were determined by Fourier Transform Infrared (FTIR) Spectroscopy, X–Ray Diffraction (XRD) and thermogravimetric (TG) analysis. The results of the chemical compositions revealed that the modified alkaline treatment was able to remove a large fraction of lignin and hemicelluloses compared to unmodified alkaline treatment. Thus, this process represents an efficient treatment in extracting cellulose of highest yield. 

Spectro-mechanical Characterization of Aromaticity and Maturity of Kerogens in Oil Shale at 6 nm Spatial Resolution

2018 ◽  
Author(s):  
Devon Jakob ◽  
Le Wang ◽  
Haomin Wang ◽  
Xiaoji Xu
Keyword(s):  
Spatial Resolution ◽  
Oil Shale ◽  
Infrared Imaging ◽  
Mechanical Characterization ◽  
Optical Diffraction ◽  
Chemical Compositions ◽  
Valuable Insight ◽  
Eagle Ford Shale

<p>In situ measurements of the chemical compositions and mechanical properties of kerogen help understand the formation, transformation, and utilization of organic matter in the oil shale at the nanoscale. However, the optical diffraction limit prevents attainment of nanoscale resolution using conventional spectroscopy and microscopy. Here, we utilize peak force infrared (PFIR) microscopy for multimodal characterization of kerogen in oil shale. The PFIR provides correlative infrared imaging, mechanical mapping, and broadband infrared spectroscopy capability with 6 nm spatial resolution. We observed nanoscale heterogeneity in the chemical composition, aromaticity, and maturity of the kerogens from oil shales from Eagle Ford shale play in Texas. The kerogen aromaticity positively correlates with the local mechanical moduli of the surrounding inorganic matrix, manifesting the Le Chatelier’s principle. In situ spectro-mechanical characterization of oil shale will yield valuable insight for geochemical and geomechanical modeling on the origin and transformation of kerogen in the oil shale.</p>

scholarly journals New Insights into the Crystal Chemistry of Elpidite, Na2Zr[Si6O15]·3H2O and (Na1+YCax□1−X−Y)Σ=2Zr[Si6O15]·(3−X)H2O, and Ab Initio Modeling of IR Spectra

Materials ◽  
2021 ◽  
Vol 14 (9) ◽  
pp. 2160
Author(s):  
Alexander Bogdanov ◽  
Ekaterina Kaneva ◽  
Roman Shendrik
Keyword(s):  
Ir Spectra ◽  
Structural Models ◽  
Chemical Characterization ◽  
Chemical Compositions ◽  
X Ray Diffraction ◽  
Special Group ◽  
X Ray ◽  
Influence Of Water ◽  
Radioactive Species

Elpidite belongs to a special group of microporous zirconosilicates, which are of great interest due to their capability to uptake various molecules and ions, e.g., some radioactive species, in their structural voids. The results of a combined electron probe microanalysis and single-crystal X-ray diffraction study of the crystals of elpidite from Burpala (Russia) and Khan-Bogdo (Mongolia) deposits are reported. Some differences in the chemical compositions are observed and substitution at several structural positions within the structure of the compounds are noted. Based on the obtained results, a detailed crystal–chemical characterization of the elpidites under study was carried out. Three different structure models of elpidite were simulated: Na2ZrSi6O15·3H2O (related to the structure of Russian elpidite), partly Ca-replaced Na1.5Ca0.25ZrSi6O15·2.75H2O (close to elpidite from Mongolia), and a hypothetical CaZrSi6O15·2H2O. The vibration spectra of the models were obtained and compared with the experimental one, taken from the literature. The strong influence of water molecule vibrations on the shape of IR spectra of studied structural models of elpidite is discussed in the paper.

scholarly journals Size-resolved characterization of organic aerosol in the North China Plain: new insights from high resolution spectral analysis

2021 ◽  
Author(s):  
Weiqi Xu ◽  
Chun Chen ◽  
Yanmei Qiu ◽  
Conghui Xie ◽  
Yunle Chen ◽  
...  
Keyword(s):  
Radiative Forcing ◽  
North China Plain ◽  
North China ◽  
Fine Particles ◽  
Large Fraction ◽  
Organic Aerosol ◽  
Size Distributions ◽  
The North ◽  
The Impact

Organic aerosol (OA), a large fraction of fine particles, has a large impact on climate radiative forcing and human health, and the impact depends strongly on size distributions. Here we...

