Construction of Supramolecular Laccase Enzymes and Understanding of Catalytic Dye Degradation Using Multispectral and Molecular Docking Approaches

A non-covalent supramolecular enzyme system, which is formed by non-covalent interactions of an enzyme with substrate analogs, shows better enzyme catalytic activity than the enzyme itself. A non-covalent supramolecular laccase-dye...

Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and Molecular docking study

Heliyon ◽

10.1016/j.heliyon.2021.e08204 ◽

2021 ◽

pp. e08204

Author(s):

Mouna Medimagh ◽

Noureddine Issaoui ◽

Sofian Gatfaoui ◽

Silvia Antonia Brandán ◽

Omar Al-Dossary ◽

...

Keyword(s):

Molecular Docking ◽

Ir Spectrum ◽

Docking Study ◽

Molecular Docking Study ◽

Ft Ir ◽

Depicting the Non-Covalent Interaction of Whey Proteins with Galangin or Genistein Using the Multi-Spectroscopic Techniques and Molecular Docking

Foods ◽

10.3390/foods8090360 ◽

2019 ◽

Vol 8 (9) ◽

pp. 360 ◽

Cited By ~ 1

Author(s):

Chun-Min Ma ◽

Xin-Huai Zhao

Keyword(s):

Molecular Docking ◽

Hydrophobic Interaction ◽

Whey Proteins ◽

Sodium Dodecyl ◽

Binding Constants ◽

Spectroscopic Techniques ◽

Stereochemical Structure ◽

Β Lactoglobulin ◽

The non-covalent interactions between a commercial whey protein isolate (WPI) and two bioactive polyphenols galangin and genistein were studied at pH 6.8 via the multi-spectroscopic assays and molecular docking. When forming these WPI-polyphenol complexes, whey proteins had changed secondary structures while hydrophobic interaction was the major driving force. Detergent sodium dodecyl sulfate destroyed the hydrophobic interaction and thus decreased apparent binding constants of the WPI-polyphenol interactions. Urea led to hydrogen-bonds breakage and protein unfolding, and therefore increased apparent binding constants. Based on the measured apparent thermodynamic parameters like ΔH, ΔS, ΔG, and donor-acceptor distance, galangin with more planar stereochemical structure and random B-ring rotation showed higher affinity for WPI than genistein with location isomerism and twisted stereochemical structure. The molecular docking results disclosed that β-lactoglobulin of higher average hydrophobicity had better affinity for the two polyphenols than α-lactalbumin of lower average hydrophobicity while β-lactoglobulin possessed very similar binding sites to the two polyphenols. It is concluded that polyphenols might have different non-covalent interactions with food proteins, depending on the crucial polyphenol structures and protein hydrophobicity.

Catalytic activity and facile recovery of a cyclometalated N‐heterocyclic carbene palladium(II) complex immobilized by non‐covalent interactions on reduced graphene oxide

Applied Organometallic Chemistry ◽

10.1002/aoc.4907 ◽

2019 ◽

Vol 33 (6) ◽

pp. e4907 ◽

Cited By ~ 2

Author(s):

Kazem Karami ◽

Azar Ramezanpour ◽

Mostafa Zakariazadeh ◽

Cristian Silvestru

Keyword(s):

Graphene Oxide ◽

Catalytic Activity ◽

Reduced Graphene Oxide ◽

Reduced Graphene ◽

A co-opted ISG15-USP18 binding mechanism normally reserved for deISGylation controls type I IFN signalling

10.1101/2021.06.01.446527 ◽

2021 ◽

Author(s):

Andri Vasou ◽

Katie Nightingale ◽

Vladimira Cetkovska ◽

Connor GG Bamford ◽

Jelena Andrejeva ◽

...

Keyword(s):

Catalytic Activity ◽

Autoinflammatory Disease ◽

Type I Interferon ◽

Negative Regulator ◽

Regulatory Function ◽

Type I ◽

Binding Mechanism ◽

Tight Control ◽

Type I interferon (IFN) signalling induces the expression of several hundred IFN-stimulated genes that provide an unfavourable environment for viral replication. To prevent an overexuberant response and autoinflammatory disease, IFN signalling requires tight control. One critical regulator is the ubiquitin-like protein ISG15, evidenced by autoinflammatory disease in patients with inherited ISG15 deficiencies. Current models suggest that ISG15 stabilises USP18, a well-established negative regulator of IFN signalling. USP18 also functions as an ISG15-specific peptidase, however its catalytic activity is dispensable for controlling IFN signalling. Here, we show that the ISG15-dependent stabilisation of USP18 is necessary but not sufficient for regulation of IFN signalling and that USP18 requires non-covalent interactions with ISG15 to enhance its regulatory function. Intriguingly, this trait has been acquired through co-option of a binding mechanism normally reserved for deISGylation, identifying an unexpected new function for ISG15.

