Structure of complexes of poly-γ-benzyl-L-glutamate with water and dioxane molecules studied by IR spectroscopy and quantum chemical calculations

© 2014 Pleiades Publishing, Ltd. The structure of supramolecular complexes of poly-γ-benzyl-L-glutamate (PBG) with water and dioxane molecules during sorption from pure liquids and their binary mixtures is studied by IR spectroscopy and quantum chemical calculations. It is shown that the sorption sites of water and dioxane in PBG are different in nature. Water molecules are bound in the monomeric form to the carbonyl groups of the ester moieties of the side chains and the helical backbone of the peptide to form complexes with two hydrogen bonds. Dioxane molecules are sorbed in a large amount in the region of the side chains of PBG, causing their repacking with preservation of the helicity of the polypeptide backbone. Under simultaneous sorption of water and dioxane vapors, the binding of the latter increases the number of water molecules bound to the carbonyl groups of PBG. In this case, there is also an additional absorption of water molecules on the oxygen atoms of dioxane molecules. Calculations have shown that in the most probable configuration of the complexes, the water molecule simultaneously forms hydrogen bonds with the carbonyl groups of the side chain and the peptide backbone. Dioxane molecules do not penetrate to the peptide groups of helical backbone of PBG due to steric hindrance and are localized in the region of the benzyl moieties of the side chains; such complexes are stabilized by weak CH...O interactions

Influence of Al on the structure and in vitro behavior of hydroxyapatite nanopowders

Nanopowders of aluminum-substituted (0-20 mol %) hydroxyapatite (HA) with the average size of 40-60 nm were synthesized by the precipitation method from nitrate solutions. A series of samples were studied by various analytical tools to elucidate the peculiarities of al introductio

Metrics of rhamnogalacturonan I with β-(1→4)-linked galactan side chains and structural basis for its self-aggregation

© 2016 Elsevier LtdWithin the family of plant cell wall polysaccharides rhamnogalacturonans I are the most diverse and structurally complex members. In present study we characterize the 3-dimensional structures and dynamic features of the constituents of RG-I along MD trajectories. It is demonstrated that extended threefold helical structure of the rhamnogalacturonan linear backbone is the most energetically favorable motif. Branching helps to stabilize a conformer of the backbone twisted along 1→2 glycosidic linkage triggering the orientation of long side chains without altering the extended overall backbone chain conformation. Formation of anti-parallel pairing of the β-galactan side chains allows us to suggest a novel mode of non-covalent cross-linking in pectins. Studied structural elements are organized to report the first attempt to characterize 3D structure of RG-I focusing on the special case of flax tertiary cell wall and elucidate the structural basis underlying the formation of RG-I self-associates and functional role of RG-I in planta

Gelation of rhamnogalacturonan I is based on galactan side chain interaction and does not involve chemical modifications

© 2017 Elsevier LtdThe article presents the structural principles of microwave-induced formation of new gel type from pectic rhamnogalacturonan I (RG-I). The backbone of gel-forming RG-I does not contain consecutive galacturonic residues and modifying groups that can be the cause of junction zone formation as it occurs in course of classical ways of pectin gelation. Microwave irradiation does not cause destruction and chemical modifications of RG-I. Removal of half of galactan chains from RG-I leads to loss of gelling capability pointing out on their leading role in this process. Rising of intensity of the bands attributed to galactose and glycosidic linkages in RG-I gel comparing to solution where this polymer exists as molecule associate indicates that the spatial organization of galactans in gel is changed. A model of the RG-I gelation is proposed: being destabilized at volumetric microwave heating RG-I associates are repacked forming network where RG-I molecules are entangled by galactan chains

Enzymatic Glyco-Modification of Synthetic Membrane Systems

The present report assesses the capability of a soluble glycosyltransferase to modify glycolipids organized in two synthetic membrane systems that are attractive models to mimic cell membranes: giant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs). The objective was to synthesize the Gb3 antigen (Galα1,4Galβ1,4Glcβ-Cer), a cancer biomarker, at the surface of these membrane models. A soluble form of LgtC that adds a galactose residue from UDP-Gal to lactose-containing acceptors was selected. Although less efficient than with lactose, the ability of LgtC to utilize lactosyl–ceramide as an acceptor was demonstrated on GUVs and SLBs. The reaction was monitored using the B-subunit of Shiga toxin as Gb3-binding lectin. Quartz crystal microbalance with dissipation analysis showed that transient binding of LgtC at the membrane surface was sufficient for a productive conversion of LacCer to Gb3. Molecular dynamics simulations provided structural elements to help rationalize experimental data

Structure and properties of aqueous dispersions of sodium dodecyl sulfate with carbon nanotubes

© 2016, Springer Science+Business Media New York.The dispersing action of the surfactant (sodium dodecyl sulfate, SDS) on the carbon nanotubes (CNT) in aqueous medium has been studied. Electron microscopy, molecular docking, NMR and IR spectroscopies were applied to determine the physical-chemical properties of CNT dispersions in SDS—water solutions. It was established that micellar adsorption of the surfactant on the surface of carbon material and solubilization of SDS in aqueous medium contribute to improving CNT dispersing in water solutions. It was shown that the non-polar hydrocarbon radicals of a single surfactant molecule form the highest possible number of contacts with the graphene surface. Upon increase of the SDS in solution these radicals form micelles connected with the surface of the nanotubes. At the sufficiently high SDS concentration the nanotube surface becomes covered with an adsorbed layer of surfactant micelles. Water molecules and sodium cations are concentrated in spaces between micelles. The observed pattern of micellar adsorption is somewhat similar to a loose bilayer of surfactant molecules

Molecular structure and properties of κ-carrageenan-gelatin gels

© 2018 Elsevier Ltd Rheological studies, FTIR spectroscopy and a molecular docking approach were used to explore the structural basis of the peculiar physicochemical properties of gelatin gels modified with a κ-carrageenan admixture. Mixed gel properties are affected by the polysaccharide-to-gelatin ratio, Z, and can be divided into two categories. At low ratios, the strength of mixed gels varies insignificantly compared to gelatin due to the similar structures of the gels. Above the threshold content of κ-carrageenan (Z > 0.1), the storage modulus and yield stress of mixed gels are significantly enhanced. The nonadditivity and threshold character of the rheological properties could be the result of conformational ordering of both gelatin and κ-carrageenan, leading to the formation of additional junction zones in the gel network. According to molecular docking studies, the junctions could be formed as a result of complementary interactions between the gelatin triple helix and the κ-carrageenan double helix. The stack formation increases the interaction energy, which explains the strengthening of the gel network

Glycosaminoglycans: What Remains To Be Deciphered?

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise “glycocodes” that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics

Structure of complexes of poly-γ-benzyl-L-glutamate with water and dioxane molecules studied by IR spectroscopy and quantum chemical calculations

© 2014 Pleiades Publishing, Ltd. The structure of supramolecular complexes of poly-γ-benzyl-L-glutamate (PBG) with water and dioxane molecules during sorption from pure liquids and their binary mixtures is studied by IR spectroscopy and quantum chemical calculations. It is shown that the sorption sites of water and dioxane in PBG are different in nature. Water molecules are bound in the monomeric form to the carbonyl groups of the ester moieties of the side chains and the helical backbone of the peptide to form complexes with two hydrogen bonds. Dioxane molecules are sorbed in a large amount in the region of the side chains of PBG, causing their repacking with preservation of the helicity of the polypeptide backbone. Under simultaneous sorption of water and dioxane vapors, the binding of the latter increases the number of water molecules bound to the carbonyl groups of PBG. In this case, there is also an additional absorption of water molecules on the oxygen atoms of dioxane molecules. Calculations have shown that in the most probable configuration of the complexes, the water molecule simultaneously forms hydrogen bonds with the carbonyl groups of the side chain and the peptide backbone. Dioxane molecules do not penetrate to the peptide groups of helical backbone of PBG due to steric hindrance and are localized in the region of the benzyl moieties of the side chains; such complexes are stabilized by weak CH...O interactions

Beta-rich intermediates in denaturation of lysozyme: accelerated molecular dynamics simulations

Amyloid fibrillar aggregates play a critical role in many neurodegenerative disorders. Conversion of globular proteins into fibrils is associated with global conformational rearrangement and involves the transformation of α-helices to β-sheets. In the present work, the accelerated molecular dynamics technique was applied to study the unfolding of hen egg-white lysozyme at elevated temperatures, and the transformation of the native structure to a disordered one was analyzed. The influence of the disulfide bonds on the conformational dynamics and the energy landscape of denaturation process was considered. Our results show that formation of the metastable β-enriched conformers of individual protein molecules may precede the aggregation process. These β-rich intermediates can play a role of bricks making up fibrils. Communicated by Ramaswamy H. Sarma