scholarly journals Size-based characterization of adalimumab and TNF-α interactions using flow induced dispersion analysis: assessment of avidity-stabilized multiple bound species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Morten E. Pedersen ◽  
Ragna M. S. Haegebaert ◽  
Jesper Østergaard ◽  
Henrik Jensen
Keyword(s):  
Protein Interactions ◽  
Free Ligand ◽  
Local Environment ◽  
Dispersion Analysis ◽  
Surface Immobilization ◽  
Covalent Bonds ◽  
Essential Information ◽  
Tnf Α

AbstractThe understanding and characterization of protein interactions is crucial for elucidation of complicated biomolecular processes as well as for the development of new biopharmaceutical therapies. Often, protein interactions involve multiple binding, avidity, oligomerization, and are dependent on the local environment. Current analytical methodologies are unable to provide a detailed mechanistic characterization considering all these parameters, since they often rely on surface immobilization, cannot measure under biorelevant conditions, or do not feature a structurally-related readout for indicating formation of multiple bound species. In this work, we report the use of flow induced dispersion analysis (FIDA) for in-solution characterization of complex protein interactions under in vivo like conditions. FIDA is an immobilization-free ligand binding methodology employing Taylor dispersion analysis for measuring the hydrodynamic radius (size) of biomolecular complexes. Here, the FIDA technology is utilized for a size-based characterization of the interaction between TNF-α and adalimumab. We report concentration-dependent complex sizes, binding affinities (Kd), kinetics, and higher order stoichiometries, thus providing essential information on the TNF-α–adalimumab binding mechanism. Furthermore, it is shown that the avidity stabilized complexes involving formation of multiple non-covalent bonds are formed on a longer timescale than the primary complexes formed in a simple 1 to 1 binding event.

scholarly journals Genetic and Molecular Characterization of the Caenorhabditis elegans Gene, mel-26, a Postmeiotic Negative Regulator of MEI-1, a Meiotic-Specific Spindle Component

Genetics ◽  
1998 ◽  
Vol 150 (1) ◽  
pp. 119-128
Author(s):  
M Rhys Dow ◽  
Paul E Mains
Keyword(s):  
Caenorhabditis Elegans ◽  
Protein Interactions ◽  
Negative Regulator ◽  
Meiotic Spindle ◽  
Loss Of Function ◽  
Protein Protein Interactions ◽  
Gain Of Function ◽  
Recessive Mutations ◽  
Female Germline

Abstract We have previously described the gene mei-1, which encodes an essential component of the Caenorhabditis elegans meiotic spindle. When ectopically expressed after the completion of meiosis, mei-1 protein disrupts the function of the mitotic cleavage spindles. In this article, we describe the cloning and the further genetic characterization of mel-26, a postmeiotic negative regulator of mei-1. mel-26 was originally identified by a gain-of-function mutation. We have reverted this mutation to a loss-of-function allele, which has recessive phenotypes identical to the dominant defects of its gain-of-function parent. Both the dominant and recessive mutations of mel-26 result in mei-1 protein ectopically localized in mitotic spindles and centrosomes, leading to small and misoriented cleavage spindles. The loss-of-function mutation was used to clone mel-26 by transformation rescue. As suggested by genetic results indicating that mel-26 is required only maternally, mel-26 mRNA was expressed predominantly in the female germline. The gene encodes a protein that includes the BTB motif, which is thought to play a role in protein-protein interactions.

Characterization of Al65.0Cu32.9Co2.1 Alloy Containing Nanofibres

2012 ◽  
Vol 186 ◽  
pp. 212-215
Author(s):  
Jacek Krawczyk ◽  
Włodzimierz Bogdanowicz ◽  
Grzegorz Dercz ◽  
Wojciech Gurdziel
Keyword(s):  
Electron Microscopy ◽  
Average Diameter ◽  
Chemical Compositions ◽  
X Ray ◽  
Transmission Electron ◽  
Orthogonal Set ◽  
T Phase ◽  
Terminal Area ◽  
Scanning Electron

Microstructure of terminal area of Al65Cu32.9Co2.1ingots (numbers indicate at.%), obtained via directional solidification was studied. Scanning Electron Microscopy, Transmission Electron Microscopy and X-ray powder diffraction were applied. Point microanalysis by Scanning Electron Microscope was used for examination of chemical compositions of alloy phases. It was found that tetragonal θ phase of Al2Cu stoichiometric formula was the dominate phase (matrix). Additionally the alloy contained orthogonal set of nanofibres of Al7Cu2Co T phase with the average diameter of 50-500 nm and oval areas of hexagonal Al3(Cu,Co)2H-phase, surrounded by monoclinic AlCu η1phase rim. Inside some areas of H-phase cores of decagonal quasicrystalline D phase were observed.

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