scholarly journals Conformational aspects of N-glycosylation of proteins. Studies with linear and cyclic peptides as probes

1982 ◽  
Vol 203 (3) ◽  
pp. 761-768 ◽  
Author(s):  
Ernst Bause ◽  
Harald Hettkamp ◽  
Günter Legler
Keyword(s):  
Hydrogen Bond ◽  
Cyclic Peptides ◽  
Degrees Of Freedom ◽  
Attachment Site ◽  
Structural Features ◽  
Peptide Chain ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Acceptor ◽  
Disulphide Bond Formation ◽  
Partial Fixation

Conformational aspects of N-glycosylation of glycoproteins have been studied by using a series of peptides which contained, in addition to the ‘marker sequence’ Asn-Gly-Thr, two cysteine residues in various positions of the peptide chain. The presence of two cysteines permitted a partial fixation of the above triplet sequence in cyclic structures of various size by intramolecular disulphide bond formation. Comparison of the glycosyl acceptor properties of the linear peptides and their corresponding cyclic analogues allows the following statements. The considerably lower acceptor capabilities of the cyclic derivatives indicate that the restriction of rotational degrees of freedom imposed by disulphide bonding results in a conformation which hinders a favourable interaction of the peptide substrate with the N-glycosyltransferase. On the other hand, the glycosylation rate of linear peptides increases with increasing chain length, suggesting that the amino acids on both the N- and C-terminal side of the ‘marker sequence’ may contribute to a considerable extent to the induction of an ‘active’ conformation. Realization of a potential sugar attachment site requires a hydrogen bond interaction within the ‘marker sequence’ between the oxygen of threonine (serine) as the hydrogen bond acceptor and the β-amide of asparagine as the donor [Bause & Legler (1981) Biochem. J.195, 639–644]. This interaction is obviously facilitated when the peptide chain can adopt a conformation which resembles a β-turn or other loop structure. The available experimental and statistical data are discussed in terms of possible structural features for N-glycosylation, with the aid of space-filling models.

SINGLE MOLECULE IMMOBILIZATION OF π-CONJUGATED MOLECULES ON Au USING DENDRIMER-BASED TEMPLATES

2005 ◽  
Vol 04 (04) ◽  
pp. 467-473 ◽  
Author(s):  
ABDELHAK BELAISSAOUI ◽  
HIDEO TOKUHISA ◽  
EMIKO KOYAMA ◽  
MASATOSHI KANESATO
Keyword(s):  
Hydrogen Bond ◽  
Ftir Spectroscopy ◽  
Single Molecule ◽  
Binding Constant ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Acceptor ◽  
Conjugated Molecules ◽  
The Core ◽  
Conjugated Molecule

We demonstrate that immobilization of a π-conjugated molecule containing a bipyridine moiety as a hydrogen bond acceptor on Au using a dendrimer-based template with 3,4-dihydroxybenzene moiety at the core as a hydrogen bond donor. The hydrogen bond interaction was used for the linkage between the conjugated molecule and the template to improve the method to fabricate single-molecule arrays we reported before.1 Although the binding constant is small ( K = 120 ± 20 M -1) in CDCl 3, it was demonstrated that the dendrimer spacer serves as a template to isolate the π-conjugated molecule, and is removable simply with a CH 2 Cl 2 rinsing by surface FTIR spectroscopy.

scholarly journals Combined Pharmacophore and Grid-Independent Molecular Descriptors (GRIND) Analysis to Probe 3D Features of Inositol 1,4,5-Trisphosphate Receptor (IP3R) Inhibitors in Cancer

2021 ◽  
Vol 22 (23) ◽  
pp. 12993
Author(s):  
Humaira Ismatullah ◽  
Ishrat Jabeen
Keyword(s):  
Hydrogen Bond ◽  
Cancer Progression ◽  
Molecular Descriptor ◽  
Pharmacophore Model ◽  
Receptor Site ◽  
Structural Features ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Design And Optimization ◽  
Trisphosphate Receptor