DFT Study of Efinaconazole, an Antifungal Drug and Its Molecular Docking against a Holoenzyme (pdb id: 3IDB)

Journal of Scientific Research ◽

10.3329/jsr.v13i2.51731 ◽

2021 ◽

Vol 13 (2) ◽

pp. 679-694

Author(s):

J. Hossen ◽

T. K. Pal

Keyword(s):

Molecular Docking ◽

Hydrogen Bonds ◽

Density Functional ◽

Computational Study ◽

Antifungal Drug ◽

Internal Displacement ◽

Chemical Hardness ◽

Discovery Studio ◽

Efinaconazole (ECZ) is an antifungal drug. Various non-covalent interactions between ECZ and a holoenzyme (protein id: 3idb) has been investigated through computational study. The structure of ECZ was optimized using density functional theory (DFT) applying B3LYP/6-311G+(d,p) method. HOMO, LUMO, chemical hardness and softness, several thermochemical parameters, electrostatic potential surface, vibrational spectrum, total energy, and maximum internal force and maximum internal displacement with respect to optimization step number have been determined. The optimized ECZ ligand was subjected to molecular docking against the protein 3idb in Autodock Vina program. The different non-covalent interactions in the ligand-protein complex were visualized in BIOVIA Discovery Studio Visualizer. Various surface plots such as hydrogen bonds, ionizability, SAS, hydrophobicity, aromatic and charge surfaces were excerpted. ECZ molecule forms three strong hydrogen bonds with amino acid residues of the holoenzyme. In addition to this, it is significantly capable to form several other bonds which strengthen the ligand-protein interaction. The result showed that the ECZ molecule posed considerable binding affinity against the macromolecule.

The Hydricity and Reactivity Relationship in [ FeFe ]-hydrogenases

10.21203/rs.3.rs-77874/v1 ◽

2020 ◽

Author(s):

Jacob Artz ◽

David Mulder ◽

Michael Ratzloff ◽

John Peters ◽

Paul King

Keyword(s):

Catalytic Activity ◽

Transition Metal ◽

Thermodynamic Properties ◽

Chemical Reactivity ◽

Chemical Compounds ◽

Transition Metal Catalysts ◽

Metal Cofactor ◽

Metal Cofactors ◽

Abstract Reactivity of transition metal catalysts is controlled by covalent and non-covalent interactions that tune thermodynamic properties including hydricity. Hydricity is critical to catalytic activity and for modulating the reduction or oxidation of chemical compounds. Likewise, enzymes can employ transition metal cofactors and use metal-hydride intermediates tuned by protein frameworks to selectively control reactivity. One example, the [FeFe]-hydrogenases, catalyze reversible H2 activation with H2 oxidation to H+ reduction ratios spanning ~107 in rate, offering a model to determine the extent that hydricity controls reactivity. To address this question, the hydricity of the catalytic H cluster of two [FeFe]-hydrogenases, CpI and CpII, were compared. We show that for CpI, the higher rates of H+ reduction correspond to a more hydridic H cluster, whereas CpII, which strongly favors H2 oxidation, has a less hydridic H cluster. The results demonstrate that enzymes manipulate metal cofactor hydricity to enable an extraordinary range of chemical reactivity.

Non covalent interactions analysis and spectroscopic characterization combined with molecular docking study of N'-(4-Methoxybenzylidene)-5-phenyl-1H-pyrazole-3-carbohydrazide

Journal of King Saud University - Science ◽

10.1016/j.jksus.2021.101778 ◽

2021 ◽

pp. 101778

Author(s):

Abir Sagaama ◽

Noureddine Issaoui ◽

Fehmi Bardak ◽

Omar Al-Dossary ◽

Aleksandr S. Kazachenko ◽

...

Keyword(s):

Molecular Docking ◽

Spectroscopic Characterization ◽

Docking Study ◽

Molecular Docking Study ◽

An Insight into Non-Covalent Interactions in Binary, Ternary and Quaternary Copper (II) Complexes: Synthesis, X-ray structure, DFT Calculations, Antimicrobial Activity and Molecular Docking Studies

Inorganica Chimica Acta ◽

10.1016/j.ica.2021.120748 ◽

2021 ◽

pp. 120748

Author(s):

Amel F. Elhusseiny ◽

Ali El-Dissouky ◽

Franz Mautner ◽

Eman M. Tawfik ◽

Doaa S. El-Sayed

Keyword(s):

Antimicrobial Activity ◽

Molecular Docking ◽

Dft Calculations ◽

Docking Studies ◽

X Ray ◽

Molecular Docking Studies ◽

Covalent Interactions ◽

Insight Into

“In situ immobilization” of a multicomponent chiral catalyst (MCC) via non-covalent interactions for heterogeneous asymmetric hydrogenation reactions

Organic Chemistry Frontiers ◽

10.1039/c9qo01331h ◽

2020 ◽

Vol 7 (2) ◽

pp. 345-349

Author(s):

Er-Jun Hao ◽

Gong-Xin Li ◽

Zhen-Zhen Lv ◽

Fu-Sheng Li ◽

Yu-Qing Chen ◽

...

Keyword(s):

Catalytic Activity ◽

Asymmetric Hydrogenation ◽

Stacking Interactions ◽

In Situ Immobilization ◽

Chiral Catalyst ◽

Hydrogenation Reactions ◽

Dehydroamino Acid ◽

Novel hybrid catalysts that resulted from the anchoring of pyrene-tagged Rh(i) complexes onto graphene materials via π–π stacking interactions show excellent catalytic activity towards the hydrogenation of dehydroamino acid.