Conformational analysis in aqueous solution and estimation of the persistence length of exopolysaccharides produced by Lactobacillus helveticus Lh59 and Streptococcus macedonicus Sc136

2006 ◽  
Vol 84 (4) ◽  
pp. 730-742 ◽  
Author(s):  
J Albert van Kuik ◽  
Sébastien JF Vincent ◽  
Bas R Leeflang ◽  
Loes MJ Kroon-Batenburg ◽  
Johannis P Kamerling
Keyword(s):  
Conformational Analysis ◽  
Molecular Modelling ◽  
Persistence Length ◽  
Lactobacillus Helveticus ◽  
Side Chain ◽  
Side Chains ◽  
Structural Elements ◽  
Monosaccharide Residue ◽  
A Value ◽  
Insight Into

The conformations of two exopolysaccharides, one produced by Lactobacillus helveticus Lh59 and one by Streptococcus macedonicus Sc136, were investigated by molecular modelling to get insight into their physical properties. In particular, the influence of side chains and glycosidic linkage types on the overall shapes and persistence lengths of the polysaccharides were studied. It appeared that the side chains had only minor effects on the persistence lengths of the polysaccharides, with the exception of the monosaccharide residue directly attached to the backbone. The extensiveness of the backbone is enhanced by β-D-Hexp-(1→4) structural elements, whereas α-D-Hexp-(1→3) and α-D-Hexp-(1→4) elements create structural variability by introducing bends. The occurrence of either (1→5)- or (1→6)-linked monosaccharides, resulting in one extra bond between monosaccharide units, causes the overall flexibility of the polysaccharide chain to be enhanced and extensiveness to be reduced. The presence of such flexible linkages in the backbone leads to a shorter persistence length than when present in the side chain: a value of only 4.5 nm was found for the L. helveticus Lh59 EPS with a (1→5) linkage in the backbone, and a value of 8.5 nm for the S. macedonicus Sc136 EPS with two (1→6) linkages in the side chain.Key words: conformational analysis, exopolysaccharide, Lactobacillus helveticus, molecular modelling, persistence length, Streptococcus macedonicus.

Comparative study of dG affinity vs. DNA methylation modulating properties of side chain derivatives of procainamide: insight into its DNA hypomethylating effect

RSC Advances ◽  
2016 ◽  
Vol 6 (7) ◽  
pp. 5350-5358 ◽  
Author(s):  
R. L. Gawade ◽  
D. K. Chakravarty ◽  
J. Debgupta ◽  
E. Sangtani ◽  
S. Narwade ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Comparative Study ◽  
Structural Features ◽  
Side Chain ◽  
Side Chains ◽  
Hypomethylating Agents ◽  
Derivatives Of ◽  
Insight Into

Structural features of side-chains govern the association of procainamide and its derivatives with dG base of CpG rich DNA, which may differentially hinder the activity of DNMT-1, thereby they act as DNA hypomethylating agents.

Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

2020 ◽  
Author(s):  
Julian Keupp ◽  
Johannes P. Dürholt ◽  
Rochus Schmid
Keyword(s):  
First Principles ◽  
Good Accuracy ◽  
Field Investigation ◽  
Square Lattice ◽  
Side Chain ◽  
Second Step ◽  
Side Chains ◽  
Dynamics Simulations ◽  
Complex Phenomena ◽  
Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br>wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br>transition by a “wine-rack” type motion of the square lattice. We studied this not<br>yet fully understood behavior using an accurate first principles parameterized force<br>field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br>benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br>cations for an interface between a closed and an open pore phase traveling through<br>the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br>conventional simulations in small supercells this mechanism is prevented by periodic<br>boundary conditions (PBC), enforcing a synchronous transformation of the entire<br>crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br>side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br>tally known to have different properties with the side-chains acting as fixed guest<br>molecules. First, in order to extend the parameterization for such flexible groups,<br>1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br>structure force based fit method. The resulting parametrization for a library of<br>fu-MOFs is then validated with respect to a set of reference systems and shows very<br>good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br>length is studied with respect to the influence of the side-chains on the breathing<br>behavior. For small supercells in PBC a systematic trend of the closed pore volume<br>with the chain length is observed. However, for a nanocrystallite model a distinct<br>interface between a closed and an open pore phase is visible only for the short chain<br>length, whereas for longer chains the interface broadens and a nearly concerted trans-<br>formation is observed. Only by molecular dynamics simulations using accurate force<br>fields such complex phenomena can be studied on a molecular level.