Inositol 1, 4, 5-trisphosphate receptor (IP3R)-mediated Ca2+ signaling plays a pivotal role in different cellular processes, including cell proliferation and cell death. Remodeling Ca2+ signals by targeting the downstream effectors is considered an important hallmark in cancer progression. Despite recent structural analyses, no binding hypothesis for antagonists within the IP3-binding core (IBC) has been proposed yet. Therefore, to elucidate the 3D structural features of IP3R modulators, we used combined pharmacoinformatic approaches, including ligand-based pharmacophore models and grid-independent molecular descriptor (GRIND)-based models. Our pharmacophore model illuminates the existence of two hydrogen-bond acceptors (2.62 Å and 4.79 Å) and two hydrogen-bond donors (5.56 Å and 7.68 Å), respectively, from a hydrophobic group within the chemical scaffold, which may enhance the liability (IC50) of a compound for IP3R inhibition. Moreover, our GRIND model (PLS: Q2 = 0.70 and R2 = 0.72) further strengthens the identified pharmacophore features of IP3R modulators by probing the presence of complementary hydrogen-bond donor and hydrogen-bond acceptor hotspots at a distance of 7.6–8.0 Å and 6.8–7.2 Å, respectively, from a hydrophobic hotspot at the virtual receptor site (VRS). The identified 3D structural features of IP3R modulators were used to screen (virtual screening) 735,735 compounds from the ChemBridge database, 265,242 compounds from the National Cancer Institute (NCI) database, and 885 natural compounds from the ZINC database. After the application of filters, four compounds from ChemBridge, one compound from ZINC, and three compounds from NCI were shortlisted as potential hits (antagonists) against IP3R. The identified hits could further assist in the design and optimization of lead structures for the targeting and remodeling of Ca2+ signals in cancer.

scholarly journals The role of the hydroxy amino acid in the triplet sequence Asn-Xaa-Thr(Ser) for the N-glycosylation step during glycoprotein biosynthesis

1981 ◽  
Vol 195 (3) ◽  
pp. 639-644 ◽  
Author(s):  
E Bause ◽  
G Legler
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Hydroxy Group ◽  
Catalytic Mechanism ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Acceptor ◽  
Hydroxy Amino Acid ◽  
Hydroxy Amino

The catalytical role of the hydroxy amino acid in the “marker sequence” Asn-Xaa-Thr(Ser) for the N-glycosylation step of glycoprotein formation was investigated by using a series of hexapeptides derived from Tyr-Asn-Gly-Xaa-Ser-Val by substituting threonine, serine, cysteine, valine and O-methylthreonine respectively for Xaa. The results, which were obtained with calf liver microsomal fractions as enzyme source and dolichyl diphosphate di-N-acetyl [14C] chitobiose as glycosyl donor showed that the threonine-, serine- and cysteine-containing derivatives could be glycosylated, although at very different rates, whereas the valine and O-methylthreonine analogues did not work as glycosyl acceptors. Replacement of threonine by serine resulted in a 4-fold decrease in Vmax, and about a 10-fold increase in Km for glycosyl transfer. Replacement of serine by cysteine again decreased acceptor activity 2-3-fold. The various results, taken together, indicate an absolute requirement for a hydrogen-bond-donor function in the side chain of the hydroxy amino acid of the “marker sequence” and furthermore, point to a considerable influence of the structure of this amino acid on binding as well as on the glycosyl transfer itself. In order to explain the observed differences in the glycosyl-transfer rates, a model is proposed with a hydrogen-bond interaction between the amide of asparagine as the hydrogen-bond donor and the oxygen of the hydroxy group of the hydroxy amino acid as the hydrogen-bond acceptor. The participation of the hydroxy group in the catalytic mechanism of glycosyl transfer in the kind of proton-relay system is discussed.

Probing the Structural Features and the Micro-heterogeneity of Various Deep Eutectic Solvents and their Water Dilutions by the Photophysical Behaviour of Two Fluorophores

2020 ◽  
Author(s):  
Matteo Tiecco ◽  
Irene Di Guida ◽  
Pier Luigi Gentili ◽  
Raimondo Germani ◽  
Carmela Bonaccorso ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Transient Absorption ◽  
Photophysical Properties ◽  
Deep Eutectic Solvents ◽  
Structural Features ◽  
Solvation Dynamics ◽  
Structured Systems ◽  
Reduced Viscosity ◽  
Bond Network ◽  
Fluorescent Molecules

<div><div><div><p>The structural features of a series of diverse Deep Eutectic Solvents (DESs) have been investigated and characterized by means of two fluorescent probes. The spectral and photophysical properties of the latter are strictly dependent on the experienced environment, so that they can provide insights into the polarity, viscosity, hydrogen-bond network, and micro-heterogeneity of the various DESs.</p><p>In fact, the investigated DESs exhibit a variety of properties with regards to their hydrophilicity, acidity, and hydrogen-bond ability, and these details were deeply probed by the two fluorescent molecules. The effect of the addition of water, which is a key strategy for tuning the properties of these structured systems, was also tested. In particular, the excited state dynamics of the probes, measured by femtosecond-resolved transient absorption, proved instrumental in understanding the changes in the structural properties of the DESs, namely reduced viscosity and enhanced heterogeneity, as the water percentage increases. Differences between the various DESs in terms of both local microheterogeneity and bulk viscosity also emerged from the peculiar multi-exponential solvation dynamics undergone by the excited states of the probes.</p></div></div></div>

Probing the Structural Features and the Micro-heterogeneity of Various Deep Eutectic Solvents and their Water Dilutions by the Photophysical Behaviour of Two Fluorophores

2020 ◽  
Author(s):  
Matteo Tiecco ◽  
Irene Di Guida ◽  
Pier Luigi Gentili ◽  
Raimondo Germani ◽  
Carmela Bonaccorso ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Transient Absorption ◽  
Photophysical Properties ◽  
Deep Eutectic Solvents ◽  
Structural Features ◽  
Solvation Dynamics ◽  
Structured Systems ◽  
Reduced Viscosity ◽  
Bond Network ◽  
Fluorescent Molecules

<div><div><div><p>The structural features of a series of diverse Deep Eutectic Solvents (DESs) have been investigated and characterized by means of two fluorescent probes. The spectral and photophysical properties of the latter are strictly dependent on the experienced environment, so that they can provide insights into the polarity, viscosity, hydrogen-bond network, and micro-heterogeneity of the various DESs.</p><p>In fact, the investigated DESs exhibit a variety of properties with regards to their hydrophilicity, acidity, and hydrogen-bond ability, and these details were deeply probed by the two fluorescent molecules. The effect of the addition of water, which is a key strategy for tuning the properties of these structured systems, was also tested. In particular, the excited state dynamics of the probes, measured by femtosecond-resolved transient absorption, proved instrumental in understanding the changes in the structural properties of the DESs, namely reduced viscosity and enhanced heterogeneity, as the water percentage increases. Differences between the various DESs in terms of both local microheterogeneity and bulk viscosity also emerged from the peculiar multi-exponential solvation dynamics undergone by the excited states of the probes.</p></div></div></div>

scholarly journals Study on the interaction between catechin and cholesterol by the density functional theory

2020 ◽  
Vol 18 (1) ◽  
pp. 357-368
Author(s):  
Kaiwen Zheng ◽  
Kai Guo ◽  
Jing Xu ◽  
Wei Liu ◽  
Junlang Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Charge Transfer ◽  
Density Functional ◽  
Antioxidant Properties ◽  
Micelle Formation ◽  
Aromatic Rings ◽  
Hydrogen Bond Interaction ◽  
Functional Theory ◽  
The Density Functional Theory

AbstractCatechin – a natural polyphenol substance – has excellent antioxidant properties for the treatment of diseases, especially for cholesterol lowering. Catechin can reduce cholesterol content in micelles by forming insoluble precipitation with cholesterol, thereby reducing the absorption of cholesterol in the intestine. In this study, to better understand the molecular mechanism of catechin and cholesterol, we studied the interaction between typical catechins and cholesterol by the density functional theory. Results show that the adsorption energies between the four catechins and cholesterol are obviously stronger than that of cholesterol themselves, indicating that catechin has an advantage in reducing cholesterol micelle formation. Moreover, it is found that the molecular interactions of the complexes are mainly due to charge transfer of the aromatic rings of the catechins as well as the hydrogen bond interactions. Unlike the intuitive understanding of a complex formed by hydrogen bond interaction, which is positively correlated with the number of hydrogen bonds, the most stable complexes (epicatechin–cholesterol or epigallocatechin–cholesterol) have only one but stronger hydrogen bond, due to charge transfer of the aromatic rings of catechins.

scholarly journals Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer’s Disease: Computational Refining and Biochemical Evaluation

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1946
Author(s):  
Nitin Chitranshi ◽  
Ashutosh Kumar ◽  
Samran Sheriff ◽  
Veer Gupta ◽  
Angela Godinez ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Hydrogen Bond ◽  
Virtual Screening ◽  
Cathepsin B ◽  
Amyloid Β ◽  
Proteolytic Degradation ◽  
Hydrogen Bond Acceptor ◽  
Starting Point ◽  
The Brain

Amyloid precursor protein (APP), upon proteolytic degradation, forms aggregates of amyloid β (Aβ) and plaques in the brain, which are pathological hallmarks of Alzheimer’s disease (AD). Cathepsin B is a cysteine protease enzyme that catalyzes the proteolytic degradation of APP in the brain. Thus, cathepsin B inhibition is a crucial therapeutic aspect for the discovery of new anti-Alzheimer’s drugs. In this study, we have employed mixed-feature ligand-based virtual screening (LBVS) by integrating pharmacophore mapping, docking, and molecular dynamics to detect small, potent molecules that act as cathepsin B inhibitors. The LBVS model was generated by using hydrophobic (HY), hydrogen bond acceptor (HBA), and hydrogen bond donor (HBD) features, using a dataset of 24 known cathepsin B inhibitors of both natural and synthetic origins. A validated eight-feature pharmacophore hypothesis (Hypo III) was utilized to screen the Maybridge chemical database. The docking score, MM-PBSA, and MM-GBSA methodology was applied to prioritize the lead compounds as virtual screening hits. These compounds share a common amide scaffold, and showed important interactions with Gln23, Cys29, His110, His111, Glu122, His199, and Trp221. The identified inhibitors were further evaluated for cathepsin-B-inhibitory activity. Our study suggests that pyridine, acetamide, and benzohydrazide compounds could be used as a starting point for the development of novel therapeutics.

On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules

1998 ◽  
Vol 279 (5) ◽  
pp. 1123-1136 ◽  
Author(s):  
Ben Luisi ◽  
Modesto Orozco ◽  
Jiri Sponer ◽  
Francisco J Luque ◽  
Zippora Shakked
Keyword(s):  
Hydrogen Bond ◽  
Nitrogen Atom ◽  
Potential Role ◽  
Amino Nitrogen ◽  
Hydrogen Bond Acceptor ◽  
Amino Nitrogen Atom

6,9-Dibromo-2a,10b-diphenyl-2a,5,10,10b-tetrahydro-2H,3H-2,3,4a,10a-tetraazabenzo[g]cyclopenta[cd]azulene-1,4-dione monohydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Supramolecular Structure ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Compound C ◽  
Bifurcated Hydrogen Bond

The title compound, C24H18Br2N4O2·H2O, forms a supramolecular structure via N—H...O, O—H...O and C—H...O hydrogen bonds. In the crystal structure, the water molecule serves as a bifurcated hydrogen-bond acceptor and as a hydrogen-bond donor.

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