scholarly journals Effects of Amino Acid Side-Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1789
Author(s):  
Dmitry Tolmachev ◽  
George Mamistvalov ◽  
Natalia Lukasheva ◽  
Sergey Larin ◽  
Mikko Karttunen
Keyword(s):  
Glutamic Acid ◽  
Chain Length ◽  
Chemical Structure ◽  
Side Chain ◽  
Side Chains ◽  
Side Chain Length ◽  
Polyelectrolyte Brushes ◽  
Grafting Density ◽  
The Difference ◽  
Cellulose Surface

We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side-chain length, the chemical structure and their interplay are required. It was found that in the case of glutamic acid oligomers, the longer side chains facilitate attractive interactions with the cellulose surface, which forces the grafted chains to lie down on the surface. The additional methylene group in the side chain enables side-chain rotation, enhancing this effect. On the other hand, the shorter and more restricted side chains of aspartic acid oligomers prevent attractive interactions to a large degree and push the grafted chains away from the surface. The difference in side-chain length also leads to differences in other properties of the brush in divalent salt solutions. At a low grafting density, the longer side chains of glutamic acid allow the adsorbed cations to be spatially distributed inside the brush resulting in a charge inversion. With an increase in grafting density, the difference in the total charge of the aspartic and glutamine brushes disappears, but new structural features appear. The longer sides allow for ion bridging between the grafted chains and the cellulose surface without a significant change in main-chain conformation. This leads to the brush structure being less sensitive to changes in salt concentration.

scholarly journals Unusual Structural Features in the Adduct of Dirhodium Tetraacetate with Lysozyme

2021 ◽  
Vol 22 (3) ◽  
pp. 1496
Author(s):  
Domenico Loreto ◽  
Giarita Ferraro ◽  
Antonello Merlino
Keyword(s):  
Anticancer Agents ◽  
Structural Features ◽  
Side Chain ◽  
Side Chains ◽  
Valuable Insight ◽  
Experimental Conditions ◽  
Egg White Lysozyme ◽  
Potential Applications ◽  
Model Protein ◽  
Hen Egg White

The structures of the adducts formed upon reaction of the cytotoxic paddlewheel dirhodium complex [Rh2(μ-O2CCH3)4] with the model protein hen egg white lysozyme (HEWL) under different experimental conditions are reported. Results indicate that [Rh2(μ-O2CCH3)4] extensively reacts with HEWL:it in part breaks down, at variance with what happens in reactions with other proteins. A Rh center coordinates the side chains of Arg14 and His15. Dimeric Rh–Rh units with Rh–Rh distances between 2.3 and 2.5 Å are bound to the side chains of Asp18, Asp101, Asn93, and Lys96, while a dirhodium unit with a Rh–Rh distance of 3.2–3.4 Å binds the C-terminal carboxylate and the side chain of Lys13 at the interface between two symmetry-related molecules. An additional monometallic fragment binds the side chain of Lys33. These data, which are supported by replicated structural determinations, shed light on the reactivity of dirhodium tetracarboxylates with proteins, providing useful information for the design of new Rh-containing biomaterials with an array of potential applications in the field of catalysis or of medicinal chemistry and valuable insight into the mechanism of action of these potential anticancer agents.

scholarly journals Synthesis of New Derivatives of BEDT-TTF: Installation of Alkyl, Ethynyl, and Metal-Binding Side Chains and Formation of Tris(BEDT-TTF) Systems

2021 ◽  
Vol 7 (8) ◽  
pp. 110
Author(s):  
Songjie Yang ◽  
Matteo Zecchini ◽  
Andrew Brooks ◽  
Sara Krivickas ◽  
Desiree Dalligos ◽  
...  
Keyword(s):  
Metal Binding ◽  
Tricarboxylic Acid ◽  
Metal Salts ◽  
Side Chain ◽  
Side Chains ◽  
Ethynyl Group ◽  
X Ray ◽  
Transition Metal Salts ◽  
Alkyl Side Chains ◽  
Derivatives Of

The syntheses of new BEDT-TTF derivatives are described. These comprise BEDT-TTF with one ethynyl group (HC≡C-), with two (n-heptyl) or four (n-butyl) alkyl side chains, with two trans acetal (-CH(OMe)2) groups, with two trans aminomethyl (-CH2NH2) groups, and with an iminodiacetate (-CH2N(CH2CO2−)2 side chain. Three transition metal salts have been prepared from the latter donor, and their magnetic properties are reported. Three tris-donor systems are reported bearing three BEDT-TTF derivatives with ester links to a core derived from benzene-1,3,5-tricarboxylic acid. The stereochemistry and molecular structure of the donors are discussed. X-ray crystal structures of two BEDT-TTF donors are reported: one with two CH(OMe)2 groups and with one a -CH2N(CH2CO2Me)2 side chain.

scholarly journals Current Understanding of the Structure, Stability and Dynamic Properties of Amyloid Fibrils

2021 ◽  
Vol 22 (9) ◽  
pp. 4349
Author(s):  
Eri Chatani ◽  
Keisuke Yuzu ◽  
Yumiko Ohhashi ◽  
Yuji Goto
Keyword(s):  
Amyloid Fibrils ◽  
Polypeptide Chain ◽  
Dynamic Properties ◽  
Protein Molecule ◽  
Side Chain ◽  
Structure Stability ◽  
Side Chains ◽  
Precise Control ◽  
Functional Amyloids ◽  
Structural Architecture

Amyloid fibrils are supramolecular protein assemblies represented by a cross-β structure and fibrous morphology, whose structural architecture has been previously investigated. While amyloid fibrils are basically a main-chain-dominated structure consisting of a backbone of hydrogen bonds, side-chain interactions also play an important role in determining their detailed structures and physicochemical properties. In amyloid fibrils comprising short peptide segments, a steric zipper where a pair of β-sheets with side chains interdigitate tightly is found as a fundamental motif. In amyloid fibrils comprising longer polypeptides, each polypeptide chain folds into a planar structure composed of several β-strands linked by turns or loops, and the steric zippers are formed locally to stabilize the structure. Multiple segments capable of forming steric zippers are contained within a single protein molecule in many cases, and polymorphism appears as a result of the diverse regions and counterparts of the steric zippers. Furthermore, the β-solenoid structure, where the polypeptide chain folds in a solenoid shape with side chains packed inside, is recognized as another important amyloid motif. While side-chain interactions are primarily achieved by non-polar residues in disease-related amyloid fibrils, the participation of hydrophilic and charged residues is prominent in functional amyloids, which often leads to spatiotemporally controlled fibrillation, high reversibility, and the formation of labile amyloids with kinked backbone topology. Achieving precise control of the side-chain interactions within amyloid structures will open up a new horizon for designing useful amyloid-based nanomaterials.

scholarly journals Structure-Activity Relationships of Sandalwood Odorants: Synthesis of a New Campholene Derivative

2010 ◽  
Vol 5 (9) ◽  
pp. 1934578X1000500
Author(s):  
Iris Stappen ◽  
Joris Höfinghoff ◽  
Gerhard Buchbauer ◽  
Peter Wolschann
Keyword(s):  
Structural Changes ◽  
Great Influence ◽  
Complete Loss ◽  
Side Chain ◽  
Side Chains ◽  
Quaternary Carbon ◽  
Structural Modifications ◽  
Structure Activity ◽  
Highly Sensitive ◽  
Sandalwood Odorants

Structural modifications of natural (-)-( Z)-β-santalol have shown that the sandalwood odor impression is highly sensitive, even to small structural changes. Particularly, the substitution of the quaternary carbon is of great influence on the scent. Epi-compounds with side chains in the endo-position possess sandalwood odor in only a few derivatives, whereas modifications at this side chain, as well as modification at the bicyclic ring systems mostly lead to a complete loss of sandalwood fragrance.

scholarly journals Binding Site of the Bridged Macrolides in the Escherichia coli Ribosome

2005 ◽  
Vol 49 (1) ◽  
pp. 281-288 ◽  
Author(s):  
Liqun Xiong ◽  
Yakov Korkhin ◽  
Alexander S. Mankin
Keyword(s):  
Escherichia Coli ◽  
Tight Binding ◽  
Dimethyl Sulfate ◽  
23S Rrna ◽  
Side Chain ◽  
Macrolide Antibiotics ◽  
Side Chains ◽  
Alkyl Aryl ◽  
E Coli ◽  
Exit Tunnel

ABSTRACT Ketolides represent the latest group of macrolide antibiotics. Tight binding of ketolides to the ribosome appears to correlate with the presence of an extended alkyl-aryl side chain. Recently developed 6,11-bridged bicyclic ketolides extend the spectrum of platforms used to generate new potent macrolides with extended alkyl-aryl side chains. The purpose of the present study was to characterize the site of binding and the action of bridged macrolides in the ribosomes of Escherichia coli. All the bridged macrolides investigated efficiently protected A2058 and A2059 in domain V of 23S rRNA from modification by dimethyl sulfate and U2609 from modification by carbodiimide. In addition, bridged macrolides that carry extended alkyl-aryl side chains protruding from the 6,11 bridge protected A752 in helix 35 of domain II of 23S rRNA from modification by dimethyl sulfate. Bridged macrolides efficiently displaced erythromycin from the ribosome in a competition binding assay. The A2058G mutation in 23S rRNA conferred resistance to the bridged macrolides. The U2609C mutation, which renders E. coli resistant to the previously studied ketolides telithromycin and cethromycin, barely affected cell susceptibility to the bridged macrolides used in this study. The results of the biochemical and genetic studies indicate that in the E. coli ribosome, bridged macrolides bind in the nascent peptide exit tunnel at the site previously described for other macrolide antibiotics. The presence of the side chain promotes the formation of specific interactions with the helix 35 of 23S rRNA.

scholarly journals Structure Formation in Anisotropic Disks

2006 ◽  
Vol 2 (S235) ◽  
pp. 143-143
Author(s):  
Eduard Vorobyov ◽  
Christian Theis
Keyword(s):  
Stability Analysis ◽  
Linear Stability ◽  
Linear Stability Analysis ◽  
Disk Galaxies ◽  
Structural Elements ◽  
Small Perturbations ◽  
Gravitational Instabilities ◽  
Hydrodynamical Simulations ◽  
Axisymmetric Structures ◽  
Insight Into

The majority of normal disk galaxies are characterized by non-axisymmetric structures like spirals or bars. These structural elements have been widely discussed in the literature as a result of gravitational instabilities which are connected to growing density waves or global instabilities of disks. A first insight into the properties of galactic discs was provided by linear stability analysis. However, a disadvantage of linear stability analysis remained its restriction to small perturbations, both in amplitude and wavelength. Thus, numerical simulations, especially hydrodynamical and stellar-hydrodynamical simulations became a primary tool for the analysis of galactic evolution.

Conformational analysis of glutamic acid analogues as probes of glutamate receptors using molecular modelling and NMR methods. Comparison with specific agonists

1997 ◽  
Vol 5 (2) ◽  
pp. 335-352 ◽  
Author(s):  
Nathalie Todeschi ◽  
Josyane Gharbi-Benarous ◽  
Francine Acher ◽  
Valery Laure ◽  
Jean-Philippe Pin ◽  
...  
Keyword(s):  
Conformational Analysis ◽  
Glutamic Acid ◽  
Glutamate Receptors ◽  
Molecular Modelling ◽  
Methods Comparison ◽  
Nmr Methods